Below you will find detailed information about the various projects proposed by researchers from the BIST centres and the DCEXS-UPF for the 2022/2023 academic year. MMRES students must choose one of these as their Major Project. During the call period, as students are admitted, their selected projects become assigned and are no longer available in later calls. Once the programme has started, each student will decide on their Minor Project together with their research supervisor.
For more information about the duration and content of the major and minor projects, see the syllabus.
Project | Course | Centre | Research Group Name | Web | Supervisor | Supervisor Last Name | Availability | Description | Co-supervisor | Co-supervisor Last Name | Tags | Keywords |
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IRBB-2211. Generative models to create precision drugs | 2022-2023 | IRB Barcelona | Structural Bioinformatics & Network Biology | WEBSITE | Patrick | Aloy | Available | Biological data is accumulating at an unprecedented rate, escalating the role of data-driven methods in computational drug discovery. The urge to couple biological data to cutting-edge machine learning has spurred developments in data integration and knowledge representation, especially in the form of heterogeneous, multiplex and semantically-rich biological networks. Today, thanks to the propitious rise in knowledge embedding techniques, these large and complex biological networks can be converted to a vector format that suits the majority of machine learning implementations. Indeed, we have generated biological embeddings (i.e. bioactivity signatures) that capture complex relationships between small molecules and other biological entities such as targets or diseases (Duran-Frigola et al. 2020 Nat Biotechnol; Bertoni et al. 2021 Nat Commun). However, only a tiny fraction of the possible chemical space has been so far explored, meaning that most compounds able to modulate biological activities (i.e. drugs) are yet to be discovered. Accordingly, the main objective of this project is to couple our bioactivity signatures to inverse design algorithms to generate new chemical entities with a desired functionality. In particular, we aim at generating new chemical entities (NCEs) to modulate the activity of a specific set of targets, selected from a combination of perturbagen profiles, to revert the pathological state induced by Alzheimer´s disease (AD) and other complex disorders (Pauls et al. 2021 Genome Med. All in all, the incorporation of machine learning methods to the drug discovery process will trigger the development of thousands of novel compounds, finally enabling precision medicine. | Martino | Bertoni | ||
DCEXS-2209. High-throughput analysis of hearing loss causative genes through cas13 technology | 2022-2023 | DCEXS-UPF | Morphogenesis and Cell Signaling in Sensory Systems | WEBSITE | Berta | Alsina | Available | The inner ear is one of the most sophisticated sensory organs of the peripheral nervous system and is responsible for the senses of audition and balance. Sensory information is captured by the Hair Cells (HC) that transmit the information to the sensory neurons of the statoacoustic ganglion. Then, the afferent neurons connect to the brain. Mutations in genes responsible for hair cell and neuronal function cause hearing loss or vertigo. Hearing loss is the most prevalent sensory deficit in the world and approximately affects 466 million people, being 34 million children. Around 122 human genes causing non-syndromic hereditary hearing loss when mutated have been identified to date. However, the exact function of many of these genes has not been assessed carefully due to the difficulty of generating mutant animals at large scale. The CRISPR/Cas9 editing system has revolutionized the genetics field by the ability to efficiently mutate or modify any desired gene. Our laboratory is interested in studying inner ear development, gene regulation and hearing loss using the zebrafish and organoids as models systems (see lab publications: https://www.upf.edu/web/alsina_lab/publications) and have set up many techniques for analysing gene function. We have identified a number of regulatory elements involved in gene regulation during otic neurogenesis. | CRISPR, imaging, sensory systems, zebrafish | |||
DCEXS-2207. Characterization of antitumor mechanisms driven by type I interferon | 2022-2023 | DCEXS-UPF | Grupo de Investigación en Proteínas NFAT y Respuesta Immunológica | WEBSITE | Jose | Aramburu | Available | Alterations in immune functions not only impair our organism defenses to pathogens but also underlie diseases such as cancer or neurodegenerative, cardiovascular and metabolic disorders. We focus our work on NFAT5, a transcription factor that regulates innate and adaptive immunity in different scenarios, such as inflammation, graft rejection, tumor progression and viral infection. By uncovering circuits by which immune cells tune their function in diverse scenarios, our work can guide innovative approaches that improve antitumor immunotherapy and anti-pathogen defense. The proposed MSc research lines connect with our recent finding of a unique transcription mechanism that restrains type I interferon (IFN-I) expression to control antiviral responses while preserving hematopoietic stem cell (HSC) function (Huerga Encabo et al. 2020 J Exp Med). Recent works have established that genomic instability in tumor cells releases DNA to the cytosol, triggering IFN-I induction. This response is dually beneficial to control tumor progression as it promotes tumor cell senescence and alerts specific antitumor immunity. We will apply our experience with tumor models, lineage-specific deficient mice, and cutting edge cell and molecular biology approaches to identify new mechanisms that boost antitumor responses by enhancing IFN-I function at two levels i) improving tumor antigen presentation by dendritic cells to cytotoxic T lymphocytes and ii) promoting tumor cell senescence. Leading recent publications: Lunazzi et al., 2021 J Immunol | Cristina | Lopez-Rodriguez | Antitumor immune responses, gene expression | |
ICN2-2201. Energy Nanomaterials at Atomic Scale I | 2022-2023 | ICN2 | Advanced Electron Nanoscopy (GAeN) | WEBSITE | Jordi | Arbiol | Available | The student will work with nanostructures based on 2D nanomaterials for applications in Energy and the Environment. The student will use the advanced tools offered by the new ICN2-ALBA synchrotron electron microscopy platform 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. | Maria Chiara | Spadaro | atomic models, Energy nanomaterials, in-situ, scanning transmission electron microscopy | |
ICN2-2202. Energy Nanomaterials at Atomic Scale II | 2022-2023 | ICN2 | Advanced Electron Nanoscopy (GAeN) | WEBSITE | Jordi | Arbiol | Available | Quantum technology is supposed to be the biggest revolution that has to happen on the next few years, implying a wide range of fields such as computational and health sciences, energy applications and even the generation of extra-secure communications and encrypting. It will come to stay and deeply change everyone’s life. This project aims to focus on the materials science that is behind quantum computation. However, multiple approaches that compete with each other, (as are carried and sponsored by the main computation companies, i.e. Microsoft, Google, IBM, Intel) are being pursued in order to reach the final common goal of the process, which is the fabrication of a fully functional and commercial quantum computer. | Sara | Martí-Sánchez | atomic models, Quantum nanomaterials, scanning transmission electron microscopy | |
DCEXS-2201. Controlling the cell cycle: elaborating an integrative map of DNA synthesis regulators and tumor progression | 2022-2023 | DCEXS-UPF | Oxidative Stress and Cell Cycle Group (OSCCG) | WEBSITE | Jose | Ayté | Available | We are ultimately interested in deciphering the mechanisms that control cell cycle progression. Inactivation of the Retinoblastoma protein (RB) leads to unregulated cell cycle progression promoting cell growth, genomic instability and aneuploidy, hallmarks of tumor progression. RB activity is achieved through binding the E2F family of transcription factors. It is well known that a tumor process is very complex, accumulating secondary mutations that eliminate the brakes to the cell cycle. Even though many regulators of the RB-E2F are known, an integrative view of all the regulatory events controlling the G1/S transition is required to anticipate putative interventions able to block proliferative processes. | Cell cycle, DNA damage, G1/S transition, replicative stress, transcription | |||
ICFO-2202. Superconductivity in twisted bilayer graphene | 2022-2023 | ICFO | Quantum Nanomechanics | WEBSITE | Adrian | Bachtold | Assigned | Two-dimensional (2D) monolayers have generated a huge research interest in the past years. The discovery of graphene was awarded with the 2010 Nobel Prize in physics. Very recently, it was realised that twisted bilayer graphene represents a promising platform for understanding the elusive properties of unconventional superconductivity. Better understanding high-temperature superconductors may allow physicists to reach superconductivity at room temperature. This would likely have an enormous impact on our society, since it could dramatically reduce energy consumption in many devices and electricity distribution. Here, we propose to explore new types of twisted bilayer graphene devices in order to understand how superconductivity emerges from the strong correlation between electrons. | cryogenics, electrical measurements, nanofabrication, Superconductivity, twisted bilayer graphene | |||
