Major Research Projects

In the MMRES Master you will join a cutting-edge research group at one of the BIST Community Centres or MELIS-UPF.

Below you will find detailed information about the various Major research projects proposed for the 2024/2025 academic year. In your application, you must choose five of these projects of your interest. During the call period, as students are admitted, their selected projects become assigned and are no longer available in later calls.

If you want to apply with a research group outside the list, check the different BIST Community Centres’ websites and confirm your acceptance with the principal investigator. Add the supervisor’s name and project, and contact education@bist.eu

Once the programme has started, you will decide on your Minor Project together with your Major Project research supervisor.

For more information about the duration and content of the major and minor projects, you can check the following sections: SyllabusResearch experience, and FAQs.

ProjectCourseCentreResearch Group NameWebSupervisorAvailabilityDescriptionCo-supervisorTagsKeywords
CRG-2401. Characterisation of highly-expressed genes in oocytes2024-2025CRGBöke labWEBSITEElvanBokeAvailable

Our lab focuses on one of the biggest problems developed nations are facing in 21st century: Late-stage motherhood, and associated fertility problems. The decrease in fertility rates is leading to a population decline in majority of the developed nations from Japan to Spain, which will have unprecedented consequences for our societies in near future. Poor oocyte quality accounts for the majority of female fertility problems, however, we know little about how oocytes can remain healthy for many years or why their health eventually declines with advanced age. World-wide data show that more than 25% of female fertility problems are unexplained, pointing to a huge gap in our understanding of female reproduction. Our lab strives to help fill this gap by studying immature oocytes.

Ageing, fertility, metabolism, oocyte, protein homeostasis
MELIS-2401. Cell Cycle Control: Regulation of the G1/S Transition2024-2025MELIS-UPFOxidative Stress and Cell Cycle Group (OSCCG)WEBSITEJoseAyteAvailable

We are ultimately interested in deciphering the mechanisms that control cell cycle progression with a special focus on the G1/S transition. In metazoans, inactivation of the Retinoblastoma protein (pRB) leads to unregulated cell cycle progression promoting uncontrolled cell growth, genomic instability and aneuploidy, hallmarks of tumor progression. pRB tumor suppressor activity is achieved through binding and regulating the E2F family of transcription factors. It is well known that a tumor process is very complex, accumulating numerous secondary mutations that aim to eliminate the brakes to the proliferative process. Even though many individual regulators of the pRB-E2F complex 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. Using reverse genetics and by introducing a set of short-lived fluorescent markers in a KO library, we have recently isolated potential genes involved in the G1/S transition. Among them, we have found some components of the TOR pathway, members of the ubiquitin-mediated protein degradation and several chromatin remodelers. The Master BIST candidate will characterize (some of) these potential regulators, measuring their direct effect on the regulation of the G1/S transcriptional wave and which is their specific impact on cell cycle progression. The experimental approach will include genome-wide approximations (RNAseq, ChIPseq, proteomics) and confocal microscopy (using a cell cycle reporter that we have also recently developed in the laboratory). 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. Also, and to analyze the results (i.e., ultrasequencing or targeted proteomics), knowledge of bioinformatics will be a plus.

Cell cycle, DNA damage, DNA synthesis, G1/S transition, replicative stress
MELIS-2402. Contribution of the ptf1a-progenitor cell pool to the glutamatergic and GABAergic Neuronal populations within the hindbrain2024-2025MELIS-UPFNeurodevelopmental DynamicsWEBSITECristinaPujadesAvailable

The host lab is interested in addressing several questions such as: how does the sequential production of the diverse neurons occur; what is the relative contribution of distinct progenitor cell pools to specific fu¬nctional circuits? and which are the Gene Regulatory Networks (GRN) operating in the transition from stem cell progenitors to differentiated neurons. Recently, we have assessed the contribution of the neurog1 expressing progenitor pool to glutamatergic and GABAergic neuronal populations, by progenitor-restricted intersectional fate mapping. In this project, the candidate will be involved in assessing the contribution of the ptf1a-progenitor cell pool to the different mature neuronal circuits by intersectional fate mapping, and in generating a temporal neuronal differentiation map of the ptf1a-progenitor derivatives. We will combine 4D-imaging, intersectional genetic analysis (Poulin et al., 2020) and computational predictions (Blanc et al., 2022) to perform dynamic studies of the specific cell populations. We propose complementary approaches using the zebrafish embryonic brainstem to fill the void between gene regulatory networks and circuit architecture.

XavierSabatemorphogenesis, neurogenesis, neuronal differentiation, Stem Cells
IRB-2401. Human microbiome in Health and Disease2024-2025IRB BarcelonaComparative GenomicsWEBSITEToniGabaldónAvailable

The human microbiome is a series of distinct communities of bacteria, fungi, viruses, archaea, protists, and other microorganisms, whose compositions vary depending on environmental conditions. Different sites of the human body can be seen as unique biomes, with drastically different environments and nutrient availabilities, which in turn promote different communities. Yet even within a particular body site, the microbiome composition can be highly variable between individuals in different states of health, with distinct lifestyles, or due to a number of other factors. In this project, the student will get exposed to varios projects related with the human oral and gut microbiomes in relation to several diseases and conditions, including cystic fibrosis, colon cancer, or Alzheimer disease. The student will learn basic techniques related to DNA extraction, amplification and sequencing, as well as culture and identification of different micro-organisms. He/She will also get involved in the analysis and interpretation of sequencing data. The balance between experimental or computational work during the stage will depend on the background and interest of the student. More information about the group http://cgenomics.org

metagenomics, microbiome
IRB-2402. Revealing the adaptions of immune functions and metabolism of dendritic cells, macrophages and neutrophils to changing environments2024-2025IRB BarcelonaInnate Immune BiologyWEBSITEStefanie KWculekAvailable

Innate immune cells, such as dendritic cells, macrophages and neutrophils, control immunity and the health of organs. Therefore, they are present in virtually all body tissues. We aim to understand how innate immune cells can persist in and adapt to different environments of tissues, such as limited nutrient concentrations and other variables. Moreover, we are investigating how they can maintain their important immune functions in distinct environments. In that regard, our main research line focuses on revealing the adjustments of cellular metabolism by dendritic cells, macrophages and neutrophils to changing environments. Our ultimate goal is to identify the metabolic requirements or vulnerabilities of innate immune cells to improve or target their dysfunctions during health and non-infectious diseases such as cancer and aging. We are looking for a motivated Master candidate to investigate the homeostatic and immunogenic behaviour of dendritic cells, macrophages and/or neutrophils under different environmental or metabolic conditions in vivo and in vitro. This will include the variation of available nutrients, genetic interference with cellular metabolism and/or other alterations of the surroundings of innate immune cells. Our main model systems are laboratory mice and we will provide training in harvesting and processing their organs for research. Moreover, the candidate will perform analyses of the functions of innate immune cells, such as T cell modulation, migration, phagocytosis, and cytokine production. Subsequent experimental techniques will include the isolation or differentiation of innate immune cells for primary cell culture, co-culture assays, flow cytometry, gene expression analysis, ELISA, fluorescence microscopy and metabolic assays. However, the detailed Master’s project is flexible and will be designed together with the successful candidate based on her/his interests within our research lines. Additionally, we offer teaching of experimental design, data analysis, visualisation and interpretation as well as help with the oral presentation of the candidate’s research results.

Dendritic cells, environment, immunometabolism, macrophages, neutrophils
ICN2-2401. Energy Nanomaterials at Atomic Scale2024-2025ICN2Advanced Electron NanoscopyWEBSITEJordiArbiolAvailable

The student will work with nanostructures based on 2D nanomaterials for Energy and Environmental applications. The student will use the advanced tools offered at the Joint Electron Microscopt Center at ALBA Synchrotron (JEMCA) to analyze at an atomic scale these materials with electrocatalytic properties. Once this challenge is met, it will create atomic models of the structures that will allow us to understand the catalytic properties of these materials. The student will participate in an interdisciplinary project with a coordinated network for the development of new materials for new energy sources and their storage. The work will include the development of 3D atomic models and their simulation to extract the properties of materials. In-situ experiments will be prepared in the working conditions during which it is intended to see the reactions on a sub-nanometer scale. Duties: 1) Participate in an interdisciplinary project with state-of-the-art nanomaterials for future applications in energy and the environment (creation of hydrogen from H2O and fuels from CO2). 2) Acquire knowledge in transmission electron microscopy at the atomic scale. 3) Create atomic models of structures and obtain their simulations of their properties. 4) Develop in-situ experiments under working conditions.The student will work with nanostructures based on 2D nanomaterials for Energy and Environmental applications.

AlbaGarzón-ManjónEnergy nanomaterials, in-situ, scanning transmission electron microscopy, tomic models
ICN2-2402. Atomic-Scale Characterization of Semiconductor Nanomaterials: Unveiling their Properties through Transmission Electron Microscopy2024-2025ICN2Advanced Electron NanoscopyWEBSITEJordiArbiolAvailable

Nanotechnology has had a profound impact on various fields, including materials science, electronics, medicine, and energy production. To gain a comprehensive understanding of nanomaterials and optimize their properties, it is essential to characterize their structure and composition at the atomic scale. Transmission Electron Microscopy (TEM) has emerged as a technique that allows for atomic scale imaging, coupled with spectroscopic methods such as energy dispersive X-ray spectroscopy (EDX) and electron energy loss spectroscopy (EELS), providing spatially resolved information about composition, valence state, and plasmonics and phononics. These techniques permit the correlation of physicochemical properties with atomic structure and composition, leading to a full understanding of nanoscale systems. In this context, the student will focus on the atomic scale characterization of 1D semiconductor materials (nanowires), aiming to unravel the role of atomic arrangement in their properties, such as defect formation and elemental segregation. The project will be in collaboration with research groups from the École Polytechnique Fédérale de Lausanne or the Niels Bohr Institute of the University of Copenhagen, and experimental measurements will be conducted at the Joint Electron Microscopy Center at ALBA Synchrotron (JEMCA) using brand new TEM facilities to analyze materials at sub-nanometer scales. The student will also create 3D atomic models to simulate and interpret the acquired data. As a summary, the student will: Participate as an active member of the Group of Advanced Electron Nanoscopy of ICN2 attending to group meetings and interacting with the rest of the team Adquire knowledge in aberration-corrected TEM and its associated spectroscopies Adquire knowledge in data interpretation and analysis combined with the creation of 3D atomic models and simulations Correlate the experimentally obtained atomic arrangement with the growth mechanisms and physicochemical properties of the nanostructures

SaraMartí-SánchezAtomic models, Quantum and electronic nanomaterials, scanning transmission electron microscopy
IRB-2403. Dissecting and Targeting Immune Determinants of Tumor Evolution2024-2025IRB BarcelonaInflammation, Tissue Plasticity & Cancer labWEBSITEDirenaAlonso CurbeloAvailable

Our lab studies the interplay between genetic mutations and pro-inflammatory insults that promote cancer development, with a focus on pancreatic and liver cancers, two clinical challenges in need of more effective early detection and treatment strategies. As tumor cells co-opt physiological immune responses that normally safeguard normal tissue homeostasis (eg wound healing/regeneration, anti-tumor immunity), we combine bulk/single-cell epigenomic profiling and flexible disease models to expose molecular and cellular traits that are unique to tissues undergoing malignant transformation, and apply functional genomics tools (RNAi/CRISPR) to pinpoint the key mechanisms responsible for driving tumor evolution. The available Master projects aim to characterize and perturb molecular programs and cellular states that are selectively induced during tumor development and metastatic progression (Alonso-Curbelo et al. Nature 2021; Burdziak*, Alonso-Curbelo* et al. Science 2023), with a focus on epigenetic mechanisms regulating immune responses and tumor-host crosstalk: 1. Genetic tagging of cellular states distinguishing tumorigenesis vs normal regeneration. 2. Functional dissection of their defining molecular programs. 3. Computational mining of tumor-specific immune biomarkers in bulk and single-cell sequencing datasets. Through this opportunity, the student will acquire training in general cancer biology, molecular cloning, functional validation approaches (RNAi/CRISPR-mediated genetic perturbations); histology (immunofluorescence/immunohistochemistry); flow cytometry; culture of organoids, cell lines and primary immune cells; and experimental design, data analysis and reporting. The student will also work with our team to set up innovative experimental pipelines and contribute to a constructive and stimulating working environment.

