Welcome by IRB Barcelona Director
2
Welcome by the Organizing Commitee
3
The IRB Barcelona Student Symposium Committee
5
Conference programme
6
Invited speakers
11
Mónica Bettencourt-Dias
12
Sarah A Teichmann
14
Julius Brennecke
16
Anne-Claude Gavin
18
Conly L Rieder
20
Aaron Ciechanover
22
Christian Griesinger
24
Piet Gros
26
Erik Sahai
28
Short talks
31
Poster Session A (poster 1-37)
44
Poster Session B (poster 38-74)
75
List of participants
104
Acknowledgements
112
Index of speakers
120
2nd IRB Barcelona
PhD Student Symposium
Contents
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Life in Motion: Dynamics of Molecules and Systems
Welcome by
IRB Barcelona Director
It is with great pleasure that I welcome you all to Life in Motion: Dynamics
of Molecules and Systems, the second IRB Barcelona International PhD
Student Symposium. This initiative first came about two years ago from
conversations with a group of motivated PhD students who wanted to create
opportunities that would allow them to expand their scientific knowledge,
to acquire new skills, and to interact and forge a network with scientists
from the wider research community.
2nd IRB Barcelona International
PhD Student Symposium
As the director of a research institute that has defined one of its core
missions as the provision of high level training to its students, I was pleased
to witness the enthusiasm of the students, and happy to provide the
institutional support necessary for them to make their vision a reality. Each
symposium is organized by a committee, which takes on all aspects of the
organization of the event, from coming up with a theme to inviting speakers
and taking care of logistical details. It has been our pleasure to support
them in this initiative, but at the same time also to stand back and allow
them to resolve some of the challenges that many scientists will confront
during their careers. Indeed, a scientist’s work is not limited to experiments
at the bench, and IRB Barcelona is committed to providing the help its
students need to acquire the wide range of skills to ensure a successful
future in the life sciences.
I would also like to thank the list of distinguished speakers who have kindly
agreed to join us for this event and the students and other scientists who
have come from near and far to participate. We hope that your input and
questions will provide the basis for dynamic and fruitful discussions and
that you will take advantage of the breaks between sessions to meet new
colleagues and make new friends.
Finally, I would like to commend the PhD Student Symposium Committee on
their effort and determination in making this symposium a reality. You do not
have to be great to start, but you have to start to be great.
Joan J Guinovart
Director, IRB Barcelona
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Welcome by the
Organizing Committee
We would like to welcome you to the Second IRB Barcelona PhD Student
Symposium “Life in Motion: Dynamics of Molecules and Systems”. This is the
follow-up of an initiative launched a couple of years ago at IRB Barcelona
by a group of students who organized the First IRB Barcelona PhD Student
Symposium “Architecture of life”, held in November 2009. That event was
a great success and served as an inspiration for future generations of IRB
students. It provided us with a good starting point, directions, inspiration
and challenge for the second edition of the IRB Barcelona PhD Student
Symposium. We would like to acknowledge the achievement of the pioneers
that initiated the IRB Barcelona PhD Student Symposium series, which we
believe will become a hallmark of IRB Barcelona.
We believe that this topic will give all those involved an equal opportunity to
explain their research focus, thus providing a diversity of perspectives, as
IRB Barcelona itself does.
Having chosen the topic, we channeled our efforts into inviting outstanding
speakers, undertaking marketing tasks, finding an appropriate venue, and
convincing and motivating participants to join us in our endeavor to make
the second edition of the IRB Barcelona PhD Student Symposium a success.
2nd IRB Barcelona
PhD Student Symposium
With the legacy of the first symposium and motivated to continue the
success of the IRB Barcelona PhD Student Symposium series we, a group of
twelve students, gathered one and a half years ago to set about designing
and organizing the second edition. With diverse scientific backgrounds
(biologists, biochemists, chemists, medical doctors, physicists and
structural biologists), we shared the motivation to put together a first-class
meeting. We used our expertise in several fields to our advantage in order to
find a central theme for the symposium. Our objective was to hit on a topic
that would accurately represent today’s science. After brainstorming and
some debate, we came up with the topic of Dynamics and Motion as it is an
intrinsic feature of all living organisms, at all levels of organization, that we,
scientists from a range of research fields, study.
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Life in Motion: Dynamics of Molecules and Systems
The symposium seeks to give participants a two-day experience of great
science and excellent professional and personal interactions. We hope to
provide you with an exceptional opportunity and environment to accomplish
this.
As participants, use this occasion to speak, ask questions, and discuss and
interact with your peers and, in particular, with the speakers. This event has
been organized with the benefits of the PhD student community in mind; you
are encouraged to use it to your full advantage.
We thank you for your participation and hope you enjoy the symposium.
2nd IRB Barcelona International
PhD Student Symposium
IRB Barcelona PhD Student Symposium Committee
IRB Barcelona, Spain
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The IRB Barcelona Student Symposium Committee
Manuel Alonso Tarajano (Structural bioinformatics and network biology)
manuel.alonso@irbbarcelona.org
Lara Barrio (Development and growth control laboratory)
lara.barrio@irbbarcelona.org
Kader Cavusoglu (Cell signaling)
kader.cavusoglu@irbbarcelona.org
Eva De Mol (Laboratory of molecular biophysics)
eva.demol@irbbarcelona.org
Andrey Dyachenko (Design, synthesis and structure of peptides and proteins)
andrey.dyachenko@irbbarcelona.org
Sabine Klischies (Microtubule organization)
sabine.klischies@irbbarcelona.org
Jordi Lanuza (Cell signaling)
jordi.lanuza@irbbarcelona.org
Laura Mendieta (Design, synthesis and structure of peptides and proteins)
laura.mendiet@irbbarcelona.org
Selma Pereira (Macrophage biology: regulation of gene expression)
selma.pereira@irbbarcelona.org
Radek Pluta (Structural biology of proteins and nucleic acids, and their complexes)
radoslaw.pluta@irbbarcelona.org
Irena Stevanovic (Genomic instability and cancer laboratory)
irena.stevanovic@irbbarcelona.org
2nd IRB Barcelona
PhD Student Symposium
Milica Pavlovic (Growth control and cancer metastasis)
milica.pavlovic@irbbarcelona.org
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Life in Motion: Dynamics of Molecules and Systems
Conference programme
Thursday, 17 November
8.30
Registration
9.00
Opening remarks by Joan J. Guinovart (IRB Barcelona Director)
Session I: Evolution of protein complexes and pathways
9.15
Invited Speaker Centrosome biogenesis and evolution
Mónica Bettencourt-Dias, Instituto Gulbenkian de Ciência
(Oeiras, Portugal)
10.05
Dynein dynamics during meiotic nuclear oscillations of fission yeast
Vaishnavi Ananthanarayanan, Max Planck Institute of Molecular Cell Biology and Genetics (Dresden, Germany)
2nd IRB Barcelona International
PhD Student Symposium
10.30 Coffee break and poster session A
11.00
Invited Speaker From protein interactions to gene expression distributions
Sarah A Teichmann, MRC Laboratory of Molecular Biology, (Cambridge, UK)
11.50 RPAP2 interaction with the RNA pol II CTD
Justyna Zaborowska, Sir William Dunn School of Pathology,