ICFO-2203. Attosecond Molecular-movies with Inner-Shell Electrons | 2022-2023 | ICFO | Attoscience and Ultrafast Optics | WEBSITE | Jens | Biegert | Available | The aim of our research is the development of tools and establishment of methodologies for investigation of the ultrafast events that are caused by electrons inside atoms, molecules, solids and biological matter. The power of attoscience and ultrafast optics lies in the incredible time resolution that gives access to observing the triggering events that are caused by electronic rearrangement and ultimately lead, at hugely varying temporal scales, to molecular dissociation, chemical reactions, excitonic energy transfer or even biological function. | Attoscience, Extreme Nonlinear Optics, Ultrafast Lasers | |||
CRG-2204. From nanoscopy observation of cell fate to tissue regeneration | 2022-2023 | CRG | Reprogramming and Regeneration | WEBSITE | Maria Pia | Cosma | Available | In our group, we are investigating the mechanisms controlling the reprogramming of somatic cells to pluripotency, and our final goal is to determine if this reprogramming contributes to tissue regeneration in higher vertebrates. In particular, we are studying how the Wnt/beta-catenin signalling pathway and cell-fusion-mediated cellular reprogramming control these processes. We tackle these questions with different approaches and through different disciplines, which range from the nanoscale level of observation of cell functions, up to the whole mouse organ. | chromatin, regeneration, reprogramming, Stem Cells, super resolution microscopy | |||
DCEXS-2204. Identification of a plasma lipidomics signature underlying the beneficial health effects of tyrosol supplementation in individuals at high cardiovascular risk. | 2022-2023 | DCEXS-UPF | Integrative Pharmacology and Systems Neurosciences Research Group | WEBSITE | Rafael | de la Torre | Available | This project is linked to a research line whose aim is to understand the health benefits provided by dietary phenolic compounds and the use of nutraceuticals as therapeutic tools in the prevention of cardiovascular and neurodegenerative diseases. In this context, we performed a randomized, double-blind, controlled clinical trial (the PENSA study) that aims to evaluate the efficacy of a personalized multimodal intervention in lifestyle (Mediterranean diet, physical activity, cognitive training and social engagement) combined with the use of epigallocatechin gallate (EGCG) during 12 months, in slowing down cognitive decline in an adult population at risk of developing Alzheimer’s disease (APOE-E4 carriers) exhibiting Subjective Cognitive Decline (SCD). Although the primary efficacy outcome is change in a composite score of cognitive performance (Alzheimer Disease Cooperative Study Preclinical Alzheimer Cognitive Composite (ADCS-PACC), further research is warranted to better understand the biological mechanisms responsible for these effects. Lipidomics is a relatively new emerging discipline with the great potential of elucidating the biochemical mechanisms underlying alterations in lipid metabolism. The first objective of this project is to study the alterations in lipid metabolism induced by the intervention with Mediterranean Diet. To do so, a targeted lipidomics analysis in plasma samples of participants of the previously mentioned study will be performed. The second objective of this study is to evaluate the correlation between clinical parameters of the study participants and specific lipid species in order to find biomarkers. | Josep | Rodríguez-Morató | Lipidomics; nutritional intervention studies; neurodegenerative diseases; cognition; dietary antioxidants; nutrition. | |
IRBB-2201. Understanding stress adaptation | 2022-2023 | IRB Barcelona | Cell Signaling group | WEBSITE | Eulàlia | de Nadal | Assigned | We aim to unravel how cells detect and respond to environmental changes. We focus our studies on the characterisation of stress signal transduction pathways, especially those regulated by MAP kinases of the Hog1/p38 family, also known as the stress-activated MAP kinases (SAPKs). Proper adaptation to stress involves the modulation of several basic aspects of cell biology, among them the cell cycle and gene expression. Using S. cerevisiae budding yeast as a model organism, as well as higher eukaryotic cells, we are dissecting the molecular mechanisms underlying cell response to changes in the extracellular environment and characterising the adaptive responses required for cell survival. | Cell cycle, MAPK, Signaling, Stress, Transcripcion | |||
ICFO-2206. Medical Optics I | 2022-2023 | ICFO | Medical Optics | WEBSITE | Turgut | Durduran | Assigned | ICFO-Medical Optics group developed techniques based on near-infrared diffuse optics that are being translated to the clinics to measure tissue physiology in neuro-critical care and in oncology. These devices deliver laser light and detect the diffuse photons in order to calculate the laser speckle statistics. These statistics are then analysed by a physical model of photon propagation in tissues to quantify parameters such as microvascular blood flow. In this project, we will test next generation single-photon counting avalanche photo-diodes developed in collaboration with IFAE as highly-sensitive fast detectors. If successful, these detectors will pave the way to next generation novel systems. | ||||
ICFO-2207. Medical Optics II | 2022-2023 | ICFO | Medical Optics | WEBSITE | Turgut | Durduran | Assigned | How does the cerebrovascular reactivity vary over days and weeks? Non-invasive, longitudinal diffuse optical neuro-monitors based on diffuse correlation spectroscopy and near-infrared spectroscopy allow us to study this topic and relate to our findings on pathological conditions (ischemic stroke, traumatic brain injury, carotid stenosis and chronic sleep apnea). This project will study this aspect by measuring healthy volunteers and carry out diffuse optical data analysis, biostatistical analysis and define the healthy variation. | ||||
ICFO-2208. Medical Optics III | 2022-2023 | ICFO | Medical Optics | WEBSITE | Turgut | Durduran | Assigned | Validation and testing of compact components for diffuse correlation spectroscopy analysis and define the healthy variation. | ||||
ICFO-2209. Medical optics group IV | 2022-2023 | ICFO | Medical optics | WEBSITE | Turgut | Durduran | Assigned | Diffuse optical instrumentation for translational and clinical biomedical research: develop state-of-the-art biomedical instrumentation for translational and clinical research. These range from portable, hybrid systems that combine diffuse correlation spectroscopy (DCS) with near-infrared diffuse optical spectroscopy (NIRS-DOS) to laser speckle based animal images. We have industrial, biomedical and clinical relationships that drive the specifications of these systems. | ||||
DCEXS-2202. Structure, function and pharmacology of ion channels: relevance to neurological disorders | 2022-2023 | DCEXS-UPF | Laboratory of Molecular Physiology | WEBSITE | José Manuel | Fernández Fernández | Available | We are interested in the functional characterization of novel genetic, molecular and cellular mechanisms underlying the pathogenesis of neurological disorders, with focus on hemiplegic migraine (HM), epileptic encephalopathy and hereditary forms of ataxia. In this sense, we have identified new genetic alterations in the CACNA1A gene (coding for the pore forming alpha subunit of the high-voltage activated CaV2.1 (P/Q) calcium channel) in a clinical background of these neurological disorders. They affect not just the structure and the biophysical features of CaV2.1 channels, but also their modulation by regulatory proteins (G proteins and SNARE proteins of the vesicle docking/fusion machinery). We also study the regulation by glycosilation of the activity and membrane trafficking of CaV2.1 and mechanosensitive Piezo channels, as Phosphomannomutase Deficiency (PMM2-CDG) (the most frequent congenital disorder of N-linked glycosylation (CDG)) includes neurological alterations triggered by mild cranial trauma and shared with patients carrying CACNA1A mutations. In an international collaboration we are now developing CaV2.1 selective tool molecules capable of reversing the functional consequences of both CACNA1A human mutations linked to HM and channel hypoglycosilation, and exploring their potential to produce a treatment for these neurological pathologies and migraine in general. | Neuronal voltage-gated calcium channels; Mechanosensitive Piezo channels; Electrophysiology; Hypoglycosylation; Neurological disorders. | |||