Cancer, CRISPR/Cas9, Epigenetics, immune system, plasticity
IRB-2404. Role of protein synthesis machinery degeneration in human aging2024-2025IRB BarcelonaGene Translational LaboratoryWEBSITELluisRibasAvailable

Transfer RNAs (tRNAs) have occupied a central spot in cell biology and the biotechnology industry in recent years. In particular, the possibility of using these molecules to treat unapproachable diseases such as Huntington’s has sparkled the emergence of new biotech companies dedicated to the engineering of tRNAs. We have very recently discovered a potential link between the mutational dynamics of tRNA genes in the human genome and the process of aging. Our working hypothesis is that cellular and tissue degeneration during aging is promoted by the loss of functional tRNAs in cells, caused by the gradual accumulation of mutations in genes coding for tRNA. This hypothesis offers a mechanistic explanation for prominent characteristics of aging, such as loss of muscle mass and neurogeneration. Moreover, it opens the door to potential anti-aging interventions directed towards the improvement of tRNA function. We will try to prove our hypothesis through the comparative analysis of short- versus long-lived reptiles and mammals, and through the implementation of experimental frameworks where the physiological impact of tRNA mutations can be directly assessed, and the potential benefits of reversing these mutations can be studied. This will be done in collaboration with IRB groups that are experts in the study of the mutational mechanisms affecting the human genome.

Aging, genome, mutations, tissue degeneration, tRNAs
ICFO-2401. Attosecond core-level X-ray spectroscopy for the investigation of condensed matter systems2024-2025ICFOAttoscience and Ultrafast OpticsWEBSITEJensBiegertAvailable

How do we track the movement of electrons inside matter? Understanding the intricacies of electron behaviour within matter demands sophisticated imaging technologies capable of capturing ultrafast processes with impeccable precision. For imaging, the shorter the time we have to track the action with the camera, the faster the “shutter” is to record it, otherwise the image will have ghost afterimages. To track this high-speed movement, imaging technology must improve its shutter speed which is temporal resolution.

If you want to record changes in the microscopic world, such as the moment of chemical reactions, the breaking and forming of chemical bonds, the rotation and vibration of molecules, the temporal resolution that ranges from picoseconds to femtoseconds (1 femtosecond = 10-15s). What is the world’s highest temporal resolution imaging technology? The 2023 Nobel Prize in physics is being recognised for the attosecond (10-18s) pulses of light for the study of electron dynamics in matter.

Jens Biegert group in ICFO, is a pioneer in the development of attosecond light sources and operates a unique facility: 165-as pulses with coverage up to 500 eV at 1 kHz. Attosecond Leveraging this technology, developing Core-level x-ray absorption fine structure (XAFS) spectroscopy by ICFO to provide unprecedented insight into multi-body physics such as electron-electron, electron-hole, electron-lattice dynamics (e.g. PRX 2021), and on ring-opening reactions elucidating vibronic couplings and conical intersection dynamics.
The integration of a tunable UV to VIS pump source, emitting few-cycle and phase-locked pulses, further amplifies the competitiveness and unique research opportunities within Laserlab-Europe. Moreover, the recent expansion of attosecond light sources into the soft x-ray spectrum has revolutionized the investigation of ultrafast dynamics in solid-state materials, presenting an unparalleled experimental capability for delving into the heart of complex material phenomena.
Utilizing XAFS spectroscopy, our research aims to delineate the electronic structure of materials, dissecting contributions from individual atoms as well as those stemming from the scattering of photoelectron wave-packets with neighbouring atoms. The former enables the probing of bound states, facilitating a comprehensive mapping of the unoccupied density of states, thereby providing crucial insights into the underlying band structure. The latter, characterized by modulations in amplitude due to the interference of outgoing and backscattered photoelectron wave-packets, offers invaluable information concerning the spatial positioning of nuclei within the material.
The student will learn cutting-edge attosecond imaging technology to unravel the motion of electrons at its most fundamental level, and investigate the real-time of correlated multi-body physics to address canonical questions such as superconductivity, Mott physics and various other phenomena critical to material science.
Your task will be to familiarize yourself with our research. (We will explain it to you)
– Learn how to use Arthemis and Python to analyze soft X-ray spectra
– Preparation of samples for a soft X-ray attosecond measurement
– Participate in a measurement campaign and analyze your data

Attosecond science, condensed matter, ultrafast dynamics
CRG-2402. Mechanosensitive cell dynamics and pattern formation in the vertebrate embryo2024-2025CRGCell and tissue dynamicsWEBSITEVerenaRuprechtAvailable

The ‘Cell and Tissue Dynamics group’ headed by Dr Verena Ruprecht combines physics and biology to study the mechanisms that control cell and tissue shape, morphodynamic plasticity and multicellular self-organization in tissue development and disease

Tissues of defined shape and function are formed in the early embryo. This process requires that embryonic stem cells organize into patterns of defined architecture. At the same time cells need to acquire specific cell fates. How changes in cell shape impact on cell states and cellular signaling is still a largely open question in biology.

In this project, we will investigate how embryonic stem cells sense and respond to mechanical forces and how changes in cell shape influence cell fate specification. We have previously shown that cells use the nucleus as a mechanosensor that regulates cellular mechanics and morphodynamic plasticity (Venturini et al. Science 2020). Here we will study how nuclear mechanotransduction controls cell fate specification and pattern formation in the early embryo. We will use the Zebrafish embryo as an in vivo model system and further employ a synthetic bottom-up approach that allows to reconstitute cellular dynamics and multicellular self-organization in the early embryo. The student will apply methods from molecular biology (mRNA microinjection, cloning), embryo micromanipulation, biomimetic 3D tissue environments, advanced live cell microscopy and quantitative data analysis. The major goal of this project is to establish a quantitative description of mechanosensitive cell state dynamics in primary embryonic stem cells. This will allow to identify fundamental mechanisms that couple cell shape and cell fate specification to build the 3D body plan of the vertebrate embryo.

We are looking for a highly motivated student with an excellent academic track record who is interested to work in an interdisciplinary team and employ quantitative methods to study fundamental processes of cell dynamics in tissue development.

Cell Signalling, Embryogensis, Mechanobiology, microscopy, synthetic biology
IFAE-2401. Search for novel flavour-violating new physics with multiple leptons at the LHC2024-2025IFAEATLAS GroupWEBSITEAurelioJuste RozasAvailable

The search for hints of physics beyond the Standard Model (BSM) at the Large Hadron Collider (LHC) is particularly promising in experimental final states with multiple leptons. In particular, by requiring at least four leptons, the SM background reduces drastically, leading to an increased sensitivity to BSM effects. We propose a search with the ATLAS experiment for a novel model involving flavour-violating decays of a heavy resonance Z’->μ𝛕, which leads to final states with 2 muons and 2 tau leptons. This model can explain the muon g-2 anomaly and a dedicated search has not been carried out at the LHC yet, thus holding significant potential for discovery. The student will use Monte Carlo simulation to optimize this search, estimate backgrounds, and eventually evaluate the expected sensitivity assuming the full Run 2 dataset.

TamaraVázquez SchröderATLAS, CERN, Large Hadron Collider, Particle physics
IFAE-2402. Enriching the reach of the search for flavour-violating heavy Higgs bosons at the LHC2024-2025IFAEATLAS GroupWEBSITEAurelioJuste RozasAvailable

For the first time at the LHC, the ATLAS experiment searched for heavy Higgs boson candidates with flavour-violating couplings to top quarks and up or charm quarks. This new model opens up new production modes and decay channels never searched for before, leading to final states with multiple leptons (i.e., one pair of same-sign electric-charge leptons, or three or more leptons). A mild tension of 2.8 σ was found in the full Run-2 dataset. But why limit the flavour-violating coupling to quarks? A natural extension of this search would involve flavour-violating decays of the heavy Higgs boson to leptons of the 2nd and 3rd generations (H->μ𝛕), allowing for even more leptons in the final states. We propose a search for this novel BSM model, which could explain some of the tensions observed in previous tt̄W, tt̄H and tt̄tt̄ searches. The student will use Monte Carlo simulation to optimize this search, estimate backgrounds, and eventually evaluate the expected sensitivity assuming the full Run 2 dataset.

TamaraVázquez SchröderATLAS, CERN, Large Hadron Collider, Particle physics
IFAE-2403. Search for leptoquarks in tau final states at the LHC2024-2025IFAEATLAS GroupWEBSITEAurelioJuste RozasAvailable

Leptoquarks (LQs) are predicted by many new physics theories to describe the similarities between the lepton and quark sectors of the Standard Model and offer an attractive potential explanation for the lepton flavour anomalies observed at the LHCb experiment and the flavour factories. The ATLAS experiment at the Large Hadron Collider has a broad program of direct searches of LQs with multiple production/decay modes in a variety of final states, with preferential couplings to tau leptons. In this project, we propose a novel common search strategy focusing on the final states including tau leptons. This project will focus on 1lepton+1tau final states with non-resonant, singly and doubly resonant LQ production channels. Machine learning (ML) techniques will be used to define orthogonal event categories for different production modes and to discriminate the signal from background in each of these categories. The student will perform the ML optimization studies to maximize the signal sensitivity, as well as estimate the sensitivity of the analysis with the full Run 2 dataset collected with the ATLAS experiment.

GabrielCorreaATLAS, CERN, Large Hadron Collider, Particle physics
IFAE-2404. Model-agnostic search for new phenomena in multilepton final states at the LHC2024-2025IFAEATLAS GroupWEBSITEAurelioJuste RozasAvailable

Many extensions of the Standard Model (SM) predict events containing multiple leptons. In particular, final states with two leptons with the same charge, or three or more leptons serve as an ideal hunting ground for physics beyond the SM (BSM), as corresponding SM backgrounds are relatively rare at the LHC. While many BSM models have probed over the years, fully exploring the vast possible model space becomes unmanageable. We propose a novel and broad model-independent multilepton search in final states containing two same-charge leptons or three leptons of any flavour (electrons, muons and taus). The student will be involved in applying state-of-the-art unsupervised machine learning techniques that allow us to identify interesting events in the data in a model-agnostic way. The student will use Monte Carlo simulation to optimize this search, estimate backgrounds, and eventually evaluate the expected sensitivity assuming the full Run 2 dataset.

