Master of Multidisciplinary Research in Experimental Sciences - Major Project List 2020/2021

 
Master of
Multidisciplinary
Research in
Experimental
Sciences
Major Project List
2020/2021
                 bist.eu/master
Major Research Projects

A key feature of the program is in-depth        Major Research Project: 6-month long
hands-on research training in multiple         project carried out under the supervision.
fields. Students undertake a 6-month long      Upon completion of the project, the
major project (Major Research Project)         student will write a research paper and
and a 10-week minor project, in two            publicly defend the work he or she has
different research disciplines in leading      done.
research     institutions. Students      are   Minor Research Project: 10-week long
provided with extensive training in            research project, complementary to the
professional research skill, and engage        student’s major research project, carried
directly with and learn from outstanding       out in a different research laboratory.
local and international researchers of a PI    Upon completion of the project, the
from one of the participating institutions.    student will prepare a poster and publicly
                                               defend the work he or she has done.

Information for Applicants

*Applicants are requested to list 5 major      **Second Call applicants who state
projects in order of preference. The           preference for a project assigned in the
Selection Committee will assign major          previous round will be informed and
projects based on said list as well as the     requested to submit new projects before
Committee’s evaluation of the student’s        the closing of the call.
candidature, the supervisors’ assessments
and the adequacy of the project to the
candidate’s profile.
Master of Multidisciplinary Research in Experimental Sciences                                                                  Major Research Projects
    BIST-UPF                                                                                                                                   2020/2021

    LIST OF PROJECTS
    THE DEPARTMENT OF EXPERIMENTAL AND HEALTH SCIENCES (DCEXS-UPF) ......................7

      DCEXS-2001. Translational Synthetic Biology .................................................................................7
      DCEXS-2002. Dynamical Systems Biology .......................................................................................7
      DCEXS-2003. Uncovering the clonal dynamics of the hindbrain: balancing proliferation
3     and differentiation ...............................................................................................................................8
      DCEXS-2004. Molecular Physiology Laboratory .............................................................................9
      DCEXS-2005. Zinc imbalance and cancer progression ............................................................. 10
      DCEXS-2006. Integrative Biomedical Materials and Nanomedicine Lab ............................. 10
      DCEXS-2007. Hypoglycosylation Of Voltage-Gated And Mechanosensitive Ion Channels:
      New Pathological Mechanisms And Therapeutic Targets For Neurological Disorders In
      Phosphomannomutase 2 Deficiency (PMM2-CDG) .................................................................... 11
      DCEXS-2008. In vivo mapping of the neuronal circuity related to vestibular and auditory
      sensory function ................................................................................................................................. 12
      DCEXS-2009. Monitoring oxidative stress in living cells – use of genetically encoded
      reporters to determine H2O2 levels linked to signalling and disease ................................. 12
      DCEXS-2010. Engineering Intracellular Nanotools To Image Protein Structures In Vivo:
      Resolving The Mechanism Of Exocytosis ..................................................................................... 13
      DCEXS-2011. Cancer Biology .......................................................................................................... 13

    CENTER FOR GENOMIC REGULATION (CRG) ...................................................................... 15

      CRG-2001. Reconstituting tissue self-organization and collective cell dynamics in early
      embryonic development via 3D synthetic culture methods ..................................................... 15
      CRG-2002. Trans-generational epigenetic influences on mutation outcome ....................... 15
      CRG-2003. Understanding the molecular basis of neuronal 3’UTR length-dependent
      mRNA sorting ..................................................................................................................................... 16
      CRG-2004. Understanding the molecular basis for bidirectional neuronal mRNA transport
      .............................................................................................................................................................. 17
      CRG-2005. X-chromosome reactivation in iPSCs and mouse embryos ................................. 18
      CRG-2006. Epigenetic reprogramming in mammalian germ cells ......................................... 18
      CRG-2007. Dynamics of Living Systems ........................................................................................ 19
INSTITUTE FOR BIOENGINEERING OF CATALONIA (IBEC) .................................................. 20

  IBEC-2001.Nanoprobes & Nanoswitches I ................................................................................... 20
  IBEC-2002. Nanoprobes & Nanoswitches II ................................................................................. 21
  IBEC-2003. Nanoprobes & Nanoswitches III ................................................................................ 22
  IBEC-2004. Improving site-specific targeting of nanomedicines for treatment of lung or
  brain diseases ................................................................................................................................... 22
  IBEC-2005. Development of computational Solutions for Ion Mobility Spectrometry Data
  Analysis ............................................................................................................................................... 23
  IBEC-2006. Equivalence of chemical measurement methods .................................................. 24
  IBEC-2007. Integrative Cell and Tissue Dynamics ...................................................................... 24
  IBEC-2008. Smart Nano-Bio-Devices I ............................................................................................ 25
  IBEC-2009. Smart Nano-Bio-Devices II ........................................................................................... 25
  IBEC-2010. Selection of DNA aptamers against Plasmodium falciparum early blood
  stages .................................................................................................................................................. 26
  IBEC-2011. Bacterial infections: antimicrobial therapies I ........................................................ 27
  IBEC-2012. Bacterial infections: antimicrobial therapies II ....................................................... 27
  IBEC-2013. Deep Mutagenesis of Prion-Like Domains............................................................... 28
  IBEC-2014. Nanoscopy for Nanomedicine.................................................................................. 28
  IBEC-2015. Developing organ-on-a-chips for the study of diabetes type II .......................... 29

THE INSTITUTE OF PHOTONIC SCIENCES (ICFO) ................................................................. 31

  ICFO-2001. Live Cell Superresolution Microscopy & Embryonic Stem Cells ......................... 31
  ICFO-2002. Medical Optics I ........................................................................................................... 32
  ICFO-2003. Medical Optics II .......................................................................................................... 32
  ICFO-2004. Medical Optics III ......................................................................................................... 32
  ICFO-2005. Medical optics group IV ............................................................................................. 33
  ICFO-2006. All-optical interrogation of synaptic transmission in C elegans......................... 33
  ICFO-2007. Engineering superconductivity in twisted bilayer graphene. .............................. 34
  ICFO-2008. Hot Atoms 1 ................................................................................................................... 34
  ICFO-2009. Quantum simulation with ultracold atoms .............................................................. 35
  ICFO-2010 Single-molecule microscopy tools to study intra-Golgi membrane traffic ........ 36
  ICFO-2011. Attosecond Molecular-movies with Inner-Shell Electrons ..................................... 37
Master of Multidisciplinary Research in Experimental Sciences                                                                Major Research Projects
    BIST-UPF                                                                                                                                 2020/2021