IRBB-2204. The oral microbiome in health and disease | 2022-2023 | IRB Barcelona | Comparative genomics | WEBSITE | Toni | Gabaldón | Available | The human oral cavity is home to an abundant and diverse microbial community (i.e., the oral microbiome), whose composition and roles in health and disease have been the focus of intense research in recent years. Thanks to developments in sequencing-based approaches, such as 16S ribosomal RNA metabarcoding, whole metagenome shotgun sequencing, or meta-transcriptomics, we now can efficiently explore the diversity and roles of oral microbes, even if unculturable. Recent sequencing-based studies have charted oral ecosystems and how they change due to lifestyle or disease conditions. As studies progress, there is increasing evidence of an important role of the oral microbiome in diverse health conditions, which are not limited to diseases of the oral cavity. This, in turn, opens new avenues for microbiome-based diagnostics and therapeutics that benefit from the easy accessibility of the oral cavity for microbiome monitoring and manipulation. The student will participate in the experimental procedures of several on-going project trying to understand the relationships of the oral microbiota and several diseases, including Alzheimer’s disease, Down Syndrom, and Cystic Fibrosis. | Ester | Saus | disease, metagenomics, microbiology, Oral microbiome | |
IRBB-2202. Adaptation in Candida pathogens | 2022-2023 | IRB Barcelona | Comparative genomics | WEBSITE | Toni | Gabaldón | Available | Fungal infections constitute an ever-growing and significant medical problem. Diseases caused by such pathogens range from simple toe nail infections, to life-threatening systemic mycoses in patients with impaired immune systems. The molecular mechanisms driving invasion of mammalian hosts by fungal pathogens poses many scientifically challenging problems, which are as yet little understood. The ability to infect humans has emerged in several lineages throughout the fungal tree of life. Therefore, the problem of elucidating the mechanism for pathogenesis of fungi, as proposed here, can be approached with an evolutionary perspective by detecting specific adaptations in pathogenic lineages. During the last years we have clarified the evolutionary paths to virulence of major fungal pathogens such as Candida glabrata and Candida parapsilosis. | Ester | Saus | ||
ICFO-2205. Single-molecule microscopy tools to study membrane contact sites | 2022-2023 | ICFO | Single Molecule Biophotonics group | WEBSITE | Maria | Garcia-Parajo | Available | We are an interdisciplinary group studying intracellular membrane morphology and dynamics, with a special focus on understanding the secretory pathway. We combine advanced microscopy techniques (single-molecule fluorescence and super-resolution nanoscopy), molecular and cell biology tools, with theoretical biophysics approaches to tackle highly controversial or still mysterious fundamental topics in cell biology with a clear pathophysiological relevance. This MSc project will verse on understanding the dynamics of membrane contact sites (MCSs), in particular those that form between the endoplasmic reticulum (ER) and the Golgi complex. The Golgi complex is the central organelle responsible of protein transport to various parts of the cell and the post-translational modification of newly synthesized proteins from the ER required for their maturation. It has been recently shown that the membranes of these two organelles come to close apposition to one another forming a dynamic but highly tethered region, termed the MCS. ER-Golgi MCSs facilitate the export of proteins and lipids from the Golgi complex to the cell surface by a still unresolved mechanism. The study of MCS dynamics using conventional microscopy tools has been challenging due to their highly dynamic nature and reduced dimensions. As a result, a clear understanding of the how MCS contribute to transport carrier formation at the Golgi complex is still lacking. The role of the MSc student will be to perform a set of innovative assays that combine different avant-garde molecular and cell biological techniques, such as the use of fluorescence complementation domains or the retention using selective hooks (RUSH)-system, with state-of-the-art microscopy and nanoscopy tools, such as STED, STORM or intracellular single particle tracking (iSPT). The data obtained will be analyzed using advanced quantitative imaging analysis to finally cast light on ER-Golgi MCS dynamics and their functional relevance for protein secretion. | Felix | Campelo | Membrane contact sites / Golgi complex / Transport carrier formation / Super-resolution microscopy / Single particle tracking | |
IBEC-2204. Nanoprobes & Nanoswitches I | 2022-2023 | IBEC | Nanoprobes & Nanoswitches | WEBSITE | Pau | Gorostiza | Assigned | 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. | optogenetics, photopharmacology | |||
IBEC-2205. Nanoprobes & Nanoswitches II | 2022-2023 | IBEC | Nanoprobes & Nanoswitches | WEBSITE | Pau | Gorostiza | Assigned | Protein mediated electron transfer (ET) is essential in many biological processes, like cellular respiration or photosynthesis. The exceptional efficacy of these processes is based on the maximization of donor/acceptor coupling and the optimization of the reorganization energy. | electron transport, interactions, Proteins, scanning probe microscopies, single molecule | |||
IBEC-2206. Nanoprobes & Nanoswitches III | 2022-2023 | IBEC | Nanoprobes & Nanoswitches | WEBSITE | Pau | Gorostiza | Assigned | Cell processes like endocytosis, membrane resealing, signaling and transcription, involve conformational changes which depend on the chemical composition and the physicochemical properties of the lipid membrane. These properties are directly related to the lateral packing and interactions at the molecular level, that govern the membrane structure and segregation into nano (or micro) domains. The better understanding of the mechanical role of the lipids in cell membrane force-triggered and sensing mechanisms has recently become the focus of attention. The local and dynamic nature of such cell processes requires observations at high spatial resolution. Atomic force microscopy (AFM) is widely used to study the mechanical properties of supported lipid bilayers (SLBs). We investigate the physicochemical and structural properties of lipid membranes combining AFM and force spectroscopy (AFM-FS) under environmentally controlled conditions. We use simplified model membranes including several lipid representatives of mammalian or bacterial cells. We also study the mechanical properties of lipid membranes from nanovesicles with technological applications, like drug delivery. | Marina I. | Giannotti | atomic force microscopy, biophysics, force spectroscopy, lipid membrane, nanomechanics | |
DCEXS-2205. Precise engineering of human genomes for therapeutic applications | 2022-2023 | DCEXS-UPF | Translational Synthetic Biology | WEBSITE | Marc | Güell | Assigned | Interested in developing a new gene writing technology? Natural gene transfer is performed by retrotransposons and retrovirus. We are combining precision of modern CRISPR systems with the efficiency of natural gene transfer mechanisms to achieve precise and efficient writing to genomes. We are offering a master thesis position to develop this technology combining library screening with mammalian directed evolution. This research is funded by an EU H2020 project with top international partners. Our laboratory is focused on applied synthetic biology for therapeutic purposes. We have two lines of research, one in technology development for gene therapy, and one in skin microbiome engineering. We are located in the PRBB, an exciting international and cutting-edge scientific environment. | cas9, CRISPR, gene editing, gene therapy, synthetic biology | |||
DCEXS-2206. Skin microbiome-based sensors | 2022-2023 | DCEXS-UPF | Translational Synthetic Biology | WEBSITE | Marc | Güell | Assigned | Interested in developing novel sensing mechanisms based on natural skin bacteria? Microbes are very sophisticated molecular machines. We have developed methodologies to modify the skin microbiome in humans (Pätzold et al, Microbiome 2019). We are using the skin microbes to expand the functionalities of the host including sensing the environment or the skin status (sebum secretion, immune state). Sensed information can be registered using real time optical reporters or recorded historically on the genome using CRISPR recording. We are offering a master thesis position to develop sensing genetic circuits to be embedded into the skin microbiome. This research is funded by a US Department of Defense grant and involves very exciting interactions with international partners. Feel free to reach me if you have any question on the project (marc.guell@upf.edu). Our laboratory is focused on applied synthetic biology for therapeutic purposes. We have two lines of research, one in technology development for gene therapy, and one in skin microbiome engineering. We are located in the PRBB, an exciting international and cutting-edge scientific environment. | genetic circuits, sensors, skin microbiome, synthetic biology, therapy | |||
CRG-2201. Cross species genome annotation | 2022-2023 | CRG | Computational Biology or RNA Processing | WEBSITE | Roderic | Guigo | Available | Understanding Earth’s biodiversity and responsibly administrating its resources is among the top scientific and social challenges of this century. The Earth BioGenome Project (EBP) aims to sequence, catalog and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of 10 years (http://www.pnas.org/content/115/17/4325). The outcomes of the EBP will inform a broad range of major issues facing humankind, such as the impact of climate change on biodiversity, the conservation of endangered species and ecosystems, and the preservation and enhancement of ecosystem services. It will contribute to our understanding of biology, ecology and evolution, and will facilitate advances in agriculture, medicine and in the industries based on life: it will, among others, help to discover new medicinal resources for human health, enhance control of pandemics, to identify new genetic variants for improving agriculture, and to discover novel biomaterials and new energy sources, among others. | Julien | Lagarde | bioinforamtics, Earth BioGenome Project, gene annotation, genomics | |