University of Oxford (Oxford, UK)
12.15 Invited Speaker The piRNA pathway: Guardian of the genome
Julius Brennecke, Institute for Molecular Biotechnology, Austrian Academy of Sciences (Vienna, Austria)
13.05 Lunch
14.30 Poster session A
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Session II: Biomolecular networks
15.30 Invited Speaker From biochemical network to phenotypes
Anne-Claude Gavin, European Molecular Biology Laboratory (Heidelberg, Germany)
16.20
Organism-wide quantitative systems biology - Lessons from a minimal bacterium
Tobias Maier, EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation - CRG (Barcelona, Spain )
16.45 Coffee break and poster session A
17.30
Dynamics of γTubulin within the mitotic spindle
Nicolas Lecland, IRB Barcelona (Barcelona, Spain)
17.55 Invited Speaker Motors and microscopic motions in mitosis
Conly L Rieder, Division of Translational Medicine, Wadsworth Center (Albany, NY, USA)
18.45 End of session
2nd IRB Barcelona
PhD Student Symposium
Evening social event: Tapas with speakers
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Life in Motion: Dynamics of Molecules and Systems
Friday, 18 November
Session III: To adapt or to degrade
9.15
Invited Speaker THE EMBO LECTURE Why our proteins have to die so we shall live: The ubiquitin proteolytic system - from basic mechanisms through human diseases and onto drug targeting
Aaron Ciechanover, Cancer and Vascular Biology Research Center, Technion-Israel Institute of Technology (Haifa, Israel)
10.05
Dengue virus life cycle reappraised: putative role of the capsid protein
João Miguel Freire, Instituto de Medicina Molecular, Universidade de Lisboa (Lisbon, Portugal)
2nd IRB Barcelona International
PhD Student Symposium
10.35 Coffee break and poster session B
11.05 Invited Speaker Fuzziness of globular and aggregating proteins in infection and neurodegeneration: an NMR spectroscopic view
Christian Griesinger, NMR based Structural Biology, Max Planck
Institute for Biophysical Chemistry (Göttingen, Germany)
11.55 Dynamic interactions of proteins and DNA related to pathogenicity
Tiago Cordeiro, IRB Barcelona (Barcelona, Spain)
12.20
Systematic measurement of protein dynamics in yeast reveals novel stress response arsenal
Michal Brecker, Department of Molecular Genetics, Weizmann Institute of Science (Rehovot, Israel)
12.45 Lunch
14.10 Poster session B
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Session IV: Invasion and defense: molecular strategies
15.10
Invited Speaker Insights into the molecular mechanisms of the complement system
Piet Gros, Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research (Utrecht, The Netherlands)
16.00
Structural and dynamic insights into the myosin light chain from the cell invasion motor of plasmodium falciparum
Christopher H Douse, Institute of Chemical Biology, Imperial College (London, UK)
16.25 Coffee break and poster session B
17.20
Invited Speaker THE EMBO LECTURE Cancer cell invasion in complex environments
Erik Sahai, Tumour Cell Biology Laboratory, Cancer Research UK London Research Institute (London, UK)
18.10 Round table
19.30 Closing remarks and poster awards
19.45 End of symposium
Evening social event: The afterparty
2nd IRB Barcelona
PhD Student Symposium
16.55 Intestinal stem cell-like cells in colorectal cancer relapse
Francisco Barriga, IRB Barcelona (Barcelona, Spain)
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2nd IRB Barcelona International
PhD Student Symposium
Life in Motion: Dynamics of Molecules and Systems
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2nd IRB Barcelona
PhD Student Symposium
Invited speakers
abstracts and bios
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Life in Motion: Dynamics of Molecules and Systems
Mónica Bettencourt-Dias
2nd IRB Barcelona International
PhD Student Symposium
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
After her degree in Biochemistry in 1996,
Mónica Bettencourt-Dias moved from
Portugal to the UK. Here she completed
her PhD at the University College of London, studying tissue regeneration
in salamanders, under the supervision of Jeremy Brockes. Later on, in
2002, Mónica started her work in Drosophila melanogaster, as a post-doc
in David Glover’s lab in Cambridge. Her work on cell-cycle-related kinases
brought some major contributions to the field, such as the identification
the centrosome biogenesis regulator, SAK/PLK4. At the end of 2006, Monica
established her lab at the Instituto Gulbenkian de Ciência in Portugal, and
has been pursuing the study of centriole evolution, biogenesis, and function
in several organisms. Not only is she working on award-winning research,
Mónica is also a very good science communicator.
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Centrosome biogenesis and evolution
Centrioles are a conserved eukaryotic feature that are essential for the
formation of several microtubule organizing structures including cilia,
flagella and centrosomes. These structures are involved in a variety of
functions, from cell motility to division. Centrosome defects are seen in
many cancers, while abnormalities in cilia and flagella can lead to a variety
of human diseases, such as polycystic kidney disease.
2nd IRB Barcelona
PhD Student Symposium
The molecular mechanisms regulating centriole biogenesis have only
recently started to be unravelled, opening new ways to answer a wide range
of questions that have fascinated biologists for more than a century. Here
I will discuss centriole and cilia biogenesis, and how this mechanism might
have evolved to generate the diversity of functions those structures have in
the eukaryotic cell.
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Life in Motion: Dynamics of Molecules and Systems
Sarah A Teichmann
2nd IRB Barcelona International
PhD Student Symposium
MRC Laboratory of Molecular Biology,
University of Cambridge (Cambridge, UK)
After completing PhD in computational
genomics with Prof. Cyrus Chothia at
University of Cambridge, Dr. Sarah
Teichmann moved to University College London where she completed a
short and successful postdoc with Prof. Janet Thornton. In 2001, she started
an independent work and became program leader of the MRC Laboratory
of Molecular Biology in Cambridge, UK. Dr. Teichmann researches on the
field of structural bioinformatics and her interests are focused on decoding
the principles of protein interactions. Her outstanding results shed light on
how protein families recombine within multi-domain proteins and on the
dynamics and evolution of transcriptional regulatory networks. Recently, she
has shown that assembly pathways reflect evolutionary pathways of protein
complexes. For her exceptional contributions, during the last two years she
has been awarded with the Women of the Future Science & Technology Prize,
the Lister Research Prize, the Colworth Medal of the Biochemical Society
and the Francis Crick Lecture of the Royal Society.
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From protein interactions to
gene expression distributions
The work in my group is focused on the evolution and dynamics of protein
interactions and transcriptional regulatory interactions. In these two areas,
we analyse large datasets using computational and mathematical methods.
In the first part of my presentation, I will talk about our work on the
evolution and assembly of protein complexes. We surveyed three-dimensional
structures of protein complexes to identify interface size as a determining
principle of both evolutionary and assembly pathways (Levy et al., Nature,
2008), and to quantify conformational change in assembly (Marsh &
Teichmann, Structure, 2011). In recent work, we show for the first time, the
importance of promiscuous protein interactions in determining a protein’s
surface residue composition (Levy et al., in preparation). These new insights
have implications for structure prediction and protein engineering.