      ICFO-2012. Real time 3D video tracking of nanoparticle motion confined in an optical
      trap ....................................................................................................................................................... 37
      ICFO-2013. Frontiers of Quantum Information Science, Quantum Simulations and Many
      Body Physics ....................................................................................................................................... 38
      ICFO-2014. Cavity quantum electrodynamics.............................................................................. 38
      ICFO-2015. Hyperfocusing infrared light for sensitive photodetection .................................. 39
      ICFO-2016. Single photons from two-dimensional materials ................................................... 39
5
    INSTITUTE OF CHEMICAL RESEARCH OF CATALONIA (ICIQ) .............................................. 41

      ICIQ-2001. Machine Learning Techniques in Electro-Catalysis................................................ 41
      ICIQ-2002. Nanomaterials for energy applications ................................................................... 41

    CATALAN INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY (ICN2) ...................... 42

      ICN2-2001. Advanced Electron Nanoscopy ................................................................................. 42
      ICN2-2002. Atomically precise graphene nanostructures for optoelectronics ..................... 43
      ICN2-2003. Complex Inorganic Nanocrystals For Artificial Photosynthesis, Biogas
      Production And Fuel Cells ............................................................................................................... 44
      ICN2-2004. Nanoremediation: Emerging-Micropollutants And Nanopharmaceuticals ...... 45
      ICN2-2005. New Transfection Agents And Nanoparticle-Antioxidant Adjuvants For
      Inflammatory Related Diseases ..................................................................................................... 46

    INSTITUTE FOR HIGH ENERGY PHYSICS (IFAE) .................................................................... 47

      IFAE-2001. Enhanced ATLAS Level-1 trigger capabilities with Artificial-Intelligence
      regression on Field-Programmable Gate Array architecture. ................................................. 47
      IFAE-2002. Impact of high-granularity timing detectors in the search for the Standard
      Model Higgs boson produced in the vector boson fusion process and decaying into a
      pair of tau leptons ............................................................................................................................ 47
      IFAE-2003. Commissioning of the first Large-Size Telescope of the Cherenkov Telescope
      Array..................................................................................................................................................... 48
      IFAE-2004. Quantum annealing with coherent superconducting qubits ................................ 48
      IFAE-2005 Large-scale correlations and cancer cell metastasis ............................................. 49
      IFAE-2006 Fractal dynamics and cancer growth ........................................................................ 50
      IFAE-2007 Avalanche Photodiodes for Medical Diffuse Optics ............................................... 50
      IFAE-2008 The PAU Survey: the potential of narrow-band observations for revealing the
      true panoply of different galaxy types ......................................................................................... 51
IFAE-2009 Gravitational Waves detection using Deep Learning with LIGO/Virgo data ... 51
  IFAE-2010 The ESA Euclid Dark Energy Survey ............................................................................ 52

INSTITUTE FOR RESEARCH IN BIOMEDICINE (IRB BARCELONA)......................................... 53

  IRBB-2001. Development and Growth Control Laboratory ....................................................... 53
  IRBB-2002. MMB ............................................................................................................................... 54
  IRBB-2003. Understanding stress adaptation from yeast to mammalian cells.................... 54
  IRBB-2004. Cell Division Laboratory .............................................................................................. 55
  IRBB-2005. Complex metabolic diseases and mitochondria ................................................... 55
  IRBB-2006. Signalling and Cell Cycle ............................................................................................ 56
  IRBB-2007. Biomedical Genomics .................................................................................................. 57
Master of Multidisciplinary Research in Experimental Sciences                    Major Research Projects
    BIST-UPF                                                                                     2020/2021

    THE DEPARTMENT OF EXPERIMENTAL AND HEALTH SCIENCES
    (DCEXS-UPF)
                                                               develop precise genetic methodologies to
                                                               modulate skin microbiome population to
    DCEXS-2001. Translational Synthetic                        enable novel therapeutic strategies for
    Biology                                                    skin disease and wellbeing.

                                                               Keywords. CRISPR, synthetic biology,
7   Supervisor. Marc Güell                                     genetic engineering, gene therapy,
    Research group. Translational Synthetic                    microbiome
    Biology

    Project Description. Our group aims to                     DCEXS-2002. Dynamical Systems Biology
    leverage synthetic biology and gene
    editing to generate technologies with                      Supervisor. Jordi Garcia-Ojalvo
    therapeutic potential. Our ability to modify
    genomes has profoundly affected how we                     Research    group.   Dynamical     Systems
    perform scientific research, and future                    Biology
    therapies. Emergent consequences of                        Project Description. The Dynamical
    reinventing biology have already started                   Systems Biology laboratory of the
    to reach society. For example, engineered                  Universitat Pompeu Fabra studies the
    human immune T cells (CAR-T) cure                          dynamics of living systems, from
    cancers with outstanding performance, or                   unicellular organisms to human beings.
    ‘ex    vivo’   applied     gene       editing              The lab uses dynamical phenomena to
    technologies have successfully cured                       identify the molecular mechanisms of a
    severe genetic diseases such as ‘bubble                    large variety of biological processes
    boys’ or sickle cell disease. Biological                   including cellular decision-making, spatial
    technology will have a growing influence                   self-organization and tissue homeostasis.
    in our lives. We have lines of research in                 We use experimental biochemical and
    developing precise tools for applied gene                  electrophysiological data to constrain
    editing technologies and in skin                           computational models of living systems,
    microbiome based therapeutics.                             and thereby unravel the underlying
    -Precise editing of mammalian genomes:                     molecular circuitry of physiological
    Despite enormous progress, precise                         processes. Using a combination of
    introduction of new alleles in mammalian                   theoretical modelling and experimental
    genomes still results difficult. Our goal is to            tools including time-lapse fluorescence
    explore novel alternatives to precisely re-                microscopy      and     microfluidics, we
    write genomes safely and efficiently.                      investigate dynamical phenomena such
    -Microbiome engineering: The skin is                       as pulses and oscillations, and study how
    populated by numerous microorganisms                       multiple instances of these processes
    which affect host health. We aim to                        coexist inside cells and tissues in a
                                                               coordinated way. At a larger level of
organization, we use conductance-based          The specific objective of the project is to
neural models to explain the emergence          uncover the clonal growth dynamics of the
of collective rhythms in cortical networks,     hindbrain in order to understand how cell
and mesoscopic neural-mass models to            proliferation and cell differentiation are
link the structural properties of brain         balanced. For this we will life-monitor the
networks with their function.                   whole embryonic hindbrain upon time and
                                                compare the growth of specific progenitor
Keywords.       Quantitative      biology,
                                                cell populations with the overall growth,
biophysics, statistical physics, nonlinear
                                                using     genetic   clonal     experiments
dynamics, complexity
                                                combined with a Machine Learning
                                                platform for their analysis. These results
                                                will provide us insights into the
DCEXS-2003. Uncovering the clonal
                                                mechanisms of segregation of progenitors
dynamics of the hindbrain: balancing
                                                within the hindbrain and how brain
proliferation and differentiation
                                                morphogenesis       and     growth      are
                                                coordinated.
Supervisor. Cristina Pujades
                                                To explore how different groups of
Research group. Development of the
                                                progenitors contribute to the growth of the
Central Nervous System
                                                hindbrain, zebrafish transgenic embryos
Project Description. Our main goal is to        will be used allowing for fluorescent life-
understand       how        spatiotemporally    monitoring clonal growth. To get insight
coordinated cell progenitor specification       into the growth of the tissue and the
and differentiation occurs alongside            specific progenitor cell populations we will
morphogenesis to construct the functional       assess: i) clonal growth, and ii)
brain. Thus, we need to blend the               morphological spatial variability of the
information provided by morphogenesis           clones. Clone tracking will allow
and tissue growth studies -balancing            deciphering modes of clonal behaviour
progenitors vs. differentiated cells-, with     (symmetric vs. asymmetric divisions). We
the reconstruction of cell lineages, with the   will develop a Machine Learning
demand to incorporate the time as a             approach for cell motion pattern
crucial factor. We make use of the              recognition and allocation, since an
zebrafish embryo because it allows to           automatised, accurate segmentation and
combine high-resolution in vivo imaging         tracking framework will represent an
with the genome-editing technology. We          improvement to identify distinct modes of
take advantage of complementary                 growth and movement patterns.
approaches       such     as     4D-imaging,
                                                The student will learn the experimental
functional perturbations, clonal growth
                                                skills for 4D-imaging and cell-tracking, and
studies and transcriptomics in order to fill
                                                the computational tools to extract
the void between gene regulatory
                                                biological insights from big-data analyses.
networks and tissue architecture.
                                                Keywords. brain morphogenesis, 4D-
                                                imaging, zebrafish, clonal growth
Master of Multidisciplinary Research in Experimental Sciences             Major Research Projects
    BIST-UPF                                                                              2020/2021