JackHarrisonATLAS, CERN, Large Hadron Collider, Particle physics
IFAE-2405. Exploring the LHC’s Hidden Secrets: Hunting for heavy scalars with flavour-violating couplings at the LHC2024-2025IFAEATLAS GroupWEBSITEAurelioJuste RozasAvailable

Since the discovery of the Higgs boson in 2012, the ATLAS and CMS experiments have tirelessly searched for hints of additional heavier Higgs bosons. Most of these searches assume that such heavy Higgs bosons couple to fermions in a flavour-conserving way (e.g., H->tt). However, there are extensions of the Standard Model (SM) that allow flavour-violating couplings (e.g., H->tc or tu), which could even be dominant, making the current search strategy ineffective. Recently, the first dedicated ATLAS search for such flavour-violating Higgs boson in the multi-lepton and multi-b-jet final state found an intriguing 2.8 σ excess using the full Run 2 dataset. With the start of Run 3 of the LHC, it is imperative to develop a much more powerful search able to reach a conclusive statement regarding the presence of a real BSM signal. The student will participate in the optimization of such a new search using Monte Carlo simulation, covering the event selection, event categorization and signal-to-background discrimination using Deep Neural Networks. If possible, the expected sensitivity of the improved search will be evaluated and compared with that of the original search.

ShaliniEpariATLAS, CERN, Large Hadron Collider, Particle physics
IRB-2405. Modulating determinants of tumour cell immunigenicity for enhanced immunotherapy effectiveness in childhood cancer2024-2025IRB BarcelonaPediatric Cancer EpigeneticsWEBSITEAlexandraAvgustinovaAvailable

Childhood cancers are biologically distinct from adult cancers. They do not display high levels of mutational accumulation, but instead are characterised by epigenetic deregulation. In the Pediatric Cancer Epigenetics Lab we ask fundamental questions about the biology of developmental tumours: How does epigenetic dysregulation lead to tumourigenesis? Which progenitor cells are amenable to epigenetically driven malignant transformation? What makes these progenitors especially susceptible, and can their transformation be reversed?

Our overall goal is to identify the specific epigenomic vulnerabilities of developmental tumours and to exploit them in the pursuit of personalised therapies to improve patient welfare and prognosis. We believe that one size does not fit all, and that we need to treat the individual, not the disease.

The Master´s student will use co-culture assays of mouse and patient-derived malignant rhabdoid tumour (MRT) cells and different immune cell types, CRISPR/Cas9 technologies and molecular profiling to identify why some MRTs are highly immunogenic, while others completely escape recognition by the immune system. We hope that understanding this dichotomy may unlock avenues to increase effectiveness of immunotherapy for MRT patients.

N/AN/AChildhood cancer, Epigenomics
IRB-2406. Exploring tumor vulnerabilities by targeting stress kinase signaling2024-2025IRB BarcelonaSignaling and Cell CycleWEBSITEAngel R. NebredaNebredaAvailable

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. We have used mouse models to demonstrate important roles for p38 MAPK signaling in tumor progression, particularly in breast, lung and colon cancer, as well as in the tumor response to chemotherapeutic drugs. Our work combines biochemical approaches and experiments in cultured cells with studies using mouse models and chemical tools. Ongoing projects in the group address the role of p38 MAPKs in two main topics: (1) Cancer cell homeostasis and chemoresistance mechanisms, and (2) Cross talk between cancer cells and stromal cells. The group has the ambition to identify new therapeutic opportunities based on the modulation of p38 MAPK signaling. We are also performing chemical and genetic screenings to find new actionable targets that can be used to boost current cancer therapies as well as to design new targeted therapies for particular cancer types.

cancer cell homeostasis, chemotherapy resistance, signaling network, targeted therapy, tumor microenvironment
IFAE-2406. from climate change to neurons and carcinogenesis using particle physics2024-2025IFAETheory GroupWEBSITEPereMasjuanAvailable

The evolution of complex systems such as neurogenesis, carcinogenesis, and the climate change, is based on multiple interactions that are very complicated to simulate, especially if the key ingredients are hidden variables. However, they all share the fate of being subject to the principle of minimal energy, which dictates their evolution. The principle can be linked to the symmetries of the system as a whole and can be studied using the mathematical tool of Group Theory. In this project, we will approach the evolution of such complex systems (following students’ preference) by exploring their physical properties and symmetries, and we will attempt to describe them mathematically using the elements of Group Theory. As such, a group of differential equations will be provided and related using the set of Renormalization Group Equations which will then be calibrated with related experiments during the associated Minor Project.

carcinogenesis, Climate change, group theory, neurogenesis, symmetries
IRB-2407. Epiegenetic and metabolic mechanisms in stem cell homeostasis, aging and cancer metastasis2024-2025IRB BarcelonaStem cells and cancerWEBSITESalvadorAznar BenitahAvailable

My lab is internationally recognized for its significant contributions on the systemic regulation and timing (circadian rhythms) of stem cell function in homeostasis and aging, how stem cell identity is epigenetically regulated during homeostasis and cancer, and for the identification of metastasis-initiating cells and how they are influenced by diet. Our group pioneered the finding that the timing of stem cell function is highly regulated and fixed, and is controlled by the circadian clock machinery. Since that finding, we have shown that circadian rhythms control many SC functions and are essential to maximize functionality while minimizing potential damages and energy expenditure. My lab is also interested in studying how the function of stem cells is regulated by epigenetic mechanisms. We were also among the first to show that epigenetic mechanisms are relatively dispensable for maintaining the identity of adult SCs, yet ensure that SCs remain flexible in response to stresses. We are also very interested in the cells that promote metastasis. We recently identified the cells responsible for metastasis in several types of tumors. These cells have intriguing characteristics: i) they are exclusive in their ability to generate metastases; ii) they express the fatty acid channel CD36, and are characterized by a unique lipid metabolic signature; iii) they are exquisitely sensitive to the levels of fat in circulation, and consequently, they relate the predisposition of metastasis to the content of dietary fat; iv) they are highly sensitive to CD36 inhibition, which almost completely abolishes their metastatic potential. We combine state-of-the-art large scale genomic and epigenomic studies, proteomics, and molecular and cellular biology approaches using in vivo genetic models in mice and patient-derived samples.

Adult stem cells, Aging, diet, Epigenetics, metastasis
IFAE-2407. Detecting gravitational waves with the Moon2024-2025IFAETheory GroupWEBSITERafelEscribanoAvailable

Gravitational waves are our newest eyes on the Universe. Their detection has brought us new key information about black holes, and many other interesting physics, such as the astrophysical origin of Gold. The quest to extend these detection to a broad spectrum is open. I recently showed that the orbit of the Moon may be affected by gravitational waves from supermassive black holes. In this TFM I want to do the data analysis required to test this with the data from laser ranging of the Moon.

Data Analysis, Gravitational waves, Moon, orbital mechanics
ICFO-2402. Characterization and optical manipulation of mechanical properties of lipid membranes2024-2025ICFOSingle Molecule BiophotonicsWEBSITEMariaGarcia-ParajoAvailable

Lipid oxidation is a natural process in which oxidants attack and transform lipids, altering the properties and mechanical behaviour of lipid membranes. Several studies have shown that oxidized lipids affect cell homeostasis and are involved in the onset of several inflammatory and neurodegenerative diseases. Understanding and controlling the initial steps of lipid oxidation as well as the effects on membranes is crucial to unveil the physiopathology and to progress in the development of novel treatments.

In our laboratory, we combine light-based tools with advanced fluorescence microscopy techniques to photo-induce the oxidation of lipids and to assess their effects on the mechanical properties of membranes with high spatiotemporal control. In particular, this project aims to (i) study the effects of controlled photo-oxidation processes on the mechanical properties of lipid membranes, including model synthetic systems and mammalian cells and, to (ii) photo-manipulate the organization of force-sensitive cellular structures in living cells. For this, the Master student will initially explore different fluorescent sensors and photosensitizing compounds, combining photophysical methods and fluorescence microscopy techniques, with particular emphasis on fluorescence lifetime imaging (FLIM). Then, he/she will study how mammalian cells respond to photo-oxidative damage by characterizing the interactions and re-organization of mechanosensitive proteins.

Candidates with a background in physics/chemistry/biology are encouraged to apply. The student will work in an interdisciplinary group and will acquire wet lab skills, hands-on experience in advanced fluorescence microscopy techniques, photophysics of fluorescent and light-activatable molecules, preparation and study of lipid membranes and cell culture. Moreover, the student will strengthen his/her writing and oral skills by regularly discussing and presenting the research progress to a multidisciplinary and international audience.

JoaquimTorraFluorescence Microscopy, lipid photo-oxidation, Mechanobiology, reactive oxygen species
IBEC-2401. Nanomechanics of lysosomal storage disorders2024-2025IBECNanoprobes & NanoswitchesWEBSITEPauGorostizaAvailable

The overall goal of the project is to study the implications of the abnormal lipid accumulation in lysosomal storage disorder lipidoses, on membrane biomechanical properties and how this correlates with endocytosis and vesicular trafficking, in order to set the basis improved treatments capable of reverting the lipid accumulation and associated biomechanical/cell biology effects. 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.

MarinaGiannottiAtomic force microscopy, Biophysics, force spectroscopy, lipid membrane, Nanomechanics
IBEC-2402. Nanoprobes & Nanoswitches II2024-2025IBECNanoprobes & 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.

MarinaGiannottielectron transport, interactions, Proteins, scanning probe microscopies, single molecule
IBEC-2403. Nanoprobes & Nanoswitches III2024-2025IBECNanoprobes & 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
IRB-2408. Understanding stress adaptation from yeast to mammalian cells.2024-2025IRB BarcelonaCell signalingWEBSITEFrancescPosasAvailable

The main focus of our group is to understand how cells detect and respond to environmental changes. We have focused our studies on the characterization of the stress signal transduction pathways, especially those controlled by MAP kinases of the Hog1/p38 family, also known as the stress-activated MAP kinases (SAPK). Using S. cerevisiae budding yeast as a model organism, as well as mammalian cells, we study the molecular mechanisms required to respond to changes in the extracellular environment and which are the adaptive responses required for cell survival. Our main research lines are:

1. SAPK signaling: Using quantitative data in single cells and mathematical modelling, together with mutational analyses, we study the basic signaling properties of stress-responsive MAP pathways and how to alter them.
2. 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 characterization of the bases of adaptation in eukaryotes. We are also using genome wide CRISPR screening to identify essential genes for stress adaptation.
3. 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.
4. 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.