2nd IRB Barcelona
PhD Student Symposium
In the second part of my presentation, I will talk about our work on
dissecting the distribution of gene expression levels in mammalian cell
populations, revealing two distinct mRNA abundance classes (Hebenstreit et
al., Mol Sys Biol, 2011). We provide evidence, including correlation of the
two mRNA abundance classes with epigenetic modifications (Hebenstreit et
al., Nucleic Acids Res, 2011), supporting the notion that these two classes
correspond to functional versus non-functional proteins in cells. These
findings now help interpret mRNA and protein abundance data in the form of
microarrays, RNA-sequencing and proteomics.
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Life in Motion: Dynamics of Molecules and Systems
Julius Brennecke
2nd IRB Barcelona International
PhD Student Symposium
Institute for Molecular Biotechnology,
Austrian Academy of Sciences (Vienna, Austria)
Julius Brennecke joined the laboratory of
Dr. Stephen Cohen at the EMBL, Heidelberg
in 2001, were he completed his PhD and
first postdoc focusing on the bantam microRNA and the computational
identification of microRNA targets in Drosophila melanogaster. Later on, in
2005, he moved to the United States where he finish his postdoctoral studies
at the Gregory Hannon’s laboratory (Cold Spring Harbor Laboratories, NY)
and the Norbert Perrimon’s laboratory (Harvard Medical School, Boston)
working on the piRNA pathway in the Drosophila germline. Since 2009 he is
a Group Leader at the Institute for Molecular Biotechnology of the Austrian
Academy of Sciences, Vienna. His work in the novel area of piRNA pathway
as the backbone of a transposon silencing system in flies brought some major
contributions to the field and several awards to him.
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The piRNA Pathway - Guardian of the Genome
Throughout the eukaryotic lineage, small RNA silencing pathways protect
the genome against the deleterious influence of selfish genetic elements
such as transposons. In animals, an elaborate small RNA pathway centered
on PIWI proteins and their interacting piRNAs silences transposons within
germline cells. In contrast to other small RNA silencing pathways, we almost
entirely lack a mechanistic under-standing of this genome defense system.
However, genetic and molecular studies have begun to uncover a fascinating
conceptual framework for this pathway that is conserved from sponges to
mammals.
2nd IRB Barcelona
PhD Student Symposium
I will discuss our current understanding of the piRNA pathway in Drosophila
with an emphasis on the biogenesis of piRNAs. I will also present powerful
genetic approaches that allow to specifically silence genes of interest in
specific cell types of the ovary and that will allow us to perform genome
wide screens to uncover novel piRNA pathway members.
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Life in Motion: Dynamics of Molecules and Systems
Anne-Claude Gavin
2nd IRB Barcelona International
PhD Student Symposium
European Molecular Biology Laboratory,
EMBL (Heidelberg, Germany)
Anne-Claude
Gavin
obtained
her
PhD at University of Geneva in 1992.
Subsequently, she spent several years
as a post-doc at EMBL Heidelberg from where she moved to Cellzome AG
(Heidelberg) to become a scientific director. In 2002 she received the
Genome Technology All-Stars Award in proteomics. Since 2005 she is a Group
Leader at EMBL Heidelberg. Her group has been proponent and pioneer
of more general strategies aiming at understanding complex biological
systems. With more than 1700 citations, the system-wide characterization
of protein complexes in a model eukaryote, Saccharomyces cerevisiae, by
affinity purification and mass spectrometry is generally considered as a
breakthrough. Her main research interest includes the study of biomolecular
interaction, the understanding of the principles that govern the assembly
and dynamics of protein networks.
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From biochemical network to phenotypes
Biological function emerges from the concerted action of numerous
interacting biomolecules. Deciphering the molecular mechanisms behind
cellular processes requires the systematic charting of the multitude of
interactions between all cellular components. Since the sequencing of the
first eukaryotic genome, Saccharomyces cerevisiae, more than 10 years
ago, an explosion of new analytical tools in the fields of transcriptomics,
proteomics and metabolomics contributes ever-growing molecular
repertoires of the building blocks that make up a cell.
The importance of protein–lipid interactions is evident from the variety of
protein domains that have evolved to bind particular lipids and from the large
list of disorders, such as cancer and bipolar disorder, arising from altered
protein–lipid interactions. The importance of lipids in biological processes
and their under-representation in current biological networks suggest the
need for systematic, unbiased biochemical screens. Here, we report a
screen to catalog protein–lipid interactions in yeast using a lipid arrays. To
illustrate the data set’s biological value, we studied further several novel
interactions with sphingolipids, a class of conserved bioactive lipids with an
elusive mode of action. Integration of live-cell imaging suggests new cellular
targets for these molecules, including several with pleckstrin homology (PH)
domains. The dataset presented here represents an excellent resource to
enhance the understanding of lipids function in eukaryotic systems.
2nd IRB Barcelona
PhD Student Symposium
Biology does not rely on biomolecules acting in isolation. Biological function
depends on the concerted action of molecules acting in protein complexes,
pathways or networks. Biomolecular interactions are central to all biological
functions. In human, for example, impaired or deregulated protein–protein
or protein–metabolite interaction often leads to disease. Recent strategies
have been designed that allow the study of interactions more globally at
the level of entire biological systems. We will discuss the use of these
biochemical approaches to genome-wide screen in model organisms. While
protein–protein and protein–DNA networks have been the subject of many
systematic surveys, other critically important cellular components, such as
lipids, have to date rarely been studied in large-scale interaction screens.
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Life in Motion: Dynamics of Molecules and Systems
Conly L Rieder
2nd IRB Barcelona International
PhD Student Symposium
Division of Translational Medicine,
Wadsworth Center (Albany, NY, USA)
After completing a PhD in the laboratory
of A.S. Bajer at the University of Oregon
in 1977, Conly Rieder spent several
years as a post-doc at the University of Wisconsin (Madison). He worked
with Prof. Hans Ris and Prof. Gary Borisy, both prominent in the fields of
microtubules and mitosis. In 1980, he moved to the Wadsworth Center,
where he is currently Chief of the Laboratory of Cell Regulation; he also
holds several academic positions at neighboring institutions, including the
State University of New York at Albany. His major research interest is in how
vertebrate cells divide; since 1977, he has published over 130 papers on
kinetochores, centrosomes and spindle function.
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Motions, motors and mitosis
In keeping with the “Life in Motion” theme of this PhD student symposium,
I will illustrate, using high resolution time-lapse video light microscopy, some
of the various visible “movements” that occur during mitosis and meiosis in
plants and animals.
I will then summarize our current understanding of the molecular
mechanisms that power such movements, most of which involve
microtubule based molecular motors. The motions that I plan to discuss
include centrosome separation and mitotic spindle rotation, chromosome
attachment and mono-orientation during spindle assembly, the motion of
“particles and states” within the spindle, chromosome congression to the
spindle equator, anaphase chromatid segregation and finally cytokinesis.
2nd IRB Barcelona
PhD Student Symposium
Although some of the information used to formulate my conclusions will
come from work conducted through the years in my own lab, much will also
be based on the findings of others.