                                                         Peroxynitrite stabilizes Aß oligomers, the
                                                         most toxic forms of Aß aggregates,
    DCEXS-2004. Molecular Physiology
                                                         impairing NMDA Rc function.
    Laboratory
                                                         - We have designed synthetic peptides
    Supervisor. Francisco José Muñoz                     with a sequence similar to that of albumin
                                                         that impairs amyloid aggregation in brain.
    Research group. Molecular Physiology
                                                         C-term from albumin impairs Aß
    Laboratory
                                                         aggregation and protects neurons.
9   Project Description.
                                                         4. Expected training outcomes:
    1. Group: Dr. Francisco J. Muñoz
                                                         - To acquire the necessary skills to become
    (University lecturer; Pubs: 64; Total
                                                         an independent researcher in the field of
    Citations: 2244; h-index: 25) is focused on
                                                         neurodegeneration.
    the study of the production, aggregation
    and cytotoxicity of amyloid ß-peptide (Aß)           - To reach scientific goals in a high quality
    in Alzheimer’s disease (AD) and its                  environment through a laboratory
    regulation by oxidative stress and nitric            equipped with state-of-the-art equipment
    oxide.                                               for the biochemical, neurobiology
    2. Proposed Project: AD is due to the Aß             (imaging,      tissue      culture)     and
    aggregation inside the brain. Aß is                  electrophysiology studies.
    produced by the enzyme BACE1 that
                                                         - To expand considerably his/her scientific
    cleavages the amyloid precursor protein
                                                         and technological base.
    (APP). Both APP and BACE1 are localized
    in the lipid rafts enriched with GM1                 - To achieve not only an assortment of both
    ganglioside. GM1 has been suggested to               theoretical and practical aspects of
    favour     Aß    aggregation       therefore         research but also the critical thinking and
    contributing to synaptic impairment. We              managing skills necessary to move his/her
    propose that during aging there is a GM1             scientific career forward and become an
    increases. Thus GM1 clusters could be                international scientific researcher.
    promoting BACE1 amiloydogenic activity.
                                                         Keywords. Alzheimer's Disease; Amyloid;
    An increase of the concentration of Aß in
                                                         GM1; hippocampal neurons; aging
    neuron extracellular matrix will favour Aß
    oligomerization by binding GM1.

    3. Preliminary results:

    - Aged primary cultured of hippocampal
    neurons have high levels of GM1.

    - The binding of Aß to GM1 is increased
    when asialyzated.

    - Aggregated Aß in synapses favours the
    production of nitro-oxidative stress.
DCEXS-2005. Zinc imbalance and cancer          DCEXS-2006. Integrative Biomedical
progression                                    Materials and Nanomedicine Lab
Supervisor. Rubén Vicente García
                                               Supervisor. Pilar Rivera Gil
Research group. Laboratory of Molecular
Physiology-Biophysics of the immune            Research group. Integrative Biomedical
system                                         Materials and Nanomedicine Lab

Project Description. The human body            Project Description. Our research lies at
contains 2–3 g of zinc. In the cell, aside     the crossroads between nanoscience and
from being a structural component of           biomedicine, the field of nanobiomecine.
many proteins, zinc plays a role as a          We convert basic research findings on
second messenger regulating different          nanobiotechnology into new approaches
signalling     cascades      involved     in   addressing biomedical challenges. We
proliferation,        migration         and    fabricate multifunctional biomaterials by
differentiation. Several transporters (Zip     integrating selected building-blocks into
and ZnT family) and zinc binding proteins      one single system depending on the
work in a coordinated way to tightly           application's       requirements       and
regulate cytosolic zinc concentrations. Zinc   considering     the    biophysicochemical
dysregulation has been described in            properties of the nanomaterial. We target
several kinds of cancers affecting both,       independently two areas: diagnostics and
the patient zinc serum levels and tumour       therapeutics of diseases but also
zinc content. The expression of certain zinc   simultaneously by creating a theranostic
transporters has been correlated with the      tool towards a more personalized
stage, progression of tumours and              medicinal approach of diseases. We focus
acquisition of pro-metastatic features.        on understanding and engineering the
However, the underlying mechanisms             nanomaterial-biological system interface.
behind zinc imbalance and cancer               We use state of the art material and
progression are not fully understood. The      biological/molecular       characterization
project is based on a multidisciplinary        methods to find predictive patterns of
approach combining molecular biology,          cellular outcomes after exposure to
biophysics and nanotechnology. The             nanomaterials for translational medicine.
students will acquire skills in different
                                               The main research lines are:
techniques of all these different
disciplines.                                   Engineering       nanomaterials       for
                                               diagnosis/sensing
Keywords.     zinc,   cancer,   transporter,
                                               Engineering nanomaterials for controlled
metastasis
                                               release
.                                              Exploring the therapeutic value of novel
                                               nanomaterials
                                               Engineering the nanomaterial-biological
                                               interface
Master of Multidisciplinary Research in Experimental Sciences              Major Research Projects
     BIST-UPF                                                                               2020/2021