Eulàliade Nadalcell cycle regulation, SAPK, Signaling, single cell analysis, Stress adaptation, transcriptional regulation
IBEC-2404. Characterisation of novel interaction in CRISPR models of glioblastoma2024-2025IBECMolecular and Cellular NeurobiotechnologyWEBSITEJosé Antoniodel Río FernándezAvailable

Glioblastomas are the most common brain tumours, with a first year survival of less than 10% of diagnosed patients. Due to the heterogeneity of these tumours no specific treatment has been developed further than surgery and radiotherapy. In our lab we have identified a novel interaction which can have a significant impact in tumour development. Our aim is to investigate this interaction using bot cellular and animal models. For this reason we are developing Crispr cell line of glioblastoma which the interested student will help to characterise. Our lab offers expertise in molecular biology, microfluidics and microscopy of a wide range of models such as cell lines, organoids, primary cultures, organotipic cultures and mouse models. We are looking for a highly motivated student with experience in cell culture and molecular biology.

PolPicón PagèsCancer, Glioblastoma, Molecular Biology, Neurobiology
ICFO-2403. Engineering new photosynthetic complexes with enhanced photoprotective functions2024-2025ICFOPhoton Harvesting in Plants and BiomoleculesWEBSITENicolettaLigouriAvailable

Our group aims at understanding how changes in light, structure and environment regulate the molecular mechanisms of photoactive (bio)molecular systems. To do so we develop and apply novel ultrafast spectroscopic tools that we combine with molecular dynamics simulations.

One goal of our group is to understand how plants thrive under natural sunlight and how we can optimise their response to sunlight changes. Indeed sunlight is a fluctuating form of energy. This means that it can suddenly spike and lead to a surplus of photoexcitations in the photosynthetic membrane, and therefore cause severe photodamage. To avoid this plants have evolved a series of ingenious mechanisms to “”get rid”” of the surplus of photoexcitations and, in this way, photoprotect themselves. It has been proposed that this photoprotective mechanism can be optimised to obtain more plant biomass, and therefore more food, but how can we do it?

The student will test whether it is possible to optimise photoprotection by engineering in vitro a set of photosynthetic complexes that can in principle accelerate the rate at which photoprotection is activated/deactivated, with the goal to make this rate more similar to the one of sunlight fluctuations. The student will use novel ultrafast time-resolved spectroscopy tools to determine the potential of the engineered complexes to accelerate the regulation of photoprotection.

For the student it would be beneficial to have a background in physics/chemistry/biotechnology/biology/material science or similar. The student will acquire wet lab skills, hands-on experience in protein engineering, hands-on experience on cutting-edge ultrafast spectroscopic techniques and experience in writing and presenting the research results to a multidisciplinary audience.”

Mutational analysis, Photoprotection, Photosynthesis, Protein engineering, Ultrafast time-resolved spectroscopy
MELIS-2403. Structure, function and pharmacology of ion channels: relevance to neurological disorders.2024-2025MELIS-UPFMolecular PhysiologyWEBSITEJosé ManuelFernández FernandezAvailable

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 1A 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 ion channels activity in heterologous expression systems and neurons from wild-type and disease model knock-in mice. In vivo analyis is also planned by using C. elegans to evaluate the effect of these CaV2.1 modulators on enhanced neurotransmission due to CACNA1A malfunction.

electrophysiology, N-glycosylation, Neurological disorders., neuronal voltage-gated calcium channels, Pharmacology
IBEC-2405. Bone Marrow-on-Chip: a sensor of early relapse in lung cancer2024-2025IBECBiosensors for BioengineeringWEBSITEJavierRamonAvailable

Cancer relapse, caused by surviving cancer cells after initial treatment, remains a significant challenge. Current chemotherapy has limitations, with a 30% relapse rate in lung cancer stages 1 to 3. Predicting relapse is difficult, relying on radiological evidence. Early detection of chemo-resistance is crucial. New tools, like Minimal Residual Disease (MRD) detection using circulating tumor DNA (ctDNA), offer post-surgery insights but lack predictive ability.
Our groundbreaking hypothesis focuses on Bone Marrow Mesenchymal Stem Cells (BM-MSCs) as early sensors of tumor development. They influence hematopoietic stem cell differentiation, potentially foretelling relapse. In early cancers, myeloid cells create supportive niches, facilitating relapse.
Our EU pathfinder project, part of the Bone Marrow-on-Chip platform (BMoC-Sense), aims to emulate human bone marrow physiology. The platform integrates POLIMI’s mechanically relevant microenvironment and LUND’s biological cues to recapitulate native signaling. Optical biosensors (MetaSense tech by IBEC) enable real-time measurements.
The project involves a retrospective study using plasma from lung cancer patients with diagnosed relapse to calibrate BMoC-Sense. A prospective study at INT will identify potential biomarkers in lung tumor relapse. If successful, BuonMarrow will be a proof-of-concept device for early detection, addressing the unmet need in 30% of lung cancer patients at stages 1 to 3.
The student will collaborate with an international team to develop sensing technology and organ-on-a-chip technology.

Biosensors, cancer relapse, Organs-on-a-Chip
ICFO-2404. AI-driven materials discovery2024-2025ICFOCO2MAPWEBSITEF. PelayoGarcia de ArquerAvailable

The is an urgent need to accelerate the transition towards sustainable energy sources. This requires the acceleration in the deployment of energy-related materials, including energy harvesting (e.g., PV) and storage (e.g., batteries, clean H2). The student will work in an exciting project seeking to use AI and high-throughput experimentation to accelerate the discovery of energy materials.

AI, energy materials, high-throughput, robots, Sustainability
MELIS-2404. Bacteria and mental health: the neuroactive potential of the gut microbiome2024-2025MELIS-UPFMicrobiome Research GroupWEBSITEMireiaValles-ColomerAvailable

The human microbiome plays a key role in maintaining our health. Through the microbiota-gut-brain axis (a bidirectional communication system between the gut microbiome and the brain) the microorganisms residing in the gut can also influence mental health and well-being. Besides modulation of neural, endocrine, and immune gut-brain signaling routes, members of the gut microbiome can also metabolize a wide range of neuroactive compounds (e.g. serotonin, GABA, or dopamine) with impact on host health. We produced the first catalogue of neuroactivity of gut bacteria (Valles-Colomer et al, Nat Microbiology 2019), and are currently expanding it by several orders of magnitude through by computational analysis of gut microbiomes.

In this project, the student will contribute to 1) the mining of genomes with neuroactive potential, and 2) the assessment of the link between gut microbiome composition and mental health outcomes. If interested, can also get involved in projects modeling the social transmission of the microbiome, another research line in the team. Notions of bioinformatics (being familiar with Python and R) and multivariate statistics are required. Experience in high-performance computing is a plus but not indispensable if you are eager to learn.

gut-brain axis, mental health, microbiome, neuroactivity
IRB-2409. Drosophila as a model in cancer biology2024-2025IRB BarcelonaDevelopment and Growth Control LaboratoryWEBSITEMarcoMILANAvailable

Cancer has been classically understood as a cell-autonomous process by which oncogenes and loss of tumor-suppressor genes drive clonal cell expansion. However, research in a variety of model organisms, including Drosophila and mice, has started to unveil the relevance of cell communication in tumor development. Chromosomal Instability (CIN), defined as an increased rate of changes in chromosome structure and number, is a feature of most solid tumors in humans. While CIN promotes the gain of oncogene-carrying chromosomes and the loss of tumor-suppressor-gene-carrying chromosomes in certain cancers, its impact on the biology of the cell and on the homeostasis of the tissue, as well as its role in tumorigenesis, are far from being fully elucidated. Of note are the highly deleterious effects of CIN as a result of the generation of highly aneuploid karyotypes and the production of DNA damage. Our lab has developed a tumor model of CIN in Drosophila where the relevant cell populations and pertinent cell interactions involved in the response of an epithelial tissue to CIN have been identified. This model has led to the identification of emerging, tumor-like, cellular behaviors such as epithelial to mesenchymal (EMT)-like cell fate transitions, senescence, cell invasiveness, metastatic behavior, and malignancy. Master students will be involved in the identification of the underlying molecular mechanisms through a functional genomics approach.
References: Dekanty et al, PNAS (2012); Clemente-Ruiz et al, Dev Cell (2016); Muzzopappa et al, PNAS (2017); Benhra et al, Dev Cell (2018); Joy et al Dev Cell (2021); Romao et al Current Biology (2021); Gracia et al Nat Comm (2022); Barrio et al Current Biology (2023).

Aneuploidy, Cancer, CIN, genetics, genomics
ICFO-2405. Using state-of-the-art fluorescence microscopy techniques to study the mechanobiology of the secretory pathway2024-2025ICFOSMB/Intracellular Dynamics and NanoscopyWEBSITEFelixCampeloAvailable

Cells interact with their environment through focal adhesions (FAs), molecular platforms that bridge the extracellular matrix (ECM) and the cytoplasm. These adhesion complexes serve as sensors of a wide variety of mechanical forces, including tensile forces or the rigidity of the ECM. These physical forces are converted into biochemical signals, acting as initiators of different signaling cascades that regulate cellular processes such as differentiation, proliferation, adhesion and migration. Despite the knowledge earned in the past decades about the role of the cell surface in mechanosensing, little is known about whether the endomembrane system inside the cells also takes part in mechanotransduction.

Recent studies have shown that mechanical forces regulate transport carrier formation in the Golgi apparatus, the central cellular organelle responsible for protein maturation, trafficking, and secretion. Moreover, those carriers are delivered near or at FAs, suggesting that there might be a bidirectional communication between the plasma membrane and the Golgi. The study of the mechanobiology of the endomembrane system has gained increasing attention in recent years, making it in one of current hot topics in cell biology. Because the field is still in its infancy, there are many questions in the need for answers, such as which are the mechanisms governing the communication between the extracellular milieu and different organelles, or how cells respond and adapt to changes in their environment. Answering these questions is crucial to understand cell behavior in physio- and pathological conditions, such as cancer. This could help opening up new venues in cancer research and treatment.

The goal of this Master Project will be to apply advanced fluorescence microscopy techniques, together with mechanical stretching devices, and molecular and cell biology tools to study how mechanical signals affect cellular trafficking, the mechanisms of communication behind such processes, and how cells adapt to changes in their environment.

JavierVera LilloFluorescence Microscopy, Golgi apparatus, Mechanobiology, protein secretion, stretching
MELIS-2405. Study of the role of mechanoreceptors in amyloid toxicity in Alzheimer’s disease2024-2025MELIS-UPFMolecular Physiology LabWEBSITEFrancisco JMuñozAvailable

Alzheimer’s disease (AD) is due to the extracellular aggregation of the amyloid ß-peptide (Aß) into oligomers and fibrils, which are synaptotoxic leading finally to cell death. There is not specific treatments that can cure, prevent of retard the disease.
The hypothesis proposes that oligomeric Aß (oAß) directly or indirectly (by oxidative stress) affect to the physiological function of mechanoreceptors that will have deleterious effects in the growth and maintenance of the synaptic spines, and a rise in intracellular calcium.
The objectives is the characterization of the effect of the oAß binding and/or the oxidative stress induced by oAß on TRPM7 and Piezo1 functions in the synaptic spines. The mechanical forces that drives dendrite growth are related to mechanoreception. In particular, spine growth and the maintenance of the functional shape of the spines are under the control of mechanoreceptors that regulates actin cytoskeleton. Therefore, we will study the effect of oAß on these receptors and how it will affect to synaptic plasticity and the existing spines, and we will also address the study of their role in the dysregulation of intracellular calcium.