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Life in Motion: Dynamics of Molecules and Systems
Aaron Ciechanover
2nd IRB Barcelona International
PhD Student Symposium
Cancer and Vascular Biology Research Center,
Technion - Israel Institute of Technology (Haifa, Israel )
Dr Aaron Ciechanover, Nobel laureate,
obtained his doctoral degree in 1981 at
Tecnion - Israel Institut of Technology. As
a graduate student, together with Dr. Hershko and in collaboration with
Dr. Irwin A. Rose, he discovered that covalent attachment of ubiquitin to
the target substrate signals its degradation. After his successful PhD, Dr.
Ciechanover joined the laboratory of Dr. Harvey F. Lodish (MIT, Cambridge,
Mass) for his postdoctoral work. After three years in US, he gained the
independent research position at Department of Biochemistry at the Faculty
of Medicine of the Technion, where in 1987 he become an associate professor
and finally a full professor in 1992. Dr. Chiechenover is currently head of
Protein Turnover lab and Distinguished Research Professor at Rappaport
Faculty of Medicine and Research Institute (Technion). The discovery of
the ubiquitin-proteasome system (UPS), with its numerous functions, has
changed the paradigm that regulation of cellular processes occurs mostly at
the transcriptional and translational levels, and has set regulated proteolysis
in a prominent position. The main focus of Dr Ciechanover laboratory is the
involvement of the UPS in the pathogenesis of malignant transformation. In
particular, they are studying two different pathways: activation of NF-κB
and evasion of apoptosis. Among many prizes and awards for his scientific
accomplishment, Dr. Ciechanover was awarded for the Nobel Prize in
Chemistry in 2004.
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Why our proteins have to die so we shall live:
The ubiquitin proteolytic system from basic mechanisms through human
diseases and onto drug targeting
Between the 50s and 80s, most studies in biomedicine focused on the
central dogma - the translation of the information coded by DNA to RNA and
proteins. Protein degradation was a neglected area, considered to be a nonspecific, dead-end process.
While it was known that proteins do turn over, the high specificity of
the process - where distinct proteins are degraded only at certain time
points, or when they are not needed any more, or following denaturation/
misfolding when their normal and active counterparts are spared - was not
appreciated. The discovery of the lysosome by Christian de Duve did not
significantly change this view, as it was clear that this organelle is involved
mostly in the degradation of extracellular proteins, and their proteases
cannot be substrate-specific.
With the multitude of substrates targeted and the myriad processes
involved, it is not surprising that aberrations in the pathway have been
implicated in the pathogenesis of many diseases, certain malignancies and
neurodegeneration among them, and that the system has become a major
platform for drug targeting.
2nd IRB Barcelona
PhD Student Symposium
The discovery of the complex cascade of the ubiquitin solved the enigma.
It is clear now that degradation of cellular proteins is a highly complex,
temporally controlled, and tightly regulated process that plays major roles
in a variety of basic cellular processes such as cell cycle and differentiation,
communication of the cell with the extracellular environment and
maintenance of the cellular quality control.
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Life in Motion: Dynamics of Molecules and Systems
Christian Griesinger
2nd IRB Barcelona International
PhD Student Symposium
NMR-based Structural Biology,
Max Planck Institute for Biophysical Chemistry
(Göttingen, Germany)
Christian Griesinger started out his
scientific career in the lab of Prof. Dr. H.
Kessler, at the University of Frankfurt,
where he focused on Nuclear Magnetic Resonance (NMR) spectroscopy for
biological molecules during his PhD. He then moved for three years to the
ETH in Zürich as a postdoctoral fellow and assistant in the Laboratory for
Physical Chemistry with Prof. Dr. R.R. Ernst, an authority in the field of NMR
spectroscopy. In 1990, he returned to the University of Frankfurt, where he
was appointed as a Full Professor for Organic Chemistry. Nine years later, he
moved to Göttingen where he was appointed Director and Scientific Member
at the Max Planck Institute for Biophysical Chemistry. The main interest of
the research group he is heading at the MPI is to study the structure-function
relationship and the dynamics of proteins, at atomic resolution, using NMR.
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Fuzziness of globular and aggregating proteins
in infection and neurodegeneration:
An NMR spectroscopic view
The possibility to explore dynamics of proteins specifically ubiquitin will
be presented based on the accurate measurement of anisotropic parameters
such as residual dipolar couplings. Rates of interconversion between
ensembles will be measured by low temperature relaxation dispersion,
dielectric relaxation and temperature jump SAXS. The amount of correlated
motion will be characterized by cross correlated relaxation. The impact
on protein recognition will be discussed on the example of Dsk2-UBA. The
second part of the talk will be devoted to Parkinson’s disease (PD). It features
aggregates of a-Synuclein, so called Lewy bodies, which are connected to
neuronal dysfunction and death.
From the structure mutants have been predicted that don’t form fibrils
but oligomers at higher concentration. They have dramatically increased
toxicity in animal models. With screening and targeted libraries we identified
compounds that reduce the size of oligomers. They are off-pathway, since
no fibrils are formed any more. Biophysically they prevent pore formation in
membranes. Application of these compounds to various animal models of PD
rescues the phenotype. Interestingly, the biophysical characteristics activity
of these compounds is not limited to PD but is also observed in Creutzfeld
Jacob and Alzheimer’s disease mouse models.
2nd IRB Barcelona
PhD Student Symposium
With NMR in liquid and solid state, we have characterized the polymorphic
forms of a-Synuclein: a) Monomers, that are considered to be the healthy
form, are so called intrinsically disordered proteins lacking secondary
structure but have partial tertiary structure which autoinhibits aggregation.
In line with this we observe that mutants that destabilize the partially
folded form aggregate faster and exhibit higher toxicity in animal models. b)
Oligomers of rather well defined size are observed that have less b-structure
than the fibrils. They are on-pathway to the fibrils. c) Fibrils are formed
which could be characterized structurally by solid state NMR and are nontoxic.
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Life in Motion: Dynamics of Molecules and Systems
Piet Gros
2nd IRB Barcelona International
PhD Student Symposium
Crystal and Structural Chemistry,
Bijvoet Center for Biomolecular Research
(Utrecht, The Netherlands)
Piet Gros studied chemistry at the
University of Groningen. He graduated
cum laude in 1985 and in 1990 he obtained his “doctorate cum laude” in
protein crystallography from Groningen as well. From 1990 to 1992 he was a
postdoc at ETH in Zurich and from 1992 to 1994 he worked at Yale University.
In 1994 he returned to the Netherlands and became a researcher at Utrecht
University. He has been a professor there since 2002. In 2004, he went to
the University of Stanford for a one-year sabbatical. In 2008, Gros received
one of the first European Advanced Grants. In 2010, he became a member
of the Royal Netherlands Academy of Arts and Sciences (KNAW) and received
Netherlands’ highest distinction in scientific research, the NWO-Spinoza
Prize. Piet Gros tackles the big challenges in his discipline with creativity,
daring and persistence. In recent years, Gros successfully determined the
3D-structure of the giant and complicated C3 protein. C3 plays a crucial
role in the complement system, which is a defense mechanism of our body.
Gros attracts young scientific talent. His versatility inspires other young
researchers within chemistry to think beyond the conventional. He has
contributed to more than 75 publications, ten of which have been published
in the top journals. He also has two patents to his name.