     Keywords.      Nanomedicine; Optical                 CDG      patients.     In   this   respect,
     biosensing; Nanomaterials; Controlled                mechanosensitive Piezo channels have
     release; Theranostics                                been suggested to underlie the
                                                          transduction of different mechanical forces
                                                          into a variety of neurological responses in
     DCEXS-2007. Hypoglycosylation Of                     the brain.
     Voltage-Gated And Mechanosensitive
                                                          Our overall objective is to study how
     Ion Channels: New Pathological
                                                          hypoglycosylation affect the function of
11   Mechanisms And Therapeutic Targets
                                                          neuronal CaV2.1 and Piezo channels, and
     For Neurological Disorders In
                                                          its relevance in neurological alterations
     Phosphomannomutase 2 Deficiency
                                                          linked     to    PMM2-CDG          by    using
     (PMM2-CDG)
                                                          heterologous expression systems and
     Supervisor. José Manuel Fernández
                                                          neurons from wild-type and PMM2-CDG
     Fernández
                                                          knock-in mice. Similar analysis will be
     Research group. Laboratory of Molecular              performed in fibroblasts of patients with
     Physiology                                           PMM2-CDG and healthy volunteers, and
                                                          iPSC-derived      neurons       from     those
     Project Description.
                                                          fibroblasts, to directly assess the degree
      "Phosphomannomutase             Deficiency          of hypoglycosylation and dysfunction of
     (PMM2-CDG) is the most frequent                      CaV2.1 and Piezos in patients with distinct
     congenital     disorder      of     N-linked         neurological      phenotypes         (moderate
     glycosylation      (CDG).       PMM2-CDG             versus severe), and initiate a study of
     symptoms include severe neurological                 correlation with their clinical and genetic
     alterations. Progressive atrophy of the              report. Finally, we will test the capability of
     cerebellum is usually found in all PMM2-             novel CaV2.1 modulators to revert
     CDG patients, leading to the ataxia                  hypoglycosylation           effects,       thus
     cerebellar syndrome. Also, the stroke-like           establishing a proof of concept to develop
     episode (SLE) is one of the unpredictable            in the future a specific treatment for
     and serious neurological complications               neurological events in PMM2-CDG."
     occurring in PMM2-CDG. Mechanisms
                                                          Keywords. Hypoglycosylation; neuronal
     underlying both SLE and cerebellar
                                                          voltage-gated      calcium   channels;
     syndrome in PMM2-CDG are unknown and
                                                          mechanosensitive      Piezo  channels;
     there are no guidelines for their
                                                          Phosphomannomutase Deficiency (PMM2-
     prevention, detection and treatment. We
                                                          CDG); electrophysiology
     have recently identified the neuronal
     voltage-gated Ca2+ channel CaV2.1 as a
     potential target of glycosylation defect in
     the Central Nervous System of PMM2-CDG
     patients, and an important contributor to
     SLEs and cerebellar syndrome in PMM2-
     CDG. Besides, we found that mild cranial
     trauma is a potential SLE trigger in PMM2-
DCEXS-2008. In vivo mapping of the              activated in order to integrate neuronal
neuronal circuity related to vestibular         circuit maps with behaviour output. We
and auditory sensory function                   aim for a student highly motivated in
                                                neurobiology, imaging and circuitry to
                                                undertake this challenging project.
Supervisor. Berta Alsina
                                                Keywords. optogenetics, in vivo imaging,
Research group. Morphogenesis and Cell
                                                neural activity, zebrafish
Signaling Sensory Systems

Project Description. The inner ear
capturing      auditory    and       balance    DCEXS-2009. Monitoring oxidative stress
information though specialized hair cells       in living cells – use of genetically
transmits the sensory information to the        encoded reporters to determine H2O2
brain through bipolar neurons. We have          levels linked to signalling and disease
investigated     though       high-resolution
imaging and genetic perturbations the
                                                Supervisor. Elena Hidalgo
development of the sensory neurons of the
inner ear in zebrafish (Hoijman et al. 2017     Research group. Oxidative Stress and
eLife, Taberner et al. biorxiv). This           Cell Cycle Group
information is currently also being
                                                Project Description. General objectives:
mapped with spatial transcriptomic data
                                                Intracellular peroxides are important
to discriminate between different neuronal
                                                drivers of both toxicity and signalling
subtypes. However, it remains unexplored
                                                events. Several genetically encoded
how different stimuli activate specific
                                                fluorescent probes have been developed
neurons of the ganglion and how neuronal
                                                to monitor H2O2 fluctuations in response
activity is mapped into the brain. Neuronal
                                                to endogenous and exogenous oxidant
activity can be monitored in vivo by the
                                                sources. We have recently developed a
use of GCAMP, a genetically encoded
                                                new reporter, based on the fission yeast
calcium sensor. The project aims at
                                                H2O2 sensor Tpx1 fused to a redox
imaging at high spatial and temporal
                                                sensitive GFP, which is more sensitive to
resolution the patterns of neuronal activity
                                                peroxide fluctuations that any other
in the statoacoustic ganglion and the
                                                reporter characterized so far. We aim at
hindbrain when specific neurons are
                                                comparing its behaviour in response to
activated or specific stimuli are presented
                                                genetic and environmental interventions.
to the zebrafish. For this aim, the student
                                                The candidate will characterize the
will use a transgenic line expressing
                                                regulation of our H2O2 reporter in
GCAMP5G in neurons, will learn how to
                                                different S. pombe backgrounds and in
image neuronal activity in vivo and will
                                                different biological situations, such as
collaborate with a laboratory with
                                                during chronological aging or cell cycle
expertise in photochemically activation of
                                                progression, to assess the role of
neuronal receptors. Moreover, analysis of
                                                moderate intracellular H2O2 fluctuations
behaviour will also be assessed when
                                                as     drivers  of    these     processes.
specific populations of neurons are
Master of Multidisciplinary Research in Experimental Sciences            Major Research Projects
     BIST-UPF                                                                             2020/2021