ICFO-2204. Frontiers of Quantum Information Science, Quantum Simulations and Many Body Physics | 2022-2023 | ICFO | Quantum Optics Theory | WEBSITE | Maciej | Lewenstein | Available | The MSc student will join one of the running research projects in the ICFO-QOT. The concrete choice will depend on the current efforts in the group (that change adjusting to scientific needs), student’s preferences and preparation, availability of supervisor/co-supervisor and resources for a specific theme. At this stage ICFO-QOT can absorb one MSc student in this area. QOT-ICFO studies and develops in particular | many body physics, quantum information, quantum simulations | |||
IRBB-2205. Biomecical Genomics-Study of DNA damage and repair mechanisms | 2022-2023 | IRB Barcelona | Biomedical Genomics Group-BBGLab | WEBSITE | Nuria | Lopez-Bigas | Assigned | In addition to contributing to finding drivers of cancer and precision medicine, our group is focused on understanding mutational processes by analysing tumour genomes. By studying the observed pattern of somatic mutations across genomic regions, we are able to explore the basic cell mechanisms that produce them. The interplay between these mechanisms, such as internal and external insults that damage DNA, chromosomal replication, transcription, and DNA repair mechanisms, leads to mutational processes that give rise to heterogeneous patterns of somatic mutations across the genome. Our efforts are now focused on generating nucleotide-resolution genome-wide maps of DNA damage and repair upon exposure to chemotherapeutic agents, as we have already optimized a protocol to map alkylation damage in human cell lines. | Víctor | González Huici | cancer, chemotherapy, DNA damage, DNA repair, mutational signature | |
ICIQ-2202. Machine learning for electrochemical processes | 2022-2023 | ICIQ | TheoHetCat | WEBSITE | Núria | López | Assigned | The project is dedicated to leverage Machine Learning techniques to new chemical processes that can improve the design of new processes to mitigate CO2 emissions and thus climate change. | CO2 reduction; Density Functional Theory; Machine learning techniques; descriptors; electrochemical interfaces | |||
IFAE-2204. Prediction of COVID-19 propagation and Cancer growth using Group Theory | 2022-2023 | IFAE | Theory Division | WEBSITE | Pere | Masjuan | Available | This project shall explore the connexion between the COVID-19 propagation and the breast cancer growth based on the mathematics of group theory. | carcinogenesis, COVID-19, group theory | |||
ICN2-2205. Atomically precise graphene nanostructures for optoelectronics | 2022-2023 | ICN2 | Atomic Manipulation and Spectroscopy Group | WEBSITE | Aitor | Mugarza | Assigned | Our group aims to understand and manipulate electronic, magnetic and optical phenomena at the atomic scale, with the final goal of searching for new ways to sense, and to store and process information. The project proposed here focuses on developing methods to tailor graphene’s properties by nanostructuration. | 2D materials, atomic scale manipulation, electronic spectroscopy, graphene nanoribbons, graphene nanostructures, materials synthesis, scanning probe microscopy | |||
DCEXS-2210. Identification of new regulators of the amyloid toxicity in Alzheimer’s disease | 2022-2023 | DCEXS-UPF | Molecular Physiology | WEBSITE | Francisco José | Muñoz López | Available | Alzheimer’s disease (AD) is the most common cause of dementia affecting more than 47 million people worldwide, being a major public health problem with a high economic impact. Due to the progressive increase in life expectancy, it has been proposed that its prevalence will triple in the next 30 years. | Alzheimer’s Disease, Amyloid, BACE1, calcium, oxidative stress | |||
ICN2-2203. Unconventional superconductivity in 2D systems | 2022-2023 | ICN2 | Theory & Simulation Group | WEBSITE | Pablo | Ordejón | Available | The kagome lattice, with an in-plane network of corner-sharing triangles made by transition metal atoms provides an exciting platform to study electronic correlations in the presence of geometric frustration and non-trivial band topology. One example that has attracted considerable interest since its discovery in 2020 is the family of metallic kagome compounds AV3Sb5 (A=K,Rb,Cs), which has shown abundant emergent quantum phenomena, including a competition between superconductivity and charge density wave. Their electronic structure is characterized by a Z2 topological invariant and shows multiple van Hove singularities coexisting near the Fermi level. Using state-of-the-art first principles electronic structure methods, this project aims for a deeper understanding of the properties of these materials. We plan to take advantage of the recent implementation of the Bogoliubov-de Gennes theory in the SIESTA package (developed in the Theory & Simulation group at ICN2) to study the superconducting properties of these fascinating compounds. | Miguel | Pruneda | computational physics, electronic structure, nanostructures, Superconductivity | |
ICN2-2204. Crossover between band and polaron-hopping in low-dimensional organic conductors | 2022-2023 | ICN2 | Theory & Simulation Group | WEBSITE | Pablo | Ordejón | Available | The goal of this project is to develop a way to understand the electronic structure of mixed-valence coordination polymers (1D-, 2D-, 3D-) using the simple but very useful Marcus-type approach based on first-principles DFT. We shall explore the conductivity of molecular or polymeric organic systems proceeding through a | Miguel | Pruneda | computational physics/chemistry, Marcus Theory, organic conductors, polarons | |
ICFO-2210. Emerging low dimensional materials for thermal radiation control and energy | 2022-2023 | ICFO | Thermal Photonics | WEBSITE | Georgia T. | Papadakis | Assigned | The challenges that are imposed onto our societies by climate change and rising temperatures are recognized internationally as one of the main threats to humankind for the next decades. In short, we reject more than half of the energy produced and consumed globally as heat, into the environment. The same problem persists in the microscale, where devices’s overheating at the microprocessor level compromises computing efficiency, data storage, and network connectivity. Standard approaches to dissipate and recycle heat into useful electricity include thermoelectric coolers and generators, steam engines, air conditioning systems and refrigirators. These are bulky, mechanically complicated, and often inefficient approaches that are based on heat conduction and heat convection. In the thermal photonics group, we are investigating means of controlling and recycling heat via thermal radiation, i.e. using infrared photons. Thermal radiation is emitted by all objects at a non-zero temperature; hence it represents an excellent energy source that we can harness. Recent advances in nanotechnology have allowed the realization of passive radiative cooling schemes where photons emitted at infrared frequencies can cool a macroscopic objects to temperatures below ambient conditions. At the same time, thermophotovoltaic systems that recycle these thermal photons into electricity promise very high efficiencies. In this Master’s project, we will leverage on the properties of emerging materials that are extremely sensitive to their immediate dielectric environment, present very sharp resonant response, and are often highly anisotropic, to control the direction of thermally emitted beams of IR radiation. The project involves analytical and semi-analytical work, numerical simulations, and measurements of thermal emission with Fourier Transform Infrared Spectroscopy. | ||||
CRG-2202. X-chromosome reactivation in iPSCs and mouse embryos | 2022-2023 | CRG | Epigenetic Reprogramming in Embryogenesis and the Germline | WEBSITE | Bernhard | Payer | Assigned | In our lab, we are studying how epigenetic information is erased during mammalian development. In particular, we study epigenetic reprogramming of the X-chromosome in mouse embryos, induced pluripotent stem cell (iPSC) and in the germ cell lineage in vivo and in vitro. Using a multidisciplinary approach, we want to gain insight into how epigenetic reprogramming is linked to its biological context, with long-term implications for regenerative and reproductive medicine. | Epigenetics, iPSC-reprogramming, Pluripotency, X-chromosome reactivation | |||
CRG-2203. Epigenetic reprogramming in mammalian germ cells | 2022-2023 | CRG | Epigenetic Reprogramming in Embryogenesis and the Germline | WEBSITE | Bernhard | Payer | Assigned | In our lab, we are studying how epigenetic information is erased during mammalian development. In particular, we study epigenetic reprogramming of the X-chromosome in mouse embryos, induced pluripotent stem cell (iPSC) and in the germ cell lineage in vivo and in vitro. Using a multidisciplinary approach, we want to gain insight into how epigenetic reprogramming is linked to its biological context, with long-term implications for regenerative and reproductive medicine. | Epigenetics, Germ cells, reproduction, X-chromosome reactivation | |||