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Insights into the molecular mechanisms
of the complement system
The complement system is an integral part of the innate immune
defense in mammals. Complement is formed by ~30 large multi-domain
plasma proteins and cell-surface receptors. This system enables to host
to recognize, lyse and clear invading microbes and altered host cells from
blood and interstitial fluids, while protecting healthy host tissue.
Through structural studies, we have revealed the molecular mechanisms
responsible for the central amplification steps, the host protection by
complement regulators and the initial events in formation of the membraneattack complex (MAC). I will discuss the structural mechanisms, which
involve large structural rearrangements due to a interplay of proteolysis and
complex formation.
Images and movies:
2nd IRB Barcelona
PhD Student Symposium
http://www.crystal.chem.uu.nl/~gros/researchhighlights.htm
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Life in Motion: Dynamics of Molecules and Systems
Erik Sahai
2nd IRB Barcelona International
PhD Student Symposium
Tumour Cell Biology Laboratory,
Cancer Research UK London Research Institute (London, UK)
Dr Erik Sahai received his PhD in 1998. at
University College London. He continued
to work as postdoctoral researcher in
Chris Marshall lab at the Institute for Cancer Research, London, as well as
in John Condeelis lab at Albert Einstein Colleege of Medicine, New York. In
2004 he started his own lab at London Research Institute. As the head of
Tumor cell biology lab, Dr. Sahai focuses his research on understanding how
tumor cells spread from the primary site. In details, he is studying tumor cell
motility with main interest in actin regulation by Rho family small GTPases
and the ROCK kinases that bind to them. The main techniques Dr. Sahai’s lab
uses are based on in vivo imaging of primary tumors, organotypic 3D culture
models, with conventional cell and molecular biology assays. Dr. Sahai was
selected as EMBO Young Investigator in 2008 and awarded with Hook Medal
of British Society for Cell Biology in 2009.
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Cancer cell invasion in complex environments
The acquisition of invasive behaviour enables the tumour cells to move
into either the surrounding tissue or the vasculature and thereby spread to
other parts of the body. The focus of our research is investigating why cancer
cells become invasive and how they move.
To study cell motility in this environment we perform intravital multiphoton confocal imaging of tumours in anaesthetised mice. This enables
the heterogeneous behaviour of cancer cells to be studied as they transit
between primary and secondary sites. It also allows direct visualisation of
the interplay between tumour cells, leukocytes, stromal fibroblasts and
endothelial cells. To complement intravital imaging, we have established
a range of three-dimensional ‘organotypic’ cultures that allow us to model
many aspects of the tumour environment in vitro.
Through a combination of screening approaches, we have identified
novel regulators of myosin light chain phosphorylation that are conserved
throughout multi-cellular organisms. We will present our new results
regarding these regulators and their role in cancer cell invasion and
metastasis.
2nd IRB Barcelona
PhD Student Symposium
By using these systems it has become clear that cancer cells can invade
both singly and collectively. These different modes of invasion have
differential requirement for Rho family small G proteins. In singly moving
cells the cortical actomyosin cytoskeleton is critically regulated by RhoAROCK function. In contrast, collectively moving cells show a ‘supra-cellular’
organisation of actomyosin that is dependent on Cdc42 and MRCK function.
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PhD Student Symposium
Life in Motion: Dynamics of Molecules and Systems
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2nd IRB Barcelona
PhD Student Symposium
Short talks
abstracts
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Life in Motion: Dynamics of Molecules and Systems
Dynein dynamics during meiotic nuclear
oscillations of fission yeast
Vaishnavi Ananthanarayanan, Martin Schattat, Sven Vogel, Alexander
Krull, Nenad Pavin and Iva Tolic-Norrelykke
Max Planck Institute of Molecular Cell Biology and Genetics
(Dresden, Germany)
2nd IRB Barcelona International
PhD Student Symposium
Cytoplasmic dynein, with the aid of microtubules (MTs), is responsible for
shaping a variety of cellular processes ranging from spindle and chromosome
positioning to chromosome movement in meiosis. In particular, during the
meiotic prophase of S. pombe, cytoplasmic dynein powers the movement of
the fused nucleus in an oscillatory motion from one cell pole to the other.
This oscillatory movement, called horse-tail nuclear movement (HNM), is
required for proper chromosome pairing1,2.
The mechanism behind HNM has been recently proposed to be the result
of asymmetric distribution of dynein on the leading and trailing MTs, which
is a consequence of the load-dependent detachment of dynein from the
trailing side3. This model requires the continuous redistribution of dynein
within the cell. To study this, we first followed single dynein molecules by
using Total Internal Reflection Fluorescence microscopy. These single dynein
molecules were tracked over time and ¬mean square displacement analysis
revealed the diffusive nature of dynein in the cytoplasm with a diffusion
coefficient of 0.64 µm2/s.
Further, dyneins diffusing in the cytoplasm were also found to be able
to bind MT. Once on the MT, surprisingly, dynein did not move to either
the (+) or (-) end of the microtubule. Instead, dynein on the MT showed
very slow diffusion (D = 0.003 µm2/s), in addition to the passive movement
together with the MT, which was brought about by the pulling of cortically
anchored dyneins on the MT. In conclusion, during HNM dynein redistributes
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in the cytoplasm by diffusion, binds to the MT from the cytoplasm and slowly
diffuses on the moving MT. This slow diffusion of dynein on the MT could help
dynein find its cortical anchor.
References
(1) Yamamoto, A., West, R. R., McIntosh, J. R. & Hiraoka, Y. A cytoplasmic dynein heavy
chain is required for oscillatory nuclear movement of meiotic prophase and efficient meiotic
recombination in fission yeast. The Journal of cell biology 145, 1233-1249 (1999).
(2) Ding, D. Q., Yamamoto, A., Haraguchi, T. & Hiraoka, Y. Dynamics of homologous chromosome
pairing during meiotic prophase in fission yeast. Developmental cell 6, 329-341 (2004).
2nd IRB Barcelona
PhD Student Symposium
(3) Vogel, S. K., Pavin, N., Maghelli, N., Julicher, F. & Tolic-Norrelykke, I. M. Self-organization of
dynein motors generates meiotic nuclear oscillations. PLoS biology 7, e1000087, doi:10.1371/
journal.pbio.1000087 (2009).
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Life in Motion: Dynamics of Molecules and Systems
RPAP2 interaction with the RNA pol II CTD
Justyna Zaborowska1, Sylvain Egloff1,2,3, Clélia Laitem1,
Tamás Kiss2,3, Shona Murphy1
1Sir
William Dunn School of Pathology, University of Oxford, (Oxford, UK);
de Toulouse, UPS, Laboratoire de Biologie Moléculaire Eucaryote,
(Toulouse, France); 3 CNRS, LBME (Toulouse, France)
2 Université
2nd IRB Barcelona International
PhD Student Symposium
The carboxyl-terminal domain (CTD) of the large subunit of RNA polymerase
II (pol II) plays an essential role in transcription. The CTD comprises multiple
heptapeptide repeats of the consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7.