The biological materials will be cell lines, neuronal primary cultures from mice and hiPSCs. Results will be validated in brain samples from APPswe/PSEN1dE9 transgenic mice and AD patients and no demented individuals.

The methodology includes molecular biology of proteins and mRNA, gene overexpression and silencing, siRNAs, confocal microscopy, spectrofluorometry, calcium image, path-clamp, flow cytometry and in silico studies.

The expected results of our project are the identification of new molecules involved in Aß pathophysiology that would be considered as therapeutic targets for the treatment of AD.

Alzheimer, Calcium, hypocampus, mechanoreceptors, memory
MELIS-2406. Implication of zinc excess in mitochondrial function in the context of neurodegeneration2024-2025MELIS-UPFLaboratory of Molecular PhysiologyWEBSITERubénVicenteAvailable

Zinc excess and its consequences on mitochondrial physiology underlies the mechanism of harmful processes that affect human health such as neurodegeneration. This is a multidisciplinary research project that focuses on the study of mitochondria zinc fluxes and their consequences, which are essential to understand and prevent certain deleterious cellular processes that are relevant in the nervous system. The methodology involves cell culture, live cell imaging and detection, confocal microscopy and molecular biology techniques.

mitochondria, zinc
IBEC-2406. Engineering mRNA for Specific Expression in Brain Endothelial Cells2024-2025IBECMolecular BionicsWEBSITEGiuseppeBattagliaAvailable

Expression of therapeutic mRNA in the brain has the potential to treat neurodegenerative diseases such as Alzheimer’s disease. However, off-target mRNA expression, particularly in scavenging organs such as the liver and spleen, limits the clinical translation of mRNA-based therapies.

We aim to achieve mRNA expression specifically in the brain vasculature by harnessing the markedly low rate of proliferation of brain endothelial cells, a key feature of their specialized phenotype. To this end, we will exploit the function of microRNA (small non-coding regulatory RNA strands) which either inhibit or enhance mRNA expression in proliferating or non-proliferating cells, respectively. Hence, by incorporating binding sites for specific microRNAs, we will engineer mRNA with enhanced expression in non-proliferating brain endothelial cells and reduced expression in proliferating liver/spleen endothelial cells.

The main objectives will be to:
1) map the RNA profile of brain/liver/spleen endothelial cells to identify suitable microRNA candidates.
2) Design reporter mRNA (luciferase) strands incorporating microRNA-binding sites in their 3’UTR
3) Transfect engineered mRNA into primary endothelial cells in vitro and assess modulation of protein expression.

The learning outcomes will be:
1) RNA profiling
a. Extraction of total RNA pool from isolated cells and sequencing of RNA
2) Cell culture
a. Extraction of primary endothelial cells from animal organs
b. Cultivation in sterile conditions
3) mRNA design and transfection
a. Constructing DNA plasmids for in vitro transcription of engineered mRNA, and incorporation of mRNA into cells through transfection
4) Reporter assays
a. Luminescence-based assays to quantify expression of engineered mRNA in primary endothelial cells

DanielGonzalez CarterBrain targeting, endothelial cells, microRNA, mRNA engineering
MELIS-2407. Advanced microscopy and new model organisms to study climate change adaptation2024-2025MELIS-UPFLive-cell structural biologyWEBSITEOriolGallegoAvailable

Ectotherms, organisms that cannot control their “body” temperature, are vulnerable to fluctuations in the ambient temperature. Eukaryotic microorganisms are especially susceptible because their survival relies on more sofisticated membrane dynamics than procaryotes. Thus, global warming is increasingly challenging the biodiversity of eukaryotic microorganisms and the ecological functions associated to these species. Unfortunately, the lack of knowledge about how species adapt their essential cellular processes to life-threating temperatures, hinders accurate predictions on the climate change impact and frustrates the efforts to develop remedies.

We offer a remunerated position for a master student to integrate advanced light and electron microscopy to investigate in situ protein networks that regulate membrane dynamics across the phylogeny of the Saccharomyces genus, including fungi species found in nature that have been poorly studied. Interestingly for us, the main phenotypic difference among these species is their ability to grow at different ambient temperatures. We will exploit the genus’ diversity to deliver mechanistic knowledge that aids the prediction of eukaryotic microorganism biodiversity loss caused by global warming and that inspires solutions to minimize such effects.

Understanding the molecular basis that constrain fungi viability to specific temperature windows will allow us to narrow the gap towards understanding the mechanism of thermal adaptation in eukaryotes. The project involves the establishment of new model organisms in the laboratory as well as gene editing techniques. The student will learn super resolution microscopy, particle tracking and image analysis. With the group of Alex De Marco, (NYSBC, US), we will also implement new cryo-electron tomography methods to resolve protein structures at atomic resolution in situ.

During the progression of the project the student will acquire a strong expertise in advanced light microscopy. Depending on the student’s skills and interest, the project could also involve modelling of 3D structures or machine learning for image analysis.

Climate change, Cryo-Electron Tomography, Machine learning, Structural biology, super resolution microscopy
CRG-2403. Machine Learning and Large Language Models for biodiveristy genomics projects2024-2025CRGComputational Biology of 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 (https://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 precise gene identification. 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, . 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 produce full-lengh RNA sequences.
Within the framework of this program, there are three possible specific projects
1. Methods for genome annotation based on long read RNAseq (experimental/computational)
2. Methods for selenoprotein prediction and annotation (bioinformatics)
3. Prediction high quality complete annotations (including lncRNAs) using Machine learning (ie. structured decoding from learning embedding) and large language models (strongly computational)

Artificial Inteligence, Biodiversity Genomics, gene annotation, long-read RNAseq, Machine learning
IBEC-2407. A computational study of the low-density lipoprotein receptor-related protein 1 (LRP1) structure and dynamics2024-2025IBECMolecular BionicsWEBSITEGiuseppeBattagliaAvailable

The Blood-Brain Barrier (BBB), a crucial interface enveloping brain capillaries, rigorously regulates the cerebral chemical balance. Nature employs receptor-mediated transcytosis, a process where a protein receptor recognizes and binds to a molecule (ligand), activating transport. This project explores the macromolecule transportation across the BBB, focusing on understanding interactions between macromolecules and receptors, particularly the LDL (Low-Density Lipoprotein) receptor family implicated in brain cancer and neurodegenerative disorders.
Our computational focus is determining the structure of LRP1 (LDL Receptor-related Protein 1), an essential receptor in the LDL family. Lacking experimental structure, we utilized tools like AlphaFold and homology modelling to predict the 3D distribution of its 61 domains. LRP1’s flexibility prompts the exploration of multiple equilibrium conformations, likely representing distinct functional forms. Subsequently, our study extends to other LDL family members.
Armed with these structures, we extensively investigate LRP1’s binding activity with known ligands using molecular docking methods. This approach unveils major binding sites and provides insights into the transport mechanism. The student actively engages in activities, learning to independently execute and analyze results from bioinformatics tools such as molecular modelling, docking, and dynamics simulations.

Gian MarcoTuveriBioinformatics LRP1 molecular dynamics docking
IBEC-2408. Engineering biohybrid soft robots based on stem cells2024-2025IBECIntegrative Cell and Tissue DynamicsWEBSITEXavierTrepatAvailable

Biohybrid devices are systems that combine living cells with soft materials to engineer functions that outperform inert machines. One example of this new type of devices is the use of muscle cells to power soft robots that perform functions such as swimming, walking, gripping or pumping. A main goal of our group is the development of a new generation of biohybrid devices based on folded stem cell tissues under optomechanical control. Thanks to the potential of stem cells, these devices will be able to self-heal, to self-assemble, to self-replicate, and to generate significant forces such as those that drive early embryonic development. In this project the student will actively engage in integrating a diverse array of tools spanning experimental bioengineering to computational modeling. On the experimental front, the student will gain hands-on experience with techniques such as micropatterning, microfluidics, and optogenetics. Micropatterning and microfluidics will be employed to sculpt tissues, while optogenetics will enable precise control over tissue movements. Complementing these experimental approaches, the computational facet of the project will involve the use of hierarchical 3D vertex models, facilitating a comprehensive understanding of the dynamics at play. The specific tasks of the project will be discussed and tailored to the student’s background and interests, with the final goal of designing and testing biohybrid soft robots with sensing, actuation and control capabilities.

imaging, microfluidics, optogenetics, Soft robotics, Stem Cells
CRG-2404. Mechanical regulation of nuclear biomolecular condensates and RNA-processing dynamics2024-2025CRGMechanics of Organelle RemodelingWEBSITEAdelAl JordAvailable

Our group is on a mission to uncover mechanisms that cells deploy to functionally remodel their organelles in health & disease. One of our key research areas focuses on the relation between biophysical forces and essential nuclear organelles known as biomolecular condensates, which are key in processing genetic information. Our goal is to understand how cytoskeletal forces mechanically impact nuclear dynamics across scales, from condensate remodeling down to RNA-processing regulation, and how this biophysical relation influences somatic cell division and specialization. By understanding these processes, we can potentially develop new ways to treat serious diseases associated with changes in cell mechanics, like cancer and conditions that cause premature aging.

Using an interdisciplinary methodology, the student will address a critical question in mechanobiology: how cytoskeletal forces in mammalian cells mechanically regulate the dynamics of nuclear RNA-processing organelles, named biomolecular condensates, to drive vital cellular processes. Our toolbox includes techniques like protein multiplexing, advanced live and super-resolution imaging, optogenetics, spatial transcriptomics, biomimetic systems, and force measurement and modulation assays.

We are looking for a student with a background in Cell Biology, Molecular Biology, or Biophysics, who is interested and excited about the mysteries of the cytoskeleton, biomolecular condensates, aging, and mechanobiology as we are.

Aging, Biomolecular condensates, Cytoskeleton, Mechanobiology, nucleus
IBEC-2409. The role of mechanics in intestinal timekeeping2024-2025IBECIntegrative cell and tissue dynamicsWEBSITEXavierTrepatAvailable

In the mammalian intestine, different cell types display distinct genetic programs not only according to their function and position within the tissue but also in a time-dependent manner. One of the main contributors to the temporal and spatial orchestration of intestinal homeostasis is the circadian clock. The circadian clock keeps the intestine synchronised with the rest of the organs and tissues in the body and with the cyclic 24-hour environment. We are progressively learning how different signalling pathways coexist and impact time in this complex tissue, but still very little is known about the role of mechanics, whose signalling is of much importance, given the intestine is subjected to considerable mechanical stress.

The student that selects this project will study the effect of mechanical constraints on the small intestine epithelium, focusing on how mechanotransduction impacts the circadian rhythms of individual cells. They will carry out this study using a multidisciplinary approach that includes cell culture (2D and 3D small intestine mouse organoids), microfabrication, microfluidics, confocal microscopy, and computational analysis, all of them technologies well established in the host lab. The main aim of this project is to help us understand if intestinal clocks are subjected not only to endocrine but also to mechanical regulation, and how this new signalling pathway differentially impacts the program of the different intestinal cell types.