ICIQ-2201. Design and development of tailored-made solutions for site-selective C-H functionalization reactions | 2022-2023 | ICIQ | Pérez-Temprano group | WEBSITE | Mónica H. | Pérez-Temprano | Available | Without any doubts, the conversion of ubiquitous and typically inert C–H bonds into C–C and C–heteroatom bonds, considered one of the Holy Grails in Chemistry, is one of the most attractive transformations in organic synthesis. Since the second half of the 20th century, the approaches for the cleavage of “unreactive” C–H bonds have evolved from classical electrophilic or radical routes to so-called ligand-directed C–H functionalization protocols. These latter strategies have the potential of simplifying reactions by minimizing the formation of undesired by-products and/or allowing the control of site-selectivity by the use of chelating functional groups present on the reagents. These directing groups (DGs) can bind to the metal center facilitating the reactivity at a specific site on molecules that contain multitude of C–H bonds. Still now, these methodologies predominantly employ precious metals. This has implications for sustainability from both the cost and environmental perspectives. | C-H functionalization, catalysis, Organic Synthesis, Organometallic Chemistry, Sustainability | |||
IBEC-2203. Optical magnetometry for skeletal muscle biomagnetic analysis | 2022-2023 | IBEC | Biosensors for Bioengineering | WEBSITE | Javier | Ramon Azcon | Available | The Biosensors for Bioengineering research group develops multi-tissue organs-on-a-chip (OOC) and integrating sensing technology with tissue engineering. Within this scope, we use in situ biosensors to study insulin release under external stimuli, changes in glucose levels, and myokines secreted by skeletal muscle (multi-OOC approach)1. This project will mimic the complex native muscle structure and organization using precursor cells encapsulated in 3D scaffolds. They support the growth and differentiation of progenitor cells and provide 3D environments to cells. We have developed hybrid biomaterials with tunable mechanical and electrical properties that give structure and support to the cells, and they are biocompatible2,3. This project’s framework will optimize biomaterials to improve other muscle cells’ functionality, longevity, and mechanical and electrical properties. Here we partner with ICFO’s Atomic Quantum Optics group to investigate myotube conductivity using exquisitely sensitive quantum devices known as optically pumped magnetometers (OPMs), which elsewhere are deployed for studies of brain and heart magnetism in vivo, i.e., magnetoencephalography and magnetocardiography4,5. The project’s main objective is to monitor myotubes’ electrical conductivity and associated magnetic field response. The expectation is for OPMs to allow real-time magnetomyography in the OOC while avoiding invasive electrode placement, unlike direct conductivity measurements6. Tasks: (1) characterize the MMG signal at the myotube level, such as the orientation of the biomagnetic field relative to the cell and temporal response to a single action potential, (2) Identify and characterize responses to chemical stimuli (e.g., drugs), introduced to the OOC. 1. Ortega, M. A. et al. Muscle-on-a-chip with an on-site multiplexed biosensing system for in situ monitoring of secreted IL-6 and TNF-α. Lab Chip 19, 2568–2580 (2019). | Michael | Tayler | optically pumped magnetometer, quantum technology, skeletal muscle, tissue engineering | |
DCEXS-2208. The mysterious biology of the most abundant microbial eukaryotes in the surface oceans | 2022-2023 | DCEXS-UPF | Biology and Ecology of Abundant Protists | WEBSITE | Daniel J. | Richter | Available | Which are the most abundant microbial eukaryotic species in the world’s sunlit oceans, and what roles do they play in global marine ecology? Currently, the answers to both these questions remain largely unknown. Microbial eukaryotes (also known as protists) are single-celled and colonial organisms that occupy the size range between bacteria (micrometers) and the smallest multicellular animals (millimeters), a critical position for the function of oceanic food webs. Recent seafaring expeditions, such as the Tara Oceans project, have produced DNA sequence-based catalogs of protists on a global scale. We previously analyzed Tara Oceans data to reveal that only 100 of the approximately 500,000 protist species in the surface ocean make up 50% of total protist abundance. Yet, 92 of these 100 species are unknown to science, and have not even been identified by light microscopy. The goal of this project is to characterize the biology, interspecies interactions, and ecosystem relevance of these 92 highly abundant, ubiquitous unknown protists. We propose two research and training objectives. First, using a novel isolation approach, we will establish robust laboratory cultures and apply single-cell transcriptome sequencing to produce gene catalogs. Second, we will apply time-lapse light and fluorescence microscopy to understand their life history and behavior and to build hypotheses about their individual and community metabolic potential, followed by laboratory manipulations to test these hypotheses. Overall, we will provide the first glimpse of the morphological, life history, behavioral and transcriptional features of currently unknown globally abundant protists. Discoveries about their biology will have immediate implications for studies of the ecology and community structure of oceanic ecosystems. Finally, we anticipate that our efforts will lead to the establishment of ecologically relevant microbial eukaryotes as new model systems whose biology can be studied intensively in the laboratory. | interspecies interaction, microscopy, new species isolation, protists, single-cell transcriptomics | |||
DCEXS-2203. Targeting a nanomedicine to pancreatic tumor | 2022-2023 | DCEXS-UPF | Integrative Biomedical Materials and Nanomedicine Lab | WEBSITE | Pilar | Rivera Gil | Assigned | Molecular mechnisms underlying the phtothermal activity of an antitumoral nanomedicine. | Nanomedicine, pancreatic cancer, targeted therapy | |||
IRBB-2203. Stress kinase signaling as target for cancer therapy | 2022-2023 | IRB Barcelona | Signaling and Cell Cycle | WEBSITE | Angel | Rodriguez Nebreda | Assigned | An important part of the group’s work focuses on the stress-activated p38 MAPK signaling pathway, investigating the mechanisms of signal integration by this pathway and its implication in physiological and pathological processes. Our results have provided in vivo evidence for the implication of p38 MAPKs in homeostatic functions, beyond the stress response, and have illustrated how dysregulation of this pathway may contribute to cancer and other diseases. Recently, we have demonstrated key roles for p38 MAPK signaling in tumor progression as well as in the resistance to chemotherapeutic drugs using mouse models. Our work combines studies using genetically modified mice and chemical inhibitors, with experiments in cancer cell lines and biochemical approaches. An important aim of our work is the identification of therapeutic opportunities based on the modulation of p38 MAPK signaling. Ongoing projects in the group address two main topics: (1) Cancer cell homeostasis and chemoresistance mechanisms, and (2) Cross talk between cancer cells and stromal cells. | cancer cell homeostasis, chemotherapy resistance, signaling network, targeted therapy, tumor microenvironment | |||
IRBB-2207. Single-cell analysis of hematopoietic and leukemic stem cell memory | 2022-2023 | IRB Barcelona | Quantitative Stem Cell Dynamics | WEBSITE | Alejo | Rodriguez-Fraticelli | Available | Our group applies single-cell and clonal analysis technologies to provide a more unbiased understanding of cellular physiology and disease. We combine single-cell sequencing with lineage tracing to understand how gene expression dynamics in stem cells (variation) contributes to distinct cellular functions. There are two Master’s thesis projects available, both focused on developing new technologies for studying stem cell dynamics in the hematopoietic system: | cellular heterogeneity, hematopoiesis, inflammation, regeneration, single cell analysis | |||
IRBB-2206. Mutagenesis in cancer genomes | 2022-2023 | IRB Barcelona | Genome Data Science | WEBSITE | Fran | Supek | Assigned | We are interested in using machine learning methodologies to analyze mutation patterns in cancer genomes, in order to (a) learn about mutagenesis and DNA repair mechanisms in human, and (b) predict cancer evolution such as the appearance of drug resistance mutations. The student will learn genomic data analyses methods (bioinformatics and statistical genomics), cancer biology,, applied machine learning and data visualization. | cancer, genetic disease, human genetics, Machine learning, mutations | |||