Dynamic phosphorylation of Ser2, Ser 5 and Ser7 underpins the function of
the CTD in expression of pol II transcribed genes [1]. For example, it has
been shown that phosphorylation of Ser7 is required for recruitment of the
gene-type-specific Integrator complex to the pol II-transcribed small nuclear
(sn)RNA genes [2, 3]. Here, we show that RNA pol II-associated protein 2
(RPAP2) specifically recognizes the phospho-Ser7 mark on the pol II CTD
and also interacts with Integrator subunits. siRNA-mediated knockdownof
RPAP2 and mutation of Ser7 to alanine cause similar defects in snRNA gene
expression. In addition, we show that RPAP2 is a CTD Ser5 phosphatase.
Taken together, our results indicate that during transcription of snRNA
genes, Ser7 phosphorylation facilitates recruitment of RPAP2, which in turn
both recruits Integrator and dephosphorylates Ser5.
References
(1) Egloff S, Murphy S: Cracking the RNA polymerase II CTD code. Trends Genet 2008,
24:280‐288.
(2) Egloff S, O’Reilly D, Chapman RD, Taylor A, Tanzhaus K, Pitts L, Eick D, Murphy S: Serine‐7
of the RNA polymerase II CTD is specifically required for snRNA gene expression. Science 2007,
318:1777‐1779.
(3) Chapman RD, Heidemann M, Albert TK, Mailhammer R, Flatley A, Meisterernst M, Kremmer E,
Eick D: Transcribing RNA polymerase II is phosphorylated at CTD residue serine‐7. Science 2007,
318:1780‐1782.
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Organism-wide quantitative systems biology
Lessons from a minimal bacterium
Tobias Maier1, Alexander Schmidt2, Marc Güell1, Sebastian Kühner3,
Anne-Claude Gavin3, Ruedi Aebersold4, Luis Serrano1
1EMBL/CRG
Biological function and cellular responses to environmental perturbations
are regulated by a complex interplay of DNA, RNA, proteins and metabolites
inside cells. To understand these central processes in living systems at the
molecular level, we integrated experimentally determined organism-wide
abundance data for mRNA, proteins, as well as individual protein half-lives
from the genome-reduced bacterium Mycoplasma pneumoniae. We provide
a fine-grained, quantitative analysis of basic intra-cellular processes under
various external conditions. Proteome composition changes in response to
cellular perturbations reveal specific stress response strategies. Protein
abundances are regulated in functional units, such as complexes or
pathways, and reflect cellular lifestyles as well as mechanistic properties
of molecular machines. The analysis of mRNA-protein correlation revealed
that the regulation of gene expression is largely decoupled from protein
abundance in M. pneumoniae. Integrating our quantitative data with protein
half-life measurements showed that translation efficiency has a higher
regulatory impact on protein abundance than protein turnover. Stochastic
simulations using in vivo data showed how low translation efficiency and long
protein half-lives effectively reduce biological noise in gene expression. Our
study provides a detailed integrative analysis of absolute cellular protein
abundances and the dynamic interplay and regulation of mRNA and proteins,
the central biomolecules of a cell.
This work was recently published in Molecular Systems Biology:
http://www.nature.com/msb/journal/v7/n1/full/msb201138.html
2nd IRB Barcelona
PhD Student Symposium
Systems Biology Research Unit, Centre for Genomic Regulation
(CRG), UPF (Barcelona, Spain); 2Proteomics Core Facility Biozentrum,
University of Basel (Basel, Switzerland); 3European Molecular Biology
Laboratory (Heidelberg, Germany); 4Institute of Molecular Systems Biology,
ETH Zürich (Zürich, Switzerland)
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Life in Motion: Dynamics of Molecules and Systems
Dynamics of γTubulin within the mitotic spindle
Nicolas Lecland and Jens Lüders
Institute for Research in Biomedicine - IRB Barcelona (Barcelona, Spain)
During mitosis, a special microtubule array is set up in order to achieve
chromosome segregation and cell division: the mitotic spindle. Both poles
of this bipolar structure are formed by centrosomes. The centrosome is
known as the major microtubule-organizing center and contributes to the
formation of the spindle. The centrosome nucleates microtubules at their
so-called minus end with the help of the γ-tubulin ring complex (γTuRC) [1].
During mitosis the majority of γTuRCs are found at centrosomes, but
some also localize along spindle microtubules. Recruitment to spindle
microtubules is mediated by the augmin complex, a recently discovered
protein complex that promotes γTuRC-dependent microtubule formation to
increase microtubule density within the spindle [2].
2nd IRB Barcelona International
PhD Student Symposium
To learn more about this novel intra-spindle microtubule nucleation
pathway we study the dynamics of spindle-bound γTuRCs during mitosis. At
the onset of mitosis the centrosome recruits a large amount of γ-tubulin,
reaching a maximum in metaphase and decreasing slowly until the end of
the mitosis [3].
FRAP experiments showed that γ-tubulin interacts relatively stably with
centrosomes in a microtubule-independent manner, while interaction of
γ-tubulin with spindle microtubules seems relatively weak and transient.
Using cells stably expressing γ-tubulin fused to photo-activatable GFP and
live cell video microscopy, I observed that γ-tubulin seems to have a stronger
attachment to the spindle than described in previous studies.
Furthermore, I also observed that γ-tubulin moves poleward on the mitotic
spindle at velocities consistent with molecular motor-driven movements.
These results would be the first experimental evidence for poleward sorting
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of microtubules minus ends, as predicted by current models for microtubule
organization during spindle assembly.
References:
(1) Raynaud-Messina B, Merdes A. (2007) Gamma-tubulin complexes and microtubule
organization. Curr Opin Cell Biol 19: 24-30.
(2) Hui Zhu et al. (2008) FAM29A promotes microtubule amplification via recruitment of the
NEDD1-gamma-tubulin complex to the mitotic spindle. J Cell Biol. 183(5):835-48.
2nd IRB Barcelona
PhD Student Symposium
(3) Khodjakov A, Rieder CL. (1999) The sudden recruitment of gamma-tubulin to the centrosome
at the onset of mitosis and its dynamic exchange throughout the cell cycle, do not require
microtubules. J Cell Biol.146(3):585-96.
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Life in Motion: Dynamics of Molecules and Systems
Dengue virus life cycle reappraised:
Putative role of the capsid protein
João Miguel Freire1, Ana Salomé Veiga1, Thaís M Conceição, Nuno C.
Santos1, Wioleta Kowalczyk2, David Andreu2, Andrea T Da Poian3 and
Miguel Castanho1
1Instituto
2nd IRB Barcelona International
PhD Student Symposium
de Medicina Molecular, Faculdade de Medicina da Universidade de
Lisboa (Lisbon, Portugal); 2Department of Experimental and Health Sciences,
Pompeu Fabra University (Barcelona, Spain); 3Instituto de Bioquímica
Médica, Universidade Federal do Rio de Janeiro (Rio de Janeiro, Brazil)
Dengue Virus (DV) causes about 20.000 deaths due to viral haemorrhagic
fever pathology and infects 50-100 million people every year. No effective
treatment is available and several aspects of the viral multiplication and
infectivity remain unclear. The functionalities of the capsid protein (DVCP),
for instance, remain elusive. Two peptides derived from two conserved
domains of DVCP as well as the full protein were studied in the presence
of oligonucleotides and biological membrane models (Large Unilamellar
Vesicles) using spectroscopic techniques (Dynamic Light Scattering - DLS,
Zeta-Potential, Fluorescence Spectroscopy and Microscopy). Peptides R
and M, these being respectively the putative DVCP RNA- and membranebinding domains, show affinity for model lipid bilayers and for membranes
BHK, PBMC and HepG2 cells. The results obtained reveal that DVCP, so far
assigned to structural functions, may play a key role during the entry steps
of DV in Cell infection. The biological implications of these results will be
discussed; mainly focusing on the fusion process of viral infection, which
until now, may have a too simplistic interpretation.
