Master of Multidisciplinary Research in Experimental Sciences - Major Project List 2020/2021
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Master of
Multidisciplinary
Research in
Experimental
Sciences
Major Project List
2020/2021
bist.eu/masterMajor 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 ........................................................................................ 19INSTITUTE 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 ......................................................................................... 51IFAE-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 oforganization, 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 growthMaster 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
interfaceMaster 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 areMaster 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 orderto 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 frommild 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 transportMaster 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 RNAbiochemistry, 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, germMaster 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. ToINSTITUTE 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 (fromMaster 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 specificIBEC-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 toMaster 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 theYou can also read