ICFO-2201. Quantum simulation with ultracold atoms | 2022-2023 | ICFO | Ultracold Quantum Gases | WEBSITE | Leticia | Tarruell | Available | In recent years, ultra-cold atomic gases have emerged as a novel platform for the study of quantum many-body systems. They provide quantum matter that can be controlled almost at will using the tools of optics and atomic physics, and allows one to engineer a very broad range of model Hamiltonians in a single table-top experiment. This bottom-up approach comes very close to Feynman’s idea of a “quantum simulator” – a special purpose quantum computer that can solve problems currently out of reach for classical machines – and, besides enabling the study of long-standing physics questions, also gives access to completely new forms of quantum matter. In our group, we have two quantum gas laboratories that focus on complementary aspects of quantum gas research. In the potassium lab, we investigate mixtures of quantum gases where the competition of interactions with different origins reveals the subtle effects of quantum fluctuations and stabilizes new phases. For instance, we exploit mixtures of Bose-Einstein condensates (BECs) to create the most dilute liquids existing in Nature, and use them to understand better the role of quantum correlations in quantum many-body physics [C. R. Cabrera et al., Science 359, 301 (2018)]. Using lasers that couple two internal states of the atoms, we also engineer collective many-body states which are described by topological gauge theories originally proposed in the context of fractional quantum Hall physics, and investigate their chiral properties. Finally, in ongoing experiments we are trying to create a supersolid liquid: a phase which exhibits simultaneously the phase coherence of a superfluid, the crystalline structure of a solid, and forms self-bound droplets like a liquid. In the strontium lab, we aim at synthesizing the cleanest and purest “solids”. To this end, we will trap quantum degenerate fermionic atoms in optical lattices – artificial crystals of light created by interfering laser beams – and probe their properties by detecting every single atom and lattice site using fluorescence imaging. With such quantum gas microscope, we want to perform quantum simulations of the Fermi-Hubbard model [L. Tarruell and L. Sanchez-Palencia, C. R. Physique 19, 365 (2018)], which is believed to hold the key of high-temperature superconductivity. Moreover, because strontium has 10 internal states, we can extend our studies to “electrons” of spin larger than 1/2, for which completely new types of quantum magnets are expected. The strontium apparatus is currently under development. Our experiment already produces laser-cooled fermionic atoms at microkelvin temperatures, and we are currently developing the quantum gas microscope part of the setup. We offer Master theses on the two laboratories. They will focus on the development of an experimental subsection of the apparatus, and will include a small theoretical part focusing on its design, and a larger experimental part consisting on its construction and characterization. Several projects are possible depending on the skills and interests of the candidates, and on the advancement of the experiments. For further information, references and a list of former Bachelor and Master projects completed in the group, please consult www.qge.icfo.es We are looking for candidates with a good background in quantum optics, atomic physics or condensed-matter physics, and a strong motivation for setting up and conducting challenging experiments in a team of three to four people. We offer training in a broad range of cutting-edge experimental techniques (from optics, electronics, ultra-high vacuum technology and computer control to quantum state engineering), as well as in theoretical atomic, quantum, statistical, and condensed matter physics. | Bose-Einstein condensates, degenerate Fermi gases, gauge theories, optical lattices, quantum gas microscope, quantum liquids, quantum magnetism, quantum simulation, supersolidity, ultracold quantum gases | |||
ICN2-2206. Ultrafast Experiments on Quantum Materials | 2022-2023 | ICN2 | Ultrafast Dynamics in Nanoscale Systems | WEBSITE | Klaas-Jan | Tielrooij | Available | In this project you will work with state-of-the-art ultrafast laser systems, in order to study optical, electrical and, especially, thermal phenomena in novel quantum materials. You will get hands-on experience with the fabrication of samples based on 2D materials with a thickness down to the atomic monolayer, and will learn how to study these exciting material systems with advanced optoelectronic setups with femtosecond time resolution. | 2D materials, heat, optics, Ultrafast | |||
IFAE-2202. CMOS Infra-red Detectors for Medical Applications | 2022-2023 | IFAE | Medical Physics | WEBSITE | Sebastian | Grinstein | Available | 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. | Stefano | Terzo | ||
IRBB-2208. Novel therapeutic approaches against intrinsically disordered protein targets | 2022-2023 | IRB Barcelona | Laboratory of Molecular Biophysics | WEBSITE | Xavier | Salvatella | Available | Intrinsically disordered proteins (IDPs) retains a large portion of flexibility that allows proteins to sample a large conformational space. Therefore, IDPs are excellent binding partners that are able to interact with a plethora of cellular components and are involved in many signaling and cell regulation events (Eftekharzadeh et al., 2019 Nat Comm.; De Mol et al., 2018 Structure). Given their increased accessibility and exposed surface, they are also tightly regulated by post-translational modifications and protein processing. Conversely, it is generally thought that the lack of a well-defined structure impedes the structure-based rationalization of small-molecules drugs, although several original approaches are being explored (Fuertes et al., 2019; Heller et al., 2020). Recently, IDPs have been reported to be involved in the formation of membrane-less organelles by phase separation (Bouchard et al. 2018 Mol. Cell). An ambitious goal of our research group is to decipher the molecular basis that regulate the phase separation propensities of IDPs and set the basis for the development of drugs that modulate their properties. To this end, novel approaches, both technical and conceptual, are under development in our group. The proposed project for a prospective master student contains (i) the biophysical characterization of an IDP liquid-liquid phase separation, (ii) the atomic-resolution study of IDP-drug interactions by nuclear magnetic resonance, and (iii) the participation in a multidisciplinary environment (from biophysics to cell biology) that aims to make a substantial contribution in the drug discovery of challenging cancer targets. | Borja | Mateos | biophysics, drug discovery, intrinsically disordered proteins, liquid-liquid phase separation, nuclear magnetic resonance | |
IRBB-2210. Uncovering and targeting early cancer-specific cell states | 2022-2023 | IRB Barcelona | Inflammation, Tissue Plasticity and Cancer | WEBSITE | Direna | Alonso Curbelo | Assigned | Our lab studies the interplay between genetic mutations and pro-inflammatory tissue signals that promotes cancer development, with a focus on pancreatic and liver cancers, two clinical challenges in dire need for early detection and interception strategies. As cancer pathogenesis hijacks processes that can be key to safeguard normal tissue homeostasis (eg wound healing), we combine bulk/single-cell epigenomic profiling and flexible disease models to uncover the molecular and cellular traits that are unique to tissues undergoing neoplastic transformation, and apply functional genomics tools (RNAi/CRISPR) to pinpoint the key mechanisms responsible for disease progression. The available Master projects will focus on developing new tools for capturing and perturbing molecular programs and cellular states that are induced by the cooperative action of oncogenic mutations and inflammation during cancer development (Alonso-Curbelo et al. Nature 2021): 1. Genetic tagging of tumor cells with unique capacities to drive and/or sense inflammation. Through this opportunity, the student will acquire training on general cancer biology, molecular cloning, functional validation approaches (RNAi/CRISPR-mediated genetic perturbations), histology (immunofluorescence/immunohistochemistry), flow cytometry, culture of pancreatic organoids and cell lines, and experimental design, data analysis and reporting. The student will also work with our team to set-up experimental pipelines in our newly opened lab and contribute to a constructive and stimulating working environment. Keywords: Cancer, inflammation, epigenetics, pancreatic cancer models, CRISPR/Cas9 | ||||
IBEC-2202. Hyperpolarisation-enhanced nuclear magnetic resonance to study metabolism in organ-on-a-chip devices | 2022-2023 | IBEC | Molecular Imaging for Precision Medicine | WEBSITE | Irene | Marco-Rius | Available | The proposed project will develop non-invasive assays based on magnetic resonance (MR) to study glucose metabolism and further the understanding of metabolic diseases such as cancer, non-alcoholic fatty liver disease and muscle dystrophy, aiming to provide a platform for personalized drug testing on organ-on-a-chip systems. | Marc | Azagra | ||