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Dynamic interactions of proteins and
DNA related to pathogenicity
Tiago Cordeiro and Miquel Pons
Institute for Research in Biomedicine - IRB Barcelona (Barcelona, Spain)
Bacterial nucleoid associated proteins act as global regulators of gene
expression facilitating the colonization of hosts. As a consequence,
understanding their function will help in the control of pathogenicity. Ler
is the master regulator of the LEE pathogenicity island in virulent strains
of Escherichia coli. We shall present the solution NMR structure of the first
complex between the DNA binding domain of Ler (CT-Ler) and a 15-mer DNA
duplex. CT-Ler recognizes a preexisting structural pattern in the DNA minor
groove. This indirect readout mechanism is also present in the abundant
repressor H-NS. This mechanism explains the capacity to regulate a large
number of genes by H-NS and the higher specificity of Ler.
References:
(1) Baños, RC et al. PLoS Genet. 5: e1000513. doi: 10.1371/journal.pgen.1000513 (2009)
(2) Cordeiro TN et al. “Indirect DNA Readout by an H-NS Related Protein. Structure of the DNA
Complex of the C-Terminal Domain of Ler” in press (2011).
(3) Cordeiro TN et al. “Protein dynamics-based decoupling of chemical equilibria underlying
independent gene regulation” submitted (2011)
(4) García et al. Biochem. J. 388, 755 (2005).
2nd IRB Barcelona
PhD Student Symposium
Proteins of the Hha/YmoA family bind to H-NS in enterobacteria and
enable the selective regulation of genes linked to pathogenicity. Using
NMR relaxation dispersion experiments we have shown that the formation
of H-NS complexes is controlled by the internal dynamics of YmoA and is
preceded by the formation of electrostatically driven encounter complexes.
We suggest that this mechanism explains the decoupling of the regulation
of pathogenicity-associated from core genes, thus improving the capacity of
enterobacteria to incorporate new horizontally acquired genes.
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Life in Motion: Dynamics of Molecules and Systems
Systematic measurement of protein dynamics in
yeast reveals novel stress response arsenal
Michal Breker1, Melissa Gymrek2 & Maya Schuldiner1
1Department of Molecular Genetics, Weizmann Institute of Science (Rehovot,
Israel); 2Massachusetts Institute of Technology (Cambridge, MA, USA)
All living cells must maintain homeostasis in a constantly changing
environment. A major goal of systems biology is to understand the spatial
and temporal changes of all cellular units and their dynamic interplay during
cellular responses to stress. Regulation of protein stability and localization
are often used to control processes quickly and independently of de-novo
protein synthesis.
2nd IRB Barcelona International
PhD Student Symposium
However, although enormous amounts of data have been collected for
transcriptional responses to stress, very little data exists, even in the
well-studied yeast Saccharomyces cerevisiae, on the dynamics of protein
abundance and localization under a variety of different environmental
conditions. Here we show a comprehensive microscopic platform for rapidly
and accurately measuring protein localization and abundance at single cell
resolution in high throughput. Using the full yeast GFP library we have used
our platform to look at protein dynamics under three different conditions
(DTT, H2O2, Nitrogen starvation).
We find that a plethora of post-transcriptional changes occur under each
condition including changes in abundance and localization for hundreds of
proteins. We show that such post-transcriptional changes can have a role in
promoting the ability of yeast to survive in stressful environments. To enable
easy access to this data we have created a database, which we call LOQATE
(LOcalization and Quantitation Atlas of YeasT ProteomE). The information
in LOQATE can be used to study new dimensions in the plasticity of yeast
responses.
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Structural and dynamic insights into
the myosin light chain from the cell invasion
motor of Plasmodium falciparum
Christopher H Douse1,2,3, Jemima C Thomas2, Paula S Salgado3, Peter
J Simpson3, Edward W Tate1,2 and Ernesto Cota1,3
of Chemical Biology, Imperial College (London, UK); 2Department
of Chemistry, Imperial College (London, UK); 3Division of Molecular
Biosciences, Imperial College (London, UK)
A key event in the complex life cycle of Plasmodium spp., the protozoan
parasites that cause malaria, is the invasion of erythrocytes by blood stages
known as merozoites. The motive force required for this invasion is provided
by a conserved actomyosin motor consisting of an unusual myosin (MyoA)
that is part of a multi-protein assembly making up the biomolecular invasion
machinery. One of these proteins is Myosin Tail Interacting Protein (MTIP),
which links the motor to the inner membrane of the merozoite [1]. The MTIP/
MyoA complex can be reconstituted in vitro using peptides mimicking the
C-terminal tail of MyoA, and since inhibition of the interaction in vivo should
prevent invasion and disrupt the parasitic life cycle, it has been identified
as a novel antimalarial drug target [2,3]. Crystallography has provided some
useful structural information [4], but an understanding of the interactions
and dynamics of the proteins in solution is also vital in terms of a structureguided drug discovery approach. In this talk I will describe the application
of multi-dimensional NMR spectroscopy and other biophysical techniques in
studying the 16.4 kDa binding domain of MTIP from Plasmodium falciparum
and the complex formed with MyoA peptides. In particular, I will show how
these experiments enabled us to extract residue-specific information on the
dynamics of this pathologically relevant system on a range of timescales.
References
(1) Green, J. L. et al. (2006), J. Mol. Biol. 355, 933-941.
(2) Bosch, J. et al. (2006), Proc. Natl. Acad. Sci. USA 103, 4832-4837.
(3) Thomas, J. C. et al. (2010), Mol. Biosyst. 6, 494-498.
2nd IRB Barcelona
PhD Student Symposium
1Institute
(4) Bosch, J. et al. (2007), J. Mol. Biol. 372, 77-88.
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Life in Motion: Dynamics of Molecules and Systems
Intestinal stem cell-like cells in
colorectal cancer relapse
Francisco Barriga, Eduard Batlle
Institute for Research in Biomedicine - IRB Barcelona (Barcelona, Spain)
2nd IRB Barcelona International
PhD Student Symposium
Mature differentiated cells of the intestinal tract are constantly renewed
by the progeny of Intestinal Stem Cells (ISCs). We report that the organization
of most human colorectal cancers (CRCs) is reminiscent of that of the normal
intestinal epithelium. CRC cells display phenotypes similar to either ISCs
or intestinal differentiated cells and recreate the formation of crypt-like
structures within tumors. We have developed a method to purify normal
intestinal cell populations including ISCs.
Comparison of the expression profiles of different crypt cell types versus
CRC patient samples led us to identify a gene program shared between
normal ISCs and the most aggressive CRCs. 30 to 40% of CRC patients
undergoing curative therapy will experience disease relapse usually in the
form of metastasis. We demonstrate that high expression levels of ISC genes
in primary tumors are associated with high risk of recurrence. Furthermore,
expression of ISC genes identifies an ISC-like tumor cell niche capable of
tumor initiation upon injection in immunodeficient mice. Our findings have
profound implications not only for the understanding of CRC biology but also
for the clinical management of CRC patients.