Juan FranciscoAbenzaCircadian, Mechanobiology, Microfabrication, microscopy, organoids
IRB-2410. Nuclear transport of intrinsically disordered proteins2024-2025IRB BarcelonaLaboratory of Molecular BiophysicsWEBSITEXavierSalvatellaAvailable

The mechanisms by which large nuclear globular proteins are transported from the cytoplasm, where they are synthesised, to the nucleus are well understood: they rely on the presence in their sequences of motifs known as nuclear localisation signals (NLSs). NLSs represent binding sites for transport proteins that also have an affinity for FG (Phe-Gly) motifs in the intrinsically disordered domains of nucleoporins that define the permeability barrier of nuclear pores: this bivalent character allows transport proteins to chaperone their cargo across the relatively hydrophobic environment of this barrier. How intrinsically disordered regions are transported to the nucleus, where they are very frequent, is instead not well understood. Since they do not fold into well-defined three-dimensional structures they can in principle thread across the permeability barrier but how their sequences influence the rate of transport is unknown. This gap in knowledge is problematic for understanding how the sequences of nuclear intrinsically disordered are shaped by nuclear transport and, especially, for understanding why mutations or aberrant post-translational modifications can clog nuclear pores in disease (Eftekharzadeh et al, 2018, Neuron). The candidate selected will contribute to answering this question by using a multidisciplinary approach involving bioinformatics, biophysical experiments with purified proteins and experiments in cells (Basu, Martínez-Cristóbal et al, 2023, in press in Nat. Struct. Mol. Biol.)

CarlaGarcia CabauBiomolecular condensation, Biophysics, cell biology, Intrinsic Disorder
IRB-2411. Decipher microtubule network organization in pluripotent stem cells and derived neuroepithelium by advanced microscopic imaging.2024-2025IRB BarcelonaMicrotubule organization in cell proliferation and differentiationWEBSITEJensLudersAvailable

The microtubule cytoskeleton provides cells with mechanical support, mediates intracellular transport, and segregates the chromosomes during cell division. These functions are crucial for cell proliferation and differentiation and thus the formation and maintenance of tissues such as the neuroepithelium. Indeed, malfunctioning of the microtubule cytoskeleton has been linked to both impaired neurodevelopment and neurodegeneration.

Most of our knowledge about how the microtubule network is organized is derived from studies in fibroblast-type of cells and cancer cell lines. However, it is unclear to what extent these concepts apply to other cell types. Moreover, significant remodeling of the microtubule network occurs during cell differentiation. In the neuroepithelium highly polarized neural progenitors are vertically aligned, with a centrosome that is localized underneath the apical membrane. Only few microtubules seem to originate from the centrosome, generally considered the main microtubule organizing center.

This project aims to elucidate how microtubules are organized in induced pluripotent stem cells (iPSCs), determine the role of the centrosome and potentially other microtubule organizing centers, and investigate microtubule network remodeling during differentiation of iPSCs into neuroepithelium-like neural rosettes. For this, cells will be subjected to microtubule nucleation and growth assays and analyzed after fixation or live by fluorescence microscopy including super resolution imaging.

The student will learn the culture and neural differentiation of iPSCs, advanced microscopic imaging techniques, and uncover fundamental principles of microtubule network organization in stem cells and derived neural rosettes that are highly relevant for development and disease.

centrosome, Cytoskeleton, microtubules, neurodevelopment, Stem Cells
CRG-2405. Building the cytoskeleton: from active matter to biological function2024-2025CRGIntracellular Self-OrganizationWEBSITEThomasSurreyAvailable

The lab of Thomas Surrey is interested in the question of biological self-organization, studying how the cytoskeleton of living cells builds itself. The goal is to understand in a quantitative manner biological network behaviour based on physico-chemical principles. The lab uses a bottom-up synthetic biology approach and has pioneered a number of novel microscopy-based in vitro reconstitutions that provide insight into the molecular mechanisms underlying microtubule cytoskeleton organization, dynamics and function. Several projects are available addressing questions of cytoskeleton self-organization and dynamics. Depending on the training and interest of the student several projects are available. They will train the student in one or several of the following methods: molecular biology, protein biochemistry, advanced biochemical in vitro reconstitutions (bottom-up biochemistry), biophysical methods, modern optical microscopy (down to single molecule imaging), microfabrication, quantitative image data analysis and computer simulations of active matter. The lab is currently particularly interested in the role of motor proteins such as dynein and kinesins for mitotic spindle assembly and the effects of molecular crowding and micro-confinement for active matter self-organization. Using the mitotic spindle as an example, the PhD projects will contribute to a better mechanistic understanding of how biological function emerges from active matter.

Selected recent publications:
Henkin, Brito, Thomas, Surrey. The minus-end depolymerase KIF2A drives flux-like treadmilling of γTuRC-uncapped microtubules. J Cell Biol 222, e202304020 (2023).
Henkin, Chew, Nédélec, Surrey. Cross-linker design determines microtubule network organization by opposing motors. PNAS 119, e2206398119 (2022).
Hannabuss, Ramirez, Cade, Fourniol, Nédélec, Surrey. Self-organization of minimal anaphase spindle midzone bundles. Curr Biol 29, 2120-2130 (2019).
Roostalu, Rickman, Thomas, Nédélec, Surrey. Determinants of Polar versus Nematic Organization in Networks of Dynamic Microtubules and Mitotic Motors. Cell 175, 796-808 (2018).
Juniper, Weiss, Platzman, Spatz, Surrey. Spherical network contraction forms microtubule asters in confinement. Soft Matter 14, 901-909 (2018).

computer simulation, in vitro reconstitution, molecular crowding, optical microscopy, synthetic biology
IBEC-2410. Photopharmacological control of dopaminergic neuronal circuits of C. elegans2024-2025IBECNanoprobes and Nanoswitches of Pau GorostizaWEBSITEGalynaMalieievaAvailable

Successful applicant will join the project that aims to study dopaminergic circuits of C. elegans using photopharmacological approach.
The brain’s dopaminergic system is involved in most higher brain functions, such as cognition, learning, pleasure sensation, and complex feeding behaviours. Despite years of sustained research, the scientific understanding of dopaminergic circuits of the brain remains fragmentary and elusive. To advance our knowledge of the principles of dopaminergic neurotransmission, new molecular tools are required to control the activity of the dopamine receptors at high spatiotemporal precision and pharmacological selectivity. The current project will combine photopharmacology, an innovative approach in neuroscience, and C. elegans, a highly convenient model organism, to study dopaminergic circuits that underlie complex behaviours.
Photopharmacology is based on using pharmacologically selective compounds with a light-sensitive switch incorporated in their structure to control endogenous neuronal receptors and specific neuronal circuits with light. We will use photo-controllable dopaminergic compounds to activate or suppress dopaminergic circuits of C. elegans with light and to study how they govern the locomotion and mechano-sensation of nematodes. The research project will be carried out in close collaboration with Dr Michael Krieg (Neurophotonics and Mechanical Systems Biology group, ICFO).

MichaelKriegC. elegans, dopamine receptors, neuronal circuits, photopharmacology
ICFO-2406. Quantum simulation and computing with ultracold neutral atoms2024-2025ICFOUltracold Quantum GasesWEBSITELeticiaTarruellAvailable

Ultra-cold atoms are a novel platform for the study of quantum many-body systems. They provide quantum matter that can be controlled almost at will using the tools of optics and atomic physics, and allow one to engineer a broad range of model Hamiltonians in table-top experiments. This bottom-up approach comes very close to Feynman’s idea of a “quantum simulator” – a special purpose quantum computer for solving problems out of reach for classical computers.

We offer Master theses in our three laboratories:

In the potassium lab, we investigate mixtures of quantum gases where the competition of interactions of different origins reveals quantum fluctuations and correlations. For instance, we exploit mixtures of Bose-Einstein condensates (BECs) to create the most dilute liquids existing in Nature [Cabrera et al., Science 359, 301 (2018)], engineer gauge theories [Frölian et al., Nature 608, 293 (2022)] and investigate exotic supersolids.

In the strontium lab, we aim at synthesizing the cleanest and purest “solids”. To this end, we trap atoms in optical lattices – artificial crystals of light created by interfering laser beams – and observe how they hop from site to site by imaging them at the single-atom level. With such quantum gas microscope, we want to perform quantum simulations of the Fermi-Hubbard model [Tarruell and Sanchez-Palencia, C. R. Physique 19, 365 (2018)], which is believed to hold the key of high-temperature superconductivity.

In the Rydberg lab, we are interested in spin physics. Our goal is to develop a very flexible platform to engineer spin models, and use them to address fundamental physics problems, focusing on lattice gauge theories for high energy physics. To this end, we are constructing a new apparatus where strontium atoms will be trapped in holographically-generated optical tweezers and will interact with each other when excited to Rydberg states.

All our projects include both experiment and theory, and are carried out in a team of 3-4 people.

Bose-Einstein condensates, microscopy, optical lattices, quantum simulation/computing, Rydberg atom arrays
IRB-2412. Mitochondrial quality control in adaptive immune responses2024-2025IRB BarcelonaMitochondrial Biology and Tissue RegenerationWEBSITEAna VictoriaLechuga-ViecoAvailable

The immune system plays a crucial role in maintaining physiological homeostasis. The ageing immune system is characterised by chronic inflammation, reduced immune function and diminished tissue repair capacity. These alterations can disrupt the equilibrium of homeostasis in energetic tissues, leading to impaired function and increased susceptibility to disease. Understanding the interactions between T cells, tissue homeostasis, and ageing holds the potential to provide new therapeutic approaches for age-related diseases. Recent studies have highlighted the importance of mitochondria in immune cell function and ageing. As mitochondrial function declines with age, immune cell metabolism and function are also compromised, contributing to immunosenescence and giving rise to various aging-related features such as metabolic and cardiovascular pathology.

This project aims to elucidate the role of mitochondrial quality control mechanisms in shaping the transcriptional programmes of immune cells and their contribution to the transition to immune senescence, cytokine production, and inflammatory responses during the aging of highly energetic tissues. This project combines diverse range of molecular biology methods and immunophenotyping, including confocal microscopy, ELISA analyses, primary cell cultures, and spectral flow cytometry. The student will correlate specific T cell subsets with tissue damage in aged mice through comprehensive metabolic immune profiling of lymphocytes, utilizing preclinical models of premature aging. Relevant mitochondrial quality control pathways will be genetically determined and validated using pharmacological treatments in mouse experimental models. Additional techniques may involve high-throughput sequencing, western blotting, immunoprecipitation, and mitochondrial biology approaches to address structure, function, and regulation, as well as their involvement in key cellular processes such as metabolism and cell signalling. The student will attend different training courses with the aim of fostering a comprehensive understanding of the diverse research techniques available at the host Institute.

Ageing, lymphocytes, metabolism, mitochondria, tissue homeostasis
ICN2-2403. Towards a universal biosensing platform based on graphene/pyrene surfaces for neurotransmitters detection2024-2025ICN2AEMDWEBSITEJose AntonioGarridoAvailable

Description: With the aim of advancing our understanding of the human brain activity we work on the development of a new generation of neural interfaces based on graphene, capable of recording electrical neural signals. Thanks to graphene´s outstanding electrical and mechanical properties we aim to overcome current technology limitations in terms of invasiveness. Moreover, graphene´s chemical and morphological properties opens the possibility of including chemical recording capabilities for developing multifunctional neural implants. We will develop a universal sensing platform based on graphene/pyrenebutyric acid (PyBA) for the detection of neurotransmitters, or other analytes of interest. For the PyBA functionalization of graphene we have develop a novel physical method based on the evaporation of PyBA, a molecule capable to interact with the  system of graphene thanks to its aromatic nature. This PyBA molecule is capable to link to bioreceptor of interest, such as specific aptamers for dopamine or serotonin.