CRG-2205. Understanding Complex Causality in Aging | 2022-2023 | CRG | Dynamics of Living Systems Group | WEBSITE | Nicholas | Stroustrup | Available | The molecular mechanisms driving aging are embedded within complex physiologic networks. At long time-scales, these mechanisms exhibit emergent, collective behaviour that is both a fascinating topic and a fundamental barrier for traditional experimental approaches to establish molecular-level causality. To understand biological aging and develop effective therapies against it, we need better and more quantitative approaches that can rapidly characterize the multiple, complex causal pathways through which molecular-level changes determine systems-level dynamics. The Dynamics of Living Systems group is an interdisciplinary team that pursues these goals through a mix of molecular genetics, synthetic biology, high-throughput imaging, machine learning, modelling, and math. We are currently looking for two candidate profiles: 1. Candidates with an interest in developing and applying data science approaches to analyze multi-omic, time-series data. 2. Candidates with an interest in primarily theoretic projects, aimed at understanding causality, interdependency, and stochastic phenomena in complex | aging, bioinformatics, interventions | |||
IFAE-2201. Charged and Neutral Pion Event Reconstruction with Machine Learning for CP Violation Measurement in the Hyper-Kamiokande experiment | 2022-2023 | IFAE | Neutrino Group | WEBSITE | Pilar | Casado | Available | The phenomenon of CP violation relates to another mystery in our understanding of the universe. If the Big Bang created matter and antimatter in equal parts, why is the universe composed of matter? In 1967 Andrei Sakharov proposed three conditions to produce an excess of matter in the early universe, and one of these is the presence of CP violation. However, it was ultimately found that the CP violation in the quarks and hadrons, such as the neutral kaons, was not sufficient to explain the imbalance in our universe. Hence, we look for new sources of CP violation, and one candidate is the phenomenon of oscillations neutrinos. | ||||
ICIQ-2203. Photocatalytic CO2 reduction in the gas phase | 2022-2023 | ICIQ | Galan-Mascaros group | WEBSITE | Jose Ramon | Galan-Mascaros | Available | The alarming increase of CO2 levels, due to anthropogenic and industrial activities, has become a serious environmental issue nowadays. A plausible solution to minimize the negative impact of CO2 emissions is to develop carbon-neutral approaches, i.e., reduction of CO2 into valuable compounds. This research project deals with the development of efficient photocatalytic systems for the gas-phase conversion of CO2 in the presence of water under sun-like irradiation and dark cycles. The main goal is to fabricate supported photocatalysts with one-dimensional (1D) heterostructures for enhancing light harvesting and electron mobility properties, which will result in higher photocatalytic performances than those obtained with bulk semiconductors. Moreover, the decoration of these photocatalytic systems with quantum dots and luminescent materials will provide them with advanced light conversion abilities, e.g., NIR-light response and light energy storage/release. Such new features will be crucial not only to promote their photoactivation in the full range of the solar spectrum (UV-vis, near-infrared) but also to maintain their photoactivity under intermittent light/dark cycles in a similar way to natural photosynthetic systems | Katherine | Villa Gómez | ||
DCEXS-2211. Genome-wide CRISPR screens to identify functional interactions of host proteins with SARS-CoV-2 proteins | 2022-2023 | DCEXS-UPF | Translational Synthetic Biology | WEBSITE | Amal | Rahmeh | Assigned | In this project, we will develop assays that recapitulate the functions of SARS-CoV-2 proteins under standard safety laboratory conditions. We will focus on the Spike protein which mediate virus entry into cells and on viral proteins that suppress the innate immune response. Using genome-wide CRISPR screens, we will identify host proteins that promote or inhibit the function of these viral proteins. We will then determine the molecular mechanisms that mediate these interactions using biochemistry and cell biology approaches.The results of this project will provide insights into the mechanistic basis of SARS-CoV-2 pathogenesis and may identify targets for anti-viral therapies. | Marc | Guell | ||
IRBB-2209. Systemic control of whole body metabolism by metastatic cells and their stroma. Impact on cancer-associated cachexia | 2022-2023 | IRB Barcelona | Stem cells and Cancer group | WEBSITE | Salvador | Aznar Benitah | Available | Cancer-associated cachexia is a nutritional wasting disorder with no effective treatment that is often fatal—up to 30% of patients who die of “cancer” in fact succumb to cachexia. Surprisingly little is known about the mechanisms underlying it, hindering any therapeutic advances. We now propose that cachexia stems from metastastic-inducing cancer cells that have “hijacked” the body’s tissue repair system, leading to energy being drained from the body and going into the metastatic cancer progression/growth. This project stems from previous work in our lab where we have identified and characterized metastatic cells in many tumor types (Nature 2021; Nature 2017; Nat Cell Biol 2018; Nat Metabolism 2020; Elife 2017). To understand this in molecular detail, we will use state-of-art technologies to examine mouse models in vivo and mouse and patient-derived cells in vitro. We aim to determine the specific molecular pathways that led to cachexia, and whether re-routed cells have a defined pro-cachexia signature. Overall, we expect to reveal actionable targets for future therapies (via drugs, diet supplements, etc), with the potential to improve quality of life and survival for patients with cancer. | Gloria | Pascual Angulo | ||
IFAE-2203. Detection of quantum properties of gravitational waves | 2022-2023 | IFAE | Theoretical Physics | WEBSITE | Diego | Blas | Available | The direct detection of gravitational waves was one of the most important milestones in Physics of recent years, as recognized by the Nobel prize of 2017. It has allowed us to explore new phenomena of the Universe, verify the existence of black holes, and confirm some of the most spectacular predictions of Einstein’s theory of general relativity. Still, an aspect of gravitational waves has remained elusive to verification. Indeed, all other interactions of Nature are quantized, a property expected also for gravity, yet not confirmed. Quite interestingly, the current developments in the precision frontier, e.g. in quantum technologies, may change this situation, and allow us to access the first hints of the quantization of gravitational radiation. In this project, we will characterize under which situations the quantum nature of gravitational waves may be relevant and how to access this regime with current or future detectors. The latter will be based on state-of-the-art technologies, as atom or light interferometers, atomic clocks, etc. The result of this project will provide insights into some of the most fundamental aspect of gravitation yet to be proven, and also will give the student the tools to continue her/his work on the frontier of fundamental physics and quantum devices. | Rodrigo | Vicente | fundamental physics, Gravitational waves, quantization of fields, quantum devices | |
IBEC-2201. Deciphering key cell-matrix interactions in differentiation and disease of the musculoskeletal system tissues | 2022-2023 | IBEC | Nanobioengineering | WEBSITE | Anna | Lagunas | Available | The Nanobioengineering group at IBEC is a multidisciplinary team applying nanotechnology for the development of new biomedical systems and devices, mainly for diagnostic purposes, and integrated microfluidic Organ-on-Chip devices for the study of organ physiology, disease etiology, or drug screening. The group uses nanotechnology applied to biomolecule interaction studies and micro/nano-environments for regenerative medicine applications. Particularly, we work on the development of bioengineered 2D and 3D micro/nanoenvironments with a topography and chemical composition controlled at the nanoscale for cell behavior studies (adhesion, proliferation, differentiation) and the biophysical description of cellular phenomena (cell migration, differentiation) using micro/nanotechnologies, cell biology tools and soft matter physics. | cell-matrix interactions, musculoskeletal system, Nanomedicine, regenerative medicine | |||
DCEXS-2213. Study of the Antibody-mediated NK cell response to Epstein-Barr Virus | 2022-2023 | DCEXS-UPF | Human Natural Killer Cell Biology Group | WEBSITE | Miguel | López-Botet | Available | The proposed project would consist in the continuation of a study on the antibody-mediated Natural Killer (NK) Cell response to Epstein Barr virus (EBV) (López-Montañés, Alari-Pahissa et al. JImmunol 2017; Alari-Pahissa et al. PlosPathogens 2021). EBV causes a highly prevalent and lifelong infection contributing to the development of some malignancies. When NK cells recognize, through the Fc receptor (CD16), antibodies (Abs) bound to EBV-antigens in the membrane of infected B cells, they become activated, produce TNFa and IFNg and release cytotoxic granules containing perforin which kills the infected B cell. We previously reported that when viral particles are attached to the B cell surface prior to infection, NK cells may be also activated by EBV-bound Abs producing TNFa but not IFNg, and releasing cytotoxic granules that, remarkably, do not result in B cell death. Recently, we showed that in this setting , NK cells may partially inhibit B cell infection, uptaking the viral particles and internalizing them through a trogocytosis-like process. We intend to investigate on one hand why the viral particle-coated B cell is not killed in spite of NK cell degranulation and, on the other hand, whether activation under these conditions may result in NK cell exhaustion. In relation to the first objective, we hypothesize that when the antigen is on the viral particle attached to the B cell, the indirect NK-B cell interaction is insufficient to promote synapse formation required to efficiently trigger effector functions. It has been recently shown that cytotoxic cells pull the membrane of target cells increasing the membrane tension, and that this makes the insertion of perforin more efficient.The project would involve the realization of molecular biology, transfection, flow cytometry, microscopy and video microscopy techniques. The main experimental line would consist in generating transfectants of viral antigens in a B cell line and comparing them with the same cell line coated with VP in the way they interact with NK cells through anti-EBV Abs in flow cytometry, microscopy and video microscopy experiments, measuring frequency and duration of synapses as well as membrane tension. | Elisenda | Alari Pahissa | ||