     Furthermore,       an      unprecedented             Therefore,     to     undertake      future
     experiment in the redox field will be to use         investigations relevant for biomedicine it
     our fluorescent reporter in different                will be necessary to perform structural
     biological models (ranging from bacteria             biology experiments in living cells.
     to human cells), to compare intracellular
                                                          The aim of the project is to develop new
     H2O2 levels using the same protein
                                                          genetically-encoded nanotools to boost
     sensor.
                                                          the power of quantitative fluorescence
     Expected training outcomes: training on              microscopy. In collaboration with the
13   cellular biology, molecular biology and              group of Alex De Marco, at the Monash
     fluorescence microscopy will be acquired             University (Australia), we will also asses
     during project execution.                            the implementation of these new
                                                          nanotools in cryo-electron tomography.
     Keywords. Redox biology, aging, H2O2,
                                                          During the progression of the project the
     yeast
                                                          student will acquire a strong expertise in
     DCEXS-2010. Engineering Intracellular                gene editing tools, advanced light
     Nanotools To Image Protein Structures                microscopy      and     image     analysis.
     In Vivo: Resolving The Mechanism Of                  Depending on the student’s skills and
     Exocytosis                                           interest, the project could also involve in
                                                          silico integration of acquired data to
                                                          model 3D structures of large protein
     Supervisor. Oriol Gallego
                                                          complexes controlling cell growth.
     Research     group.     Live-cell   Structural
                                                          Keywords. Genetic engineering, light
     Biology
                                                          microscopy, molecular mechanisms, cell
     Project Description. Our group develops              growth
     new methods of fluorescence microscopy
     that allow the study of macromolecular
     complexes directly in living cells beyond            DCEXS-2011. Cancer Biology
     the limits of current approaches.

     Understanding the molecular mechanisms               Supervisor. Ana Janic
     that drive life (and those that lead to
                                                          Research group. Cancer Biology
     death) requires structural characterisation
     of the protein machinery sustaining the              Project     Description.      The     tumour
     biology of the cell, both in a healthy and           suppressor gene p53 is mutated in half of
     in a pathological situation. Historically,           the human cancers. Given the difficulties in
     structural biology has been largely                  developing strategies for targeting wild-
     centred around in vitro approaches.                  type or mutant p53, further understanding
     However, the degree of knowledge                     of its basic biology is required for
     acquired to improve human health will be             successful clinical translation. The present
     determined not only by the precision of the          project focuses on understanding the
     experimental measurements but also by                complexity of the p53 network in tumour
     their proximity to a physiological context.          suppression in different contexts, in order
to determine which p53 downstream
function should be targeted for treatment
of different tumour types, without targeting
p53 itself. The successful candidate will be
involved in the use of a wide variety of
experimental techniques, including mouse
models       of    cancer,     tissue/tumour
pathology, CRISPR-Cas9 gene-editing
technology, next-generation sequencing,
molecular biology, cell culture and flow
cytometry.

Keywords. Cancer, tumour suppression,
p53, DNA damage
Master of Multidisciplinary Research in Experimental Sciences            Major Research Projects
     BIST-UPF                                                                             2020/2021

     CENTER FOR GENOMIC REGULATION (CRG)

     CRG-2001. Reconstituting tissue self-                signals to instruct cell fates and dynamic
     organization and collective cell                     cell behaviour. Recent work from our lab
     dynamics in early embryonic                          has identified that mechanical tissue
     development via 3D synthetic culture                 crowding and geometrical boundary
     methods                                              constraints from the 3D tissue environment
     Supervisor. Verena Ruprecht                          critically influence dynamic cell migration
15                                                        behaviour (Ruprecht et al., Cell 2015).
     Research     group.     Cell   and     Tissue
                                                          These results highlight the relevance of
     Dynamics
                                                          mechanosensitive signalling pathways
     Project Description. The Ruprecht lab                and cellular adaption to physical tissue
     studies multi-scale dynamics of cell and             parameters in early embryogenesis. In this
     tissue       organization       in   early           research project, we will address how
     embryogenesis. We have a key focus on                multicellular tissue dynamics and self-
     understanding           biological    self-          organization is controlled by mechanical
     organization, cell and tissue shape                  and physical processes in early
     formation and dynamic cell behaviour in              embryogenesis. We aim at identifying key
     3D tissues. Our lab follows a highly                 molecular and cellular modules that
     interdisciplinary approach combining                 enable cellular information processing of
     molecular and cell biological tools with             physical tissue parameters and how they
     advanced biophysical methods and                     regulate single and collective cell
     quantitative live cell imaging approaches.           dynamics to build the shape of an embryo.