General Objectives:

– Optimization of the PyBA evaporation conditions on graphene supported on a variety of substrates
– Control and quantification of PyBA layers on the surface of graphene
– Validation of the electrical and chemical sensing capabilities of the graphene devices. Study of the graphene device response to media conditions (pH, ionic strength) and explore the biosensing capability, targeting dopamine.

Training outcomes:
– Graphene based technology microfabrication
– Graphene functionalization strategies
– Advanced characterization of bidimensional materials and devices
– Electrical characterization of graphene transistor technology in different media
– In vitro dopamine sensing experimentation

Elenadel Corrographene transistors, neural interfaces, neurotransmitters biosensing
ICN2-2404. 2D Memristors for Neuromorphic Computing2024-2025ICN2AEMDWEBSITEJose AntonioGarridoAvailable

What we want? Inspired by our brain (the most efficient “computing machine” that exists), you work will represent an initiative to lay the foundations for a nanotechnology based on two-dimensional (2D) materials that imitates neural networks. In our commercial neural interfaces (www.inbrain-neuroelectronics.com), graphene is used as the advanced sensing element of the brain activity owing to its extraordinary electrical performances. The potential integration of flexible 2D electronics logics would place this computing in sensor technology as one of the most advanced worldwide.
Who we are? The Advanced Electronic Material and Devices (AEMD) group at ICN2 develops either, materials, such as high quality single layer graphene and 2D semiconductors (e.g. MoS2) and devices, like sensors, transistors for a range of applications such as neural interface technologies. Currently, we can produce high quality single layer graphene by chemical vapour deposition (CVD). The group also produce homogeneous sheets of monolayer MoS2 by metal organic CVD (MOCVD) up to 4-inch wafer size. The AEMD group is currently capable of wafer scale production of flexible electronics based on field-effect transistor (FET) configuration and has extensive experience in FET electrical characterization.
What you will do? You will assist senior and junior (PhD) personnel of the AEMD to develop arrays of 2D vertical memristors based on MoS2.
General Objectives:
• (Assist) Transfer MoS2: 1L, 2L, 3L. High density of nucleation points/Lower density of nucleation points
• (Assist) Fabrication of Arrays (New mask) – Electrochemical Bridge Au/2D/Cu Measure Arrays
• Look for Neural Paterns e.g., Spike Timing Dependent Plasticity (STDP) and Spike Timing Dependent Delay Plasticity (STDDP).
What you will learn? Training outcomes
• 2D materials semiconductor technology
• Nano and microelectronic fabrication (chips)
• Electronic Characterization
• Neuromorphic, edge computing and AI

Elenadel Corroneural interfaces, Neuromorphic computing
ICN2-2405. Triboelectric solution for energy autonomous neural interfaces2024-2025ICN2AEMDWEBSITEJose AntonioGarridoAvailable

Medical technologies have experience major advances thanks to the discover of new materials. But active implantable medical devices (AIMDs) still largely rely on conventional energy sources, delivered using bulky batteries, with typically shorter lifetimes than the implant itself. In an ideal scenario, AIMDs would be powered using long-lasting powering systems fully wireless for improved patient quality of life. A flexible and implantable device able to transform and use energy from our living environment to feed AIMDs would be a gamechanger. Our vision is to develop miniaturized triboelectric energy generators using wafer-scale microfabrication technology, with the goal of using them to feed medical implants as well as other portable devices. To this end, we will target neuromodulation applications, in particular peripheral nerve stimulation implants, developed in the Advanced Electronic Materials and Devices group. The technological breakthrough of this project is to develop and integrate this energy harvesting system with the medical implant into a flexible and biocompatible substrate.

General Objectives:

1. Develop micro-triboelectric generator devices at using wafer-scale thin film technology, providing practical levels of power.
2. Develop strategies (materials engineering based) to exploit the triboelectric performance of gold/polyimide devices
3. Integrate the energy harvesting technology into a flexible platform, together with the medical implant, and validate the completion of AIMDs requirements of stimulation capabilities, biocompatibility, conformability and durability.

Training outcomes:
– Thin film technology developed (clean room facilities)
– Advanced characterization of thin film materials and devices
– Actuation and electrical characterization of triboelectric devices

Elenadel CorroAutonomous neural interfaces, triboelectric energy generators
MELIS-2408. Synthetic evolution of RNA writers for advanced human genome engineering2024-2025MELIS-UPFTranslational Synthetic BiologyWEBSITEMarcGüellAvailable

We are offering a master position in AI-aided synthetic evolution of RNA-based gene writers. This project is framed within our recently financed ERC consolidator grant to general new principles of human genome engineering.

AI, CRISPR-cas, directed evolution, gene editing, synthetic biology
ICFO-2407. 1. Probing the effects of protein conformational changes on the spectroscopic properties of photoactive systems in real time2024-2025ICFOPhoton Harvesting in Plants and BiomoleculesWEBSITENicolettaLigouriAvailable

Our group aims at understanding how changes in light, structure and environment regulate the molecular mechanisms of photoactive (bio)molecular systems. To do so we develop and apply novel ultrafast spectroscopic tools that we combine with molecular dynamics simulations.
The student will play a key role in an ambitious project focused on monitoring real-time changes in the microenvironment and structure on the function of photoactive proteins. With this project we aim to probe, for the first time, how these perturbations impact both the excited and ground state properties of proteins in real time. The student will be engaged with a state-of-the-art ultrafast TA spectroscopy setup, comprising synchronized femtosecond lasers capable of triggering and measuring the effects of proteins’ conformational changes in real time.
A beneficial (but not necessary) background for the student includes experience in experimental physics, proficiency in optics with hands-on familiarity working with optical tables, and an understanding of biochemistry. Additionally, basic knowledge of coding languages such as Python and LabVIEW would be advantageous.

optics, Photoactive biomolecules, real time changes, ultrafast TA spectroscopy
ICFO-2408. 2. Understanding and manipulating photosynthesis by setting proteins in motion2024-2025ICFOPhoton Harvesting in Plants and BiomoleculesWEBSITENicolettaLigouriAvailable

In our multidisciplinary group, we develop and apply new approaches from chemistry, biology, and optics to probe the effect of structural, light and environmental dynamics in photoactive (bio)molecular systems. Our studies are mainly focused on learning how photosynthesis is regulated using ultrafast spectroscopy. Photocontrollable proteins offer exciting prospects for remote, precise, and reversible regulation of biochemical processes. This approach provides a common strategy for mechanistic understanding of a biological system by selective perturbation of the protein structure, and probing of the response occurring over femtoseconds to milliseconds timescales. For example, the combination of chemical engineering of small molecule photosensitive effectors, such as photocage compounds, and transient spectroscopic techniques now allows exquisite control over target protein domains, allowing to probe in real time the effect of local conformational changes. However these tools have never been used to investigate the role of protein dynamics on photosynthesis regulation. Therefore, a major objective of this project is to achieve conformational control of proteins from plants through the rational design of photoswitches and incorporation of these photoswitches into plant protein systems. The candidate will: 1) Design and prepare a range of photoswitches or photocages; 2) Develop efficient incorporation and conjugation approaches to couple the obtained photoresponsive elements into photosynthetic proteins; 3) Characterize optical properties and the stability of the photoswitchable photosynthetic proteins using techniques such as steady-state and ultrafast spectroscopy. We are seeking a highly motivated students with strong experience in physical chemistry, biochemistry or chemical engineering. Hand-on experience in protein functional characterisation, organic synthesis. and ultrafast spectroscopy are very appreciated.

optics, Photoactive biomolecules, photoswitches, Proteins, ultrafast spectroscopy
ICFO-2409. Extracting the colours of cyanobacterial photosynthesis2024-2025ICFOPhoton Harvesting in Plants and BiomoleculesWEBSITENicolettaLigouriAvailable

While we typically associate photosynthesis with the green colour, in some key organisms in the global photosynthetic carbon dioxide fixation – cyanobacteria – the photosynthetic molecular machinery also contains pigment-protein complexes of other colours. For example, the complexes involved in photoregulation in cyanobacteria are the Orange Carotenoid Protein (which changes colour from orange to red when activated) and blue, light-harvesting antennae complexes, the Phycobilisomes (which emit pink fluorescence), are essential from the perspective of the long term efficiency and productivity of photosynthesis. To further explore how photosynthesis is regulated and learn how to increase its yields, we need to perform advanced spectroscopic studies on isolated pigment-protein complexes. The successful candidate will learn how to selectively isolate various pigment-protein complexes and will get involved in the spectroscopic characterisation of these complexes. A perfect candidate with a background in biochemistry or biophysics with particular interests in bioenergetics and protein biochemistry.

Carbon dioxide fixation, cyanobacteria, pigment-protein complexes, spectroscopy
MELIS-2409. Unrevealing mechanism for p53-mediated tumour suppression2024-2025MELIS-UPFCancer BiologyWEBSITEAnaJanicAvailable

Research project summary: The tumour suppressor gene p53 is mutated in half of the human cancers, and there is still extensive morbidity and mortality associated with cancers bearing p53 mutations. Given the difficulties in developing strategies for targeting wild-type or mutant p53, further understanding of its basic biology is required for successful clinical translation. Recent studies, including ours, have challenged the previously understood model of how the p53 gene is involved in tumour suppression. We found that several p53 activated target genes implicated in DNA repair have critical functions in suppressing lymphoma/leukaemia development. Based on this observation, we hypothesise that coordination of DNA damage repair is the most critical mechanism by which p53 suppresses tumour development. The present PhD project focuses on understanding the complexity of the p53 network in tumour suppression in different contexts, in order to determine which p53 downstream function should be targeted for treatment of different tumour types, without targeting p53 itself.
Training objectives: The role will involve the use of a wide variety of experimental techniques, including  tissue/tumour pathology, CRISPR-Cas9 gene-editing technology,  molecular biology, cell culture and flow cytometry. In addition, successful candidate will have access to a wide range of academic activities; UPF and Barcelona Biomedical Research Park seminars, conferences and symposia.

Cancer Biology, Immunotherapy, p53, Tumour supression
IFAE- 2408. Infra-red Detectors for Medical Applications based on CMOS2024-2025IFAEMedical PhysicsWEBSITESebastianGrinsteinAvailable

Semiconductor detectors are being increasingly used in medical applications and, in general, as imaging systems. The IFAE Medical Physics group is developing a new generation of silicon devices for radiation detection that is based on the commercial CMOS technology. The devices are designed to be sensitive to infrared radiation (IR) for usage in neuromonitoring systems (brain blood flow measurements). In the course of this program, the selected candidate will work on the development of a system to operate these novel avalanche photo-didoes, carry out their characterization in the IFAE laboratory and test them at ICFO on tissue simulating phantoms.