DCEXS-2212. Identification of a plasma lipidomics signature underlying the beneficial health effects of tyrosol supplementation in individuals at high cardiovascular risk | 2022-2023 | DCEXS-UPF | Integrative Pharmacology and Systems Neurosciences Research Group | WEBSITE | Rafael | de la Torre | Available | This project is linked to a research line whose aim is to understand the health benefits provided by dietary phenolic compounds and the use of nutraceuticals as therapeutic tools in the prevention of cardiovascular and neurodegenerative diseases. In this context, we performed a randomized, double-blind, controlled clinical trial (the PENSA study) that aims to evaluate the efficacy of a personalized multimodal intervention in lifestyle (Mediterranean diet, physical activity, cognitive training and social engagement) combined with the use of epigallocatechin gallate (EGCG) during 12 months, in slowing down cognitive decline in an adult population at risk of developing Alzheimer’s disease (APOE-E4 carriers) exhibiting Subjective Cognitive Decline (SCD). Although the primary efficacy outcome is change in a composite score of cognitive performance (Alzheimer Disease Cooperative Study Preclinical Alzheimer Cognitive Composite (ADCS-PACC), further research is warranted to better understand the biological mechanisms responsible for these effects. Lipidomics is a relatively new emerging discipline with the great potential of elucidating the biochemical mechanisms underlying alterations in lipid metabolism. The first objective of this project is to study the alterations in lipid metabolism induced by the intervention with Mediterranean Diet. To do so, a targeted lipidomics analysis in plasma samples of participants of the previously mentioned study will be performed. The second objective of this study is to evaluate the correlation between clinical parameters of the study participants and specific lipid species in order to find biomarkers. | Josep | Rodríguez-Morató | cognition, dietary antioxidants, Lipidomics, neurodegenerative diseases, nutrition., nutritional intervention studies | |
ICFO-2213. Emerging approaches for CO2 capture and conversion | 2022-2023 | ICFO | CO2MAP | WEBSITE | F. Pelayo | García de Arquer | Available | CO2 capture and conversion using renewable energy stands out as one promising strategy to revert global warming. CO2 electroreduction (CO2R), in particular, enables the transformation of CO2 into widely used chemicals that could be readily used in our society as fuels and chemicals. Suggested literature: | ||||
ICFO-2212. AI-driven Accelerated Materials Discovery | 2022-2023 | ICFO | CO2MAP | WEBSITE | F. Pelayo | García de Arquer | Available | The discovery of new materials has fueled the most relevant technological advances across history. Advances in modern chemistry and physics, combined with nanotechnology have enabled a rapid growth in the knowledge and utilization of emerging materials, offering guidance into their design from the atomic level, synthesis, and discovery of new classes of materials. There are virtually infinite combinations of materials in terms of composition and structure. To date, the discovery of new materials has been based on serendipity, empirical observations, or time-consuming computational modeling. In this project, we will utilize artificial intelligence to accelerate the design of new materials for energy harvesting and storage applications. The prospective student will combine work on some of the next: Suggested literature: | ||||
ICFO-2211. Hot Atoms | 2022-2023 | ICFO | Atomic Quantum Optics | WEBSITE | Morgan | Mitchell | Available | “Our group studies the interactions between light and the quantized states of electrons in atoms. The electronic states of alkali atoms, in Our lab develops new ways to improve atomic magnetometer performance, as well as new applications: https://www.youtube.com/watch?v=CZZrfKs2VfI Projects are available in the following areas:(1) We use microfabricated atomic cells, targeted at wearable devices for the healthcare sector; (2) We “quantum enhancement” approaches, such as polarization squeezing, that have the potential to surpass standard quantum noise limits in magnetometers; (3) We apply optimal signal-tracking approaches, such as a Kalman filtering, to magnetometry (4) We apply magnetometers to detect magnetic activity of biological systems, e,g, muscle (5) We apply magnetometers as sensors for magnetic resonance imaging (MRI) of soft matter (6) We investigate techniques to transfer alkali atoms polarization to nuclear spin species in inert gases (e.g. 129Xe, N2, 3He), for use in gas-phase imaging applications The student will have the opportunity to learn about cutting-edge devices in quantum sensing and magnetometry within the environment of an international research team. The project will be experimentally focused, allowing the student to address a scientific question. Some fluency in programming is required (C/C++, python, Matlab or Mathematica) for data analysis and to perform simulations of the experiment on a computer. Please see the group webpage for recent publications: http://mitchellgroup.icfo.es/mg/pmwiki.php | Atomic sensors, Magnetic Resonance, Magnetometry, Quantum optics, Rubidium vapors | |||
IRBB-2212. Drug discovery innovation for cancer treatment | 2022-2023 | IRB Barcelona | Targeted protein degradation and drug discovery | WEBSITE | Cristina | Mayor Ruiz | Available | Despite tremendous progress in therapeutic drug development, more than 80% of all human proteins remain beyond the reach of inhibitor-centric traditional drug discovery, including some of the most prolific cancer targets. | CRISPR, degraders, drug discovery, screenings, Targeted protein degradation | |||
IRBB-2213. Drosophila as a model in cancer biology | 2022-2023 | IRB Barcelona | Development and Growth Control Laboratory | WEBSITE | Marco | Milán | Available | Cancer is a multi-hit process involving mutations in oncogenes and tumor suppressors, as well as interactions between the tumor cells and the surrounding stroma. Cancer as a disease is characterized by a series of hallmarks, which include sustained proliferative signalling, resistance to growth suppressors and to cell death, increased replicative immortality, invasiveness and metastasis, energy metabolism reprogramming, genome instability, and inflammation. We are interested in the cellular and molecular mechanisms underlying the regulation of many of these hallmarks, especially the role of Genome Instability in tumourigenesis. The fruit fly, Drosophila, is an excellent, genetically-tractable system for modelling the development of cancer, due to the conservation of signaling pathways, cell proliferation and survival genes between fly and humans, its suitability for genetic and molecular manipulations, and its well-described developmental biology. Working with flies (an in vivo approach) allows the analysis of tumours at the cell autonomous level but also at the systemic level (relationship between tumours and the rest of the body). Drosophila is also useful to perform high-throughput screening of small molecule inhibitors that can be developed to combat human cancer. | cancer, Chromosomal Instability, Drosophila | |||
DCEXS-2214. Zinc imbalance and cancer progression | 2022-2023 | DCEXS-UPF | Laboratory of Molecular Physiology | WEBSITE | Rubén | Vicente | Available | The human body contains 2–3 g of zinc.Deficiency in zinc causes impairment in body growth, neurological disorders and immunosuppression, leading to morbidity and an increased infection rate. In this context, our group has recently published an observational study showing that COVID-19 patients with lower plasma zinc content have worse prognosis, increased time of hospitalization and mortality. The general goal of the project is to better understand the potential benefits of using zinc as a nutriceutic in infectious diseases. The specific objectives are: i) to characterize the impact of zinc supplementation in the immune system and ii) to study at the cellular level the signalling pathways implicated in this regulation.The project is based on a multidisciplinary approach combining immunology and biophysics. The students will acquire skills in different techniques of both disciplines. | COVID-19, immunology, zinc |
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