     In this research project, we will establish          Keywords. Biological Self-organization,
     synthetic 3D culture methods that enable             Multicellular dynamics, Cytoskeleton,
     to mimic tissue self-organization of early           Mechanobiology, Biophysics
     embryonic development in synthetic
     culture environments. During gastrulation,
     an unstructured mass of pluripotent                  CRG-2002. Trans-generational
     embryonic stem cells undergoes cell fate             epigenetic influences on mutation
     specification and acquires a defined                 outcome
     shape, laying the foundation for the future
     body plan. Morphodynamic shape
                                                          Supervisor. Ben Lehner
     formation depends on precise spatio-
     temporal positioning of three distinct germ          Research group. Genetic Systems
     layers (mesoderm,         ectoderm and
                                                          Project Description. "Many detrimental
     endoderm) that give rise to different
                                                          mutations only cause disease in a subset
     organs of the organism. Both chemical
                                                          of their carriers, a phenomenon known as
     signals (morphogens) and physical stimuli
                                                          incomplete         penetrance.    Further,
     (as geometry, cell density, adhesion and
                                                          individuals     often   display  variable
     cell deformation) serve as information
                                                          expressivity of a disease, ranging from
mild to severe health impairments. Animal      CRG-2003. Understanding the molecular
studies show that incomplete penetrance        basis of neuronal 3’UTR length-
and variable expressivity are still present    dependent mRNA sorting
in the absence of environmental or
genetic variation, with inter-individual
                                               Supervisor. Sebastian Maurer
variation in gene expression during
development able to predict to some            Research group. Cytoskeleton dependent
extent whether an individual is affected or    RNA localisation mechanisms
not by an inherited mutation [1, 2]. We
                                               Project Description. The Maurer Lab
hypothesized that an additional influence
                                               wants to understand the biochemical
on mutation penetrance and expressivity
                                               processes that drive the generation of
might be the environment or physiological
                                               neuronal mRNA distributions. Thousands
state of an individual’s parents or even
                                               of mRNAs are transported into axons and
previous generations. To test this
                                               dendrites and their local translation at the
hypothesis, we have established an
                                               right location is important for neuron
automated screening platform to quantify
                                               development, polarization and synaptic
how environmental perturbations in
                                               plasticity which underlies long-term
previous generations influence the
                                               memory formation. How motor proteins
outcome of inherited mutations in C.
                                               such as kinesins and dynein recognise
elegans.     We       identified     several
                                               their mRNA cargo and transport them to
environmental factors that altered
                                               their destination is not understood. The
mutation     outcome      in     subsequent
                                               Maurer lab develops new single-molecule
generations that were never directly
                                               assays in microfluidic chambers to
exposed to the environmental challenge.
                                               assemble neuronal mRNA transport
Your master thesis project will investigate
                                               complexes from purified components.
possible      molecular         mechanisms
                                               Through this approach, the Maurer Lab
underlying the multi-generation memory of
                                               recently revealed the essential building
environmental perturbations. To this end,
                                               blocks of a minimal mammalian mRNA
you will use transgenic C. elegans lines,
                                               transport system and their function
time-lapse       microscopy,         protein
                                               (Baumann et al. bioRxiv, 2019). To further
biochemistry, as well as genetic
                                               understand which different mRNA
techniques.”
                                               transport pathways exist, the Maurer Lab
References:                                    develops new high-throughput protein-
                                               protein and protein-RNA interaction
1. Burga, A., Casanueva, O., and Lehner,
                                               assays      (Yang     et     al.     Nature
B. Nature, 480, 250-253 (2011)
                                               Communications, 2018).
2. Casanueva, O., Burga, A., and Lehner,
B. Science, 335, 82-85 (2012)
                                               The project the successful candidate will
Keywords. epigenetic inheritance, C.
                                               work on is based on a validated result
elegans
                                               from     our    high-throughput   protein
                                               interaction screen. We identified a new
                                               link between a nuclear mRNA transport
Master of Multidisciplinary Research in Experimental Sciences            Major Research Projects
     BIST-UPF                                                                             2020/2021

     factor and different motor proteins. The             memory formation. How motor proteins
     candidate will work with a PhD student in            such as kinesins and dynein recognise
     the lab to characterise these new                    their mRNA cargo and transport them to
     interactions with pure proteins and RNAs             their destination is not understood. The
     to understand how they interact and                  Maurer lab develops new single-molecule
     assemble into functional complexes. To               assays in microfluidic chambers to
     this end, the student will learn how to              assemble neuronal mRNA transport
     design recombinant protein expression                complexes from purified components.
     constructs, how to purify proteins with              Through this approach, the Maurer Lab
17   different techniques and how to                      recently revealed the essential building
     fluorescently tag proteins. Furthermore,             blocks of a minimal mammalian mRNA
     the student will be trained in bioanalytical         transport system and their function
     techniques to quantify affinities between            (Baumann et al. bioRxiv, 2019). To further
     proteins and proteins and RNAs. Finally, if          understand which different mRNA
     time permits, the student will learn how to          transport pathways exist, the Maurer Lab
     design and conduct Total-Internal-                   develops new high-throughput (HT)
     Reflection-Microscopy (TIRF-M) coupled in            protein-protein      and      protein-RNA
     vitro reconstitution experiments to analyse          interaction assays (Yang et al. Nature
     the function of purified factors during              Communications, 2018).
     mRNA transport.
                                                          The successful candidate will help to
     Keywords. Neuronal mRNA localisation,                design new approaches to reveal which
     motor proteins, RNA binding proteins,                different mRNA transport pathways exists
     single-molecule microscopy, biophysics               in induced mammalian neurons. To this
                                                          end, the student will work closely together
                                                          with a PhD student and use CRISPR-Cas9
     CRG-2004. Understanding the molecular                to create cell lines with degron-tagged
     basis for bidirectional neuronal mRNA                candidate proteins, which were detected
     transport                                            as potential mRNA-cargo adapters by our
                                                          HT-screening approaches. To enable live
                                                          cell imaging of mRNA transport dynamics,
     Supervisor. Sebastian Maurer
                                                          the student will further validate molecular
     Research group. Cytoskeleton dependent               beacons on in vitro transcribed mRNAs
     RNA localisation mechanisms                          and help to implement mRNA live-imaging
                                                          protocols. If time permits, the project
     Project Description. The Maurer Lab
                                                          further foresees to generate photo-
     wants to understand the biochemical
                                                          cleavable motor proteins which have to be
     processes that drive the generation of
                                                          first validated in vitro before they will be
     neuronal mRNA distributions. Thousands
                                                          used as a tool in induced neurons to test
     of mRNAs are transported into axons and
                                                          which motor are responsible for axonal or
     dendrites and their local translation at the
                                                          dendritic mRNA localisation.
     right location is important for neuron
     development, polarization and synaptic               Keywords. Neuronal mRNA localisation,
     plasticity which underlies long-term                 live cell imaging, protein and RNA
biochemistry, auxin-induced       degrons,     Besides adding a piece to the X-
photo-inactivation                             reactivation puzzle, the student will be
                                               immersed within a young team inside a
                                               dynamic         international    research
CRG-2005. X-chromosome reactivation            environment at CRG, which will help
in iPSCs and mouse embryos                     her/him to gain skills furthering his/her
                                               scientific career.

Supervisor. Bernhard Payer                     Keywords. Pluripotency, Epigenetics, iPSC-
                                               reprogramming,             X-chromosome
Research      group.     Epigenetic
                                               reactivation
Reprogramming in Embryogenesis and
the Germline