StefanoTerzoneuromonitoring, semiconductors, tissue simulating phantoms
ICFO-2410. Gas sensors based on two-dimensional polaritonic platforms2024-2025ICFOQuantum Nano-optoelectronicsWEBSITEFrankKoppensAvailable

Gas sensors are becoming an essential component of modern life across a range of applications, from environmental control to breath analysis for diagnosing diseases. The information collected by the sensors enables us to predict, prevent and act in potentially dangerous situations. Commercially available gas sensors typically present limitations to fully exploit the mentioned applications. These limitations are the following: slow response time, low sensitivity combined with non-selective detection, high power consumption and bulky platforms.

In our group, we have developed a fast and highly sensitive sensing platform based on two-dimensional polaritons. The sensing scheme consists of using infrared optics since most of the gases have vibrational resonances at this spectral range. We have achieved remarkable sensing capabilities such as a limit of detection of ~1 ppm, detection speed below 1 sec, high selectivity by measuring gases in mixtures and more. The project will focus on measurements under relevant conditions of gas mixtures to mimic potential industrial applications. Moreover, during the project it will be studied the interactions between gases and polaritons that become enhanced at the two-dimensional limit. The objectives of the project are the following:
– To perform optical sensing experiments based on the detection of gas mixtures using novel two-dimensional polaritonic platforms
– Analysis of the acquired data using machine learning algorithms (developed by the group)
– To improve the experimental setup to enhance the sensing capabilities: data acquisition time, noise reduction and introduction of ultra-low gas concentrations.

SebastiánCastillaGas sensors, graphene, optical sensing, plasmonics, quantum sensing
IBEC-2411. Systematic study of stress-induced amyloids2024-2025IBECPhase Transitions in Health and DiseaseWEBSITEBenedettaBolognesiAvailable

The aggregation of proteins into insoluble fibrils is the key pathological mechanism in more than 40 incurable human diseases. However, the self-assembly of proteins into fibrillar structures can also fulfill biological functions. Despite decades of research, why and how the process of protein aggregation initiates, and the sequence-dependencies of this phenomenon in function and dysfunction remain one of the most complex unsolved problems in biology, with implications all the way from therapeutic development in an aging population, to fundamental biophysics, bioengineering and synthetic biology. In order to reach the transition state and overcome the kinetic barrier to amyloid aggregation, some proteins need to be destabilized by really harsh conditions (e.g pH2, 60C) that would hardly occur in the cytoplasm of living systems. However, intrinsically disordered proteins are extremely sensitive to even relatively minor environmental changes in temperature, pH and or ionic strength, as they inhabit an ensemble of conformations in what is a relatively flat energy landscape. While intrinsically disordered regions make up roughly 30% of the human and yeast proteome, how likely it is for them to cross the barrier to amyloid formation has not been systematically elucidated. In addition, some confusion exists, even in nomenclature, on the ways in which these proteins can self-assemble upon stress, partially due to the many different techniques used to report on protein self-assembly. Being able to quantify a specific phenotype, i.e. amyloid nucleation, at scale (the whole disordered proteome), our lab has now the possibility to quantify to what extent stress conditions promote amyloid nucleation of IDPs, as well as the sequence-dependencies of these events. The success of AlphaFold suggests that deep learning strategies to decipher sequence-ensemble relationships for IDRs are potentially possible, as long as we are able to increase the throughput of quantitative approaches to study these regions, which will also be a major outcome of this project.

Amyloid, deep mutagenesis, neurodegeneration, protein disorder
ICFO-2410. PV/PEC tandem structures based on organic photoabsorbers for solar synthetic fuels generation.2024-2025ICFOOrganic Nanostructured PhotovoltaicsWEBSITECarlesRosAvailable

Worldwide energy consumption requires energy vectors capable to store and distribute energy for many applications for which direct electrification or battery storage is not suitable. Solar synthetic fuels, based on the photoelectrochemical (PEC) conversion and storage of solar light in the chemical bond of molecules such as H2 or other carbon-based fuels allows for long term storage and distribution, identified as a key scientific and technological field by the EU. Tandem PV-PEC structures have been largely researched using metal oxide photoelectrodes, but large bandgaps and recombination rates limit their performance to few milliamperes. Taking advantages of the advancements of organic photovoltaics (OPVs), tuneable band gap photoelectrodes and photovoltaic cells can be fabricated with competitive photocurrents if adequate polymers and blends can be selected.

Energy, Nanostructures, Photovoltaics
ICIQ-2401. Wearable biosensors for therapeutic drug monitoring.2024-2025ICIQBioinspired nanotechnologiesWEBSITEBeatrizPrieto SimónAvailable

We aim to deliver nanoarchitectures to build bespoke diagnostics, by harnessing high-precision fabrication methods, and advances in engineering surface functionalities. Our interest lies in gathering knowledge on the relationship between morphological properties/chemical functionalities and function, to design biosensors underpinning personalised clinical management of infections. Specifically, we aim to exploit the potential of these tools to guide antibiotics choice, as a key driver toward effective treatment, protecting patients from antibiotics adverse effects, and dwindling antibiotic resistance.

To this purpose, we work on developing diagnostics for:
– early diagnosis of infectious diseases, by targeting key host immune response biomarkers;
– infectious disease detection and aetiology identification;
– detection of antimicrobial resistance;
– therapeutic drug monitoring of antibiotics via wearable biosensors.

General objectives:
– To explore the fabrication of nanostructured materials (e.g., via polymeric replica moulding, 3D printing) to produce wearable biosensors;
– To test sensing performance when analysing antibiotics in biofluids to support therapeutic drug monitoring.

Expected training outcomes: The candidate will be trained in fabricating, functionalising and characterising nanomaterials. S/he will acquire knowledge and expertise to perform bioassays and adapt them to electrochemical biosensors. S/he will learn to use a range of electrochemical techniques. S/he will test the developed biosensor in simulated biofluids. The candidate will acquire skills to develop tools for infection diagnosis by strengthening her/his capacity of critical thinking, searching for alternatives, taking the initiative and making appropriate decisions. S/he will learn to produce reports, papers and presentations of the highest quality. S/he will get used to collaborate with researchers working on multidisciplinary research areas, preparing presentations and participating in group discussions to assess project progress, and confirm or address the direction of future research. S/he will be trained to maintain professional and ethical standards in the conduct of research according to the protocols established by ICIQ.

Antimicrobial resistance, Biosensors, Infection, Nanostructures
ICIQ-2402. Construction and Investigation of Chromophore-Protein Assemblies to Build Photovoltaic and Lighting Devices2024-2025ICIQDr. Elisabet Romero GroupWEBSITEElisabetRomeroAvailable

In nature, the photosynthetic machinery of plants and algae is composed by pigments placed in specific positions within protein matrices, which assist on the regulation of the embedded pigments’ electronic states playing a key role in energy absorption, transfer and conversion processes. Taking advantage of the design principles underlying natural photosynthesis, we aim to design artificial protein scaffolds capable of performing similar functions, opening the door to the coupling of custom-made light-harvesting complexes into photovoltaics or devices for lightning.

In this project, the student will be able to develop skills on photophysics and photochemistry by means of steady-state electronic spectroscopy techniques (e.g., Absorption, Fluorescence, Circular Dichroism, Linear Dichroism), and time-resolved Fluorescence spectroscopy in the range of pico to microseconds. By applying these techniques, the student will be able to learn about: the factors responsible for the tunning of chromophores electronic states (polarity, the protein’s environment), the chromophore to protein binding mechanism, the chromophores orientation into the proteins, the chromophores emission capacity, and the energy transfer process between the chromophores ligated to the proteins. During the project, the student will acquire wet lab skills with the handling of different biomolecules and chromophores, on protein labelling protocols; as well as technical skills on the above-mentioned spectroscopic techniques. In addition, the student will enhance her/his writing and oral skills with the composition of reports and the presentation of her/his research to an international community, together with the participation in group discussions to support the project progress. Knowledge in physics, chemistry or materials science will be beneficial to fulfil the project objectives.

Luís GustavoTeixeira Alves DuarteEnergy transfer, Lightening Devices, Photosynthesis, Photovoltaics, spectroscopy
ICFO-2411. Exploring Quantum Dynamics through Sonification: Advancing the Intersection of Quantum Physics and Sound2024-2025ICFOQuantum Optics TheoryWEBSITEMaciejLewensteinAvailable

While the visualization of quantum dynamics has seen significant development and has established itself as an industry, the realm of sonification, the process of translating quantum dynamics into sounds, remains relatively unexplored. This involves the generation of sounds, either digitally (via classical or quantum computer) or analogically (using musical instruments) derived from simulations or laboratory data across diverse quantum systems.

The Master’s project is profoundly interdisciplinary, encompassing: a) the fundamentals of quantum mechanics, with a focus on the theory of individual quantum trajectories, quantum many-body physics, and quantum many-body dynamics; b) diverse approaches to mapping quantum data to sound; c) the utilization of specialized audio programs (such as SuperCollider) to translate data into various sound parameters; and d) foundational knowledge in acoustics, music theory, and data sonification.

The ideal candidate will possess a solid background in quantum physics and computer simulations. A basic understanding of acoustics and music theory is required, coupled with an openness to experimental music research. While experience in audio synthesis, coding (with various audio programming environments), and algorithmic composition is highly advantageous, it is not mandatory.

ReikoYamadaAcoustics, Art-Science, Interdisciplinary research, Sonification
IBEC-2412. Characterization of clonal patterns in solid tumors2024-2025IBECSpatial BiotechnologyWEBSITEXavierRovira ClavéAvailable

Tumors typically harbor diverse populations of genetically distinct cancer cells, or subclones, that coexist with sources of heterogeneity from the tumor microenvironment, such as the presence of stromal and immune cells, hypoxic regions, and areas with unique extracellular matrix components. This complexity confounds accurate cancer diagnosis, treatment selection, and prediction of therapeutic response. Understanding how subclones arise and evolve will help design more effective tumor therapies and diagnostic tools to predict clinical outcomes.

Our group is focused on the development of high-throughput and spatial perturbation technologies and their application to understand how cancer cell clones spatially organize to drive solid tumor development. Some of the questions we are interested in, include:

– How is clonal cooperation established and maintained?
– How does metabolite accessibility regulate growth of neighboring cancer cell clones?
– How do clonal populations and microenvironments evolve in primary tumors?

We seek a motivated student with interest in biomedicine and background in one or more of the following areas: cell biology, chemistry, biotechnology, microscopy, and/or bioinformatics. The specific aims of the project will be tailored to the student, depending on his/her scientific interests and background, and within the framework of the group. We study clonal behaviors in solid tumors and use clinical sources, murine models, and in vitro tissues as a model. We profile them using a variety of technologies that include highly multiplexed tissue imaging, classical molecular and cellular biology methods, super-resolution, mass spectrometry, and multimodal microscopy, genetic screens, assay automation strategies, cell engineering approaches, and computational tools for deconstructing spatial patterns. The student joining the lab will be trained in basic cancer cell biology, experimental design, data analysis, and oral presentation skills. The student will learn to independently perform multiplexed antibody-based tissue imaging, including 1) antibody conjugation, 2) tissue handling, and 3) analysis of spatial data.

Cancer, Data Analysis, imaging, Single-cell, Spatial biology