Project Description. In our lab, we are
studying how epigenetic information is
                                               CRG-2006. Epigenetic reprogramming in
erased during mammalian development.
                                               mammalian germ cells
In particular, we study epigenetic
reprogramming of the X-chromosome in
mouse embryos, induced pluripotent stem        Supervisor. Bernhard Payer
cell (iPSC) and in the germ cell lineage in
                                               Research      group.     Epigenetic
vivo and in vitro. Using a multidisciplinary
                                               Reprogramming in Embryogenesis and
approach, we want to gain insight into
                                               the Germline
how epigenetic reprogramming is linked
to its biological context, with long-term      Project Description. In our lab, we are
implications    for    regenerative     and    studying how epigenetic information is
reproductive medicine.                         erased during mammalian development.
                                               In particular, we study epigenetic
In this project, the prospective student
                                               reprogramming of the X-chromosome in
would study the function of candidate
                                               mouse embryos, induced pluripotent stem
factors for X-chromosome reactivation in
                                               cell (iPSC) and in the germ cell lineage in
iPSCs and early mouse embryos. The
                                               vivo and in vitro. Using a multidisciplinary
project will involve iPSCs reprogramming
                                               approach, we want to gain insight into
and monitoring X-chromosome activity
                                               how epigenetic reprogramming is linked
using an XGFP-reporter. Using knockdown
                                               to its biological context, with long-term
and/or CRISPR deletion, the mechanism
                                               implications    for    regenerative     and
will be studied, by which the candidate
                                               reproductive medicine.
acts on epigenetic reprogramming and at
which stage X-reactivation is affected. The    In this project, the student would work with
student will learn a number of methods         germ cells from mouse embryos and/or
including iPSC reprogramming, shRNA            differentiated in vitro from embryonic stem
knockdown,           FACS         analysis,    cells (ESCs). The in vitro approach has the
immunohistochemistry, RNA-FISH, qPCR,          advantage of providing more material
etc.                                           and      being      more     amenable     to
                                               perturbation. On the other hand, germ
Master of Multidisciplinary Research in Experimental Sciences             Major Research Projects
     BIST-UPF                                                                              2020/2021

     cells from embryos can provide the                   tackle this complexity, we incorporate
     accurate biological context for testing the          techniques from a wide range of fields--
     applicability of our findings from the in            molecular genetics, reliability engineering,
     vitro system. Momentarily, we use this two-          bioinformatics, statistical physics, survival
     system strategy to elucidate the signals             analysis, high-throughput imaging, and
     and mechanisms responsible for X-                    stochastic modelling. Focusing on
     reactivation in mouse and human germ                 C.elegans as a model system, we seek to
     cells.                                               develop experimental and computational
                                                          methods in parallel to help us characterize
     Besides adding a piece to the X-
19                                                        where, when, and why aging occurs, and
     reactivation puzzle, the student will be
                                                          how we might effectively intervene in its
     immersed within a young team inside a
                                                          progression.
     dynamic         international    research
     environment at CRG, which will help                  Objectives: contribute to the development
     her/him to gain skills furthering his/her            of our high-throughput imaging technology
     scientific career.                                   Training outcomes: learn how to work with
                                                          a complex experimental apparatus
     Keywords. Keywords: Germ cells,
                                                          involving hardware, software, and
     Epigenetics, X-chromosome reactivation,
                                                          biological components.
     reproduction.
                                                          Keywords. Aging, microscopy, stochastic
     CRG-2007. Dynamics of Living Systems
                                                          processes

     Supervisor. Nicholas Stroustrup

     Research group. Dynamics of Living
     Systems

     Project Description. Our research group
     seeks to link the macroscopic symptoms of
     aging to their molecular origins. In aging,
     a variety of mechanisms contribute at
     short, medium, and longtime scales.
     Furthermore, aging appears to involve a
     substantial degree of random chance. To
INSTITUTE FOR BIOENGINEERING OF CATALONIA                               (IBEC)

IBEC-2001.Nanoprobes & Nanoswitches I        analyze receptors, ion channels and
                                             synaptic networks in the brain. These tools
Supervisor. Pau Gorostiza                    are synthetic compounds with a double
Research group. Nanoprobes &                 functionality: They are pharmacologically
Nanoswitches                                 active, binding specifically to certain
                                             proteins and altering their function, and
Project description. One of the group’s      they do so in a light-regulated manner that
research lines is focused on developing      is built in the same compound usually by
nanoscale tools to study biological          means of photoisomerizable azobenzene
systems.       These     tools     include   groups. Recent projects in this area
instrumentation based on proximity           include the development of light-regulated
probes, such as electrochemical tunneling    peptide inhibitors of endocytosis named
microscopy and spectroscopy (ECSTM,          TrafficLights and the synthesis of small
ECTS), atomic force microscopy (ECAFM)       molecule photochromic inhibitors to
and single molecule force spectroscopy       manipulate several G protein-coupled
(SMFS) that we apply to investigate          receptors like adenosine A2aR and
electron transfer in metal oxides and        metabotropic glutamate receptors mGlu5.
individual redox proteins. These studies     In addition, some of these light-regulated
are relevant to the development of           ligands also bear an additional
biosensors and molecular electronics         functionality: a reactive group for covalent
devices. Recent advances include the         conjugation to a target protein. Examples
following projects: methods for nanoscale    include      a    photochromic      allosteric
conductance          imaging         under   regulator of the G protein-couple receptor
electrochemical control, measurement of      mGlu4 that binds irreversibly to this
the nanomechanical stability and electron    protein and allows photocontrolling its
transfer distance decay constants of         activity in a mouse model of chronic pain
individual redox proteins. Based on our      and a targeted covalent photoswitch of
development of nanoscale field-effect        the kainate receptor-channel GluK1 that
transistors using redox proteins, we have    enables          photosensitization         of
recently published a method to measure       degenerated retina in a mouse model of
conductance switching in proteins “wired”    blindness. We also demonstrated for the
between two electrodes and their current-    first time two-photon stimulation of neurons
voltage characteristics.                     and astrocytes with azobenzene-based
The objective of the research line on        photoswitches.
nanoswitches is to develop molecular         Students can expect to learn the relevant
switches that are regulated with light in    techniques for the proposed project in one
order to manipulate and functionally         of    the      research    lines     (from
Master of Multidisciplinary Research in Experimental Sciences            Major Research Projects
     BIST-UPF                                                                             2020/2021

     electrochemistry to scanning probe                   conditions that allow for an effective
     microscopies           and          surface          protein-protein ET. We use scanning probe
     functionalization; from synthetic chemistry          microscopies, SPMs (scanning tunneling
     to electrophysiology and fluorescence                and atomic force microscopies and
     imaging, in vitro and in vivo) and to work           spectroscopies -STM and AFM-), to
     independently within a team of highly                evaluate immobilized proteins under
     multidisciplinary      and       motivated           electrochemical control.
     researchers.
                                                          The student will perform studies at the
     Keywords.     electrochemistry,   redox              nanoscale using SPMs to measure ET
21   proteins,   photosynthetic    complexes,             currents and interaction forces between
     optogenetics, photopharmacology                      partner proteins, under controlled
                                                          environmental and biologically relevant
                                                          conditions (electrochemical potential,
     IBEC-2002. Nanoprobes & Nanoswitches                 temperature, pH, ionic environment). The
     II                                                   student will learn to work with SPMs but
                                                          also on protein immobilization protocols,
                                                          surface functionalization, electrochemical
     Supervisor. Pau Gorostiza
                                                          studies. He/she will also learn on
     Research group. Nanoprobes &                         bibliographic search, data treatment and
     Nanoswitches                                         presentation (written and oral) of the
                                                          results. The student will incorporate to the
     Project description. Protein mediated
                                                          Nanoprobes & Nanoswithces research
     electron transfer (ET) is essential in many
                                                          group and will actively participate in the
     biological    processes,     like    cellular
                                                          meetings and discussions. He/she will
     respiration or photosynthesis. The
                                                          acquire basic competences related to the
     exceptional efficacy of these processes is
                                                          experimental work in a multidisciplinary
     based      on    the     maximization      of
                                                          lab on nanobiotechnology.
     donor/acceptor coupling           and     the
     optimization of the reorganization energy.           Keywords. Proteins; electron transport;
                                                          scanning probe microscopies; single
     Single molecule techniques can provide
                                                          molecule; interactions
     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
IBEC-2003. Nanoprobes & Nanoswitches           properties of model membranes, including
III                                            the presence of glycosphingolipids
                                               related to specific pathologies, and
                                               associate them to their role processes at
Supervisor. Pau Gorostiza
                                               the cellular level. The student will be
Research group. Nanoprobes &                   involved in the design and building of
Nanoswitches                                   supported lipid membranes, and their
                                               characterization using force spectroscopy
Project description. Cell processes like
                                               (indentation and tube-pulling) based on
endocytosis,     membrane        resealing,
                                               AFM. The student will be trained on lipid
signaling and transcription, involve
                                               vesicles and membranes preparation,
conformational changes which depend on
                                               surfaces functionalization, and to work
the chemical composition and the
                                               with SPMs techniques. He/she will also
physicochemical properties of the lipid
                                               learn on bibliographic search, data
membrane. These properties are directly
                                               treatment and presentation (written and
related to the lateral packing and
                                               oral) of the results. The student will
interactions at the molecular level, that
                                               incorporate to the Nanoprobes &
govern the membrane structure and
                                               Nonsnitches research group and will
segregation into nano (or micro) domains.
                                               actively participate in the meetings and
The better understanding of the
                                               discussions. He/she will acquire basic
mechanical role of the lipids in cell
                                               competences related to the experimental
membrane force-triggered and sensing
                                               work in a multidisciplinary lab on
mechanisms has recently become the
                                               nanobiotechnology.
focus of attention. The local and dynamic
nature of such cell processes requires         Keywords. lipid membrane; biophysics;
observations at high spatial resolution.       atomic    force    microscopy; force
Atomic force microscopy (AFM) is widely        spectroscopy; nanomechanics
used to study the mechanical properties of
supported lipid bilayers (SLBs). We
investigate the physicochemical and
structural properties of lipid membranes
                                               IBEC-2004. Improving site-specific
combining AFM and force spectroscopy
                                               targeting of nanomedicines for
(AFM-FS) under environmentally controlled
                                               treatment of lung or brain diseases
conditions. We use simplified model
                                               Supervisor. Silvia Muro
membranes including several lipid
representatives     of    mammalian      or    Research group. Targeted
bacterial cells. We also study the             Nanotherapeutics and Nanodevices
mechanical       properties     of    lipid
                                               Project     description.   Novel    drug
membranes from nanovesicles with
                                               nanocarriers improve the solubility,
technological applications, like drug
                                               biodistribution, and overall performance
delivery.
                                               and safety of therapeutic agents. Their
The general goal is to assess the structure,   functionalization with targeting moieties
phase behavior and nanomechanical              enables site-specific drug delivery to
Master of Multidisciplinary Research in Experimental Sciences            Major Research Projects
     BIST-UPF                                                                             2020/2021

     selected cells. Although this paradigm is            process of designing, executing, recording
     easily achieved in cell mono-culture                 and reporting of research, oral and written
     models, in vivo specificity of targeted              communication skills, authorship if
     vehicles remains a challenge. The                    publishable results are used for
     complexity        of     the     physiological       conference presentations or article
     environment within the body and its                  submissions, and overall participation in a
     diversity in cellular phenotypes contribute          stimulating,     interdisciplinary     and
     to this. The project will focus on examining         innovative research program.
     specific targeting of nanocarriers in
                                                          Keywords: Drug delivery, nanocarriers,
23   complex and physiologically relevant co-
                                                          site-specific   targeting,    multicellular
     culture models, providing guidance for
                                                          models, lung or brain disease
     future design of nanomedicines. This will
     be examined for one of two relevant
     organs: (1) the brain, a part of the central
                                                          IBEC-2005. Development of
     nervous system very difficult to reach from
                                                          computational Solutions for Ion Mobility
     the circulation due to the blood-brain
                                                          Spectrometry Data Analysis
     barrier, vs. (2) the lung, a peripheral organ
     which receives full cardiac output after i.v.
     injection. Different diseases affecting each         Supervisor. Santiago Marco
     organ require targeting drugs to particular
                                                          Research group. Signal and Information
     cell types, but not all, for which the project
                                                          Processing for Sensing Systems
     will broadly help design more precise
     systems for efficiency and safe treatment.           Project Description. In the group we
     Three aims will be encompassed,                      develop full computational workflows for
     including (a) biological characterization a          the analysis of metabolomics data based
     new co-culture cell model, (b) synthesis             on NMR, GC-MS or LC-MS techniques. Gas
     and       characterization     of    targeted        Chromatography-Ion                Mobility
     nanocarriers, and (c) examination of the             Spectrometry is a novel technique for the
     specific interaction of said nanocarriers            analysis of the volatile fraction of the
     with said co-culture models vs. more                 metabolome. Based on previous research
     classical systems. Techniques to be used             at the group, the main aim is to produce
     include solvent-evaporation methods for              an R-package that integrates basic GC-
     polymer nanoparticle synthesis, dynamic              IMS signal processing. The student will get
     light scattering, electrophoretic mobility           training in signal processing in the R
     and electron microscopy for nanoparticle             technology and in the development of
     size/shape and surface charge, human                 software packages.
     cell culture and fluorescence microscopy
                                                          Keywords.      Data   Analysis,  Signal
     to visualize nanoparticle-cell interactions,
                                                          Processing, R language, Metabolomics
     and image analysis algorithms for
     semiquantitative              measurements.
     Additional experiences to be gained
     include training on research safety and
     ethical conduct, participation in the
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