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PhD Student Symposium
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Life in Motion: Dynamics of Molecules and Systems
Poster Session A
Poster Session A comprises all posters
(abstract numbers) from 1 to 37. You
should install you poster until Thursday 17th of November, before 10 am
the latest, and you should remove it
Friday 18th before 10 am since there
will be another poster session.
Please remember that the Thursday’s
poster session will be divided in two
sections, one in the morning at 10.30
and the other in the afternoon at
14.30 and that poster authors should
be present on both sessions.
POSTER 1
The role of a novel exonuclease,
Exd2, in the maintenance of mitochondrial DNA
2nd IRB Barcelona International
PhD Student Symposium
Suvi Aivio1, Irena Stevanovic1, Andreu
Casali1, Laura Bailey2, Sean Rudd2,
Stefan Balint3, Travis Stracker1
1IRB
Barcelona (Barcelona, Spain);
Genome Damage and Stability
Centre (Brighton, UK) 3ICFO - Institut de Ciències Fotònique (Barcelona,
Spain)
2MRC
Abstract
Metabolic dysfunction is a hallmark
of cancer cells that undergo a switch
from mitochondrial (Mt) respiration
to aerobic glycolysis for ATP production. Mutations in MtDNA and nuclear
genes encoding Mt maintenance pro-
teins have been described in cancer
cells but the mechanisms of MtDNA repair and maintenance, and their role
in disease remain poorly understood.
Exonuclease 3’-5’ containing protein
2 (Exd2) is an uncharacterized protein
with a putative mitochondrial targeting signal in its N-terminus and a DEDDy family nuclease domain.
The structural similarity of its exonuclease-domain to WRN, a nuclear DNArepair protein mutated in Werner’s
syndrome progeria, suggested that it
might have a similar role in MtDNA repair or replication. We have confirmed
biochemically that Exd2 is an active
3’-5’ exonuclease that can act on DNA
and RNA with little preference for secondary structure. In addition, it localizes primarily to the mitochondria in
human cells.
To address the role of Exd2 in MtDNA
homeostasis, we have created several
cells lines with reduced levels of Exd2
protein and generated a non-functional allele in mice. The reduction of
Exd2 leads to increased MtDNA copy
number as well as numerous metabolic
changes, including increased ROS. We
did not observe differences in MtDNA
replication structures and cells with
reduced Exd2 showed increased autophagy and transcriptional upregulation of inflammatory genes.
Our working hypothesis is that Exd2
regulates MtDNA copy number by clearing Mt genomes after auto/mitophagy,
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POSTER 2
Conformational consequences upon
binding of aggregation inhibitors to
monomeric Tau protein
Akoury, Elias
Max Planck Institute for Biophysical
Chemistry (Goettingen, Germany)
Abstract
In many neurodegenerative disorders,
wrongly folded species form abnormal
deposits in the brain. In this study, we
focus on the intrinsically disordered
protein Tau (1), the major hallmark
associated with Alzheimer’s disease
(AD). The physiological role of Tau is
the stabilization and regulation of
microtubules and the support of the
outgrowth of axons (2,3). In AD, an extensively phosphorylated Tau no longer
binds to microtubules and aggregates
into intracellular neurofibrillary tangles. There is great interest in finding
small molecules that can inhibit tau
aggregation and understanding their
mechanisms of action (4).
Here, we probe the impact of a selected Tau aggregation inhibitor on the
conformational sampling of the Tau
backbone using Residual Dipolar Couplings (RDCs). Quantitative analysis of
N-HN, Cα-Hα, CO-Cα, CO-HN RDCs of
both [1H-13C] aromatic, aliphatic and
[1H 15N] HSQC spectra of K32 and K18
Tau constructs bound to the inhibitor B4A1 provide first insights into its
mechanism of action.
POSTER 3
DNA damage induced senescence
and apoptosis of two spontaneously
immortalized cell lines from NBS patients
O.Alster1, A. Bielak-Żmijewska1, G.
Mosieniak1, Z.Korwek1, J. K. Siwicki2
and E. Sikora1
1Nencki
Institute of Experimental Biology, Polish Academy of Sciences
(Warsaw, Poland); 2Department of Immunology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of
Oncology (Warsaw, Poland)
Abstract
Nijmegen Breakage Syndrome (NBS)
is a rare autosomal recessive disorder
characterized by: genomic instability, immunodeficiency, radiosensitivity
and increased risk of cancer development. NBS is caused by a mutation in
the NBS1 gene, which codes a protein
involved in the repair of DNA double
strand breaks. It is commonly known
that senescence can be induced by
treatment with a DNA damaging agent,
which is a consequence of the activation of the DNA damage pathway.
Moreover NBS is considered to be a
progeroid syndrome. We wanted to
verify whether we could induce senescence, in two spontaneously immortalized NBS cell lines (S3R and S4), by
treatment with a DNA damaging agent
(doxorubicin).
We used two spontaneously immortal-
2nd IRB Barcelona
PhD Student Symposium
thus preventing an innate immune mediated inflammatory response.
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Life in Motion: Dynamics of Molecules and Systems
ized NBS cell lines (S3R and S4). Cells
were treated with a DNA damaging
agent- doxorubicin for 24h and afterwards cultured in a drug free medium
for 4 days. In the case of the first cell
line- S3R we observed an induction of
p21, which was not accompanied by
the presence of other markers of senescence, while in the S4 cells a time
dependent increase in the level of p21
and as well as other markers of senescence (SA-β-Gal positive cells) could
be found.
In case of both of the cell lines doxorubicin treatment led to the activation
of p53, Chk1 and Chk2, which are part
of the DNA damage pathway. Based on
the obtained results we can say that
the different fate of the analyzed cells
is not connected with the mutation
causing the NBS syndrome, but different factors can be implicated such as
genomic instability.
2nd IRB Barcelona International
PhD Student Symposium
POSTER 4
Structural study of proteasome regulatory particle proteins
46
Juliana Amodio, Fabio Sessa, Miquel
Coll
IRB Barcelona and Institut de Biología
Molecular de Barcelona - CSIC (Barcelona, Spain)
Abstract
In eukaryotes protein lifespan is regulated by the Ubiquitin Proteasome System, by degrading short-lived regulatory or structurally aberrant proteins,
which are tagged with ubiquitin; as
lifeinmotion_booklet.indd 46
a consequence controls almost all
basic cellular processes (such as protein quality control, DNA repair, signal
transduction, etc).
The UPS is composed by a cascade
of ubiquitin ligases that tag the substrate with ubiquitin chains, allowing
the proteasome to recognize it and
degrade it. The proteasome is a large
protein complex composed by two distinct sub complexes: the Core particle
that presents a barrel-like shape, were
the proteolytic active sites are sequestered within a inner chamber; and appended to either or both ends of the
CP is the Regulatory Particle which is
responsible for fundamental upstream
processes such as recognition, unfolding, deubiquitination and finally
translocation of the substrate to the
CP. The RP comprises two distinct subcomplexes, the lid and the base.
Although much is known about the
structure and the biology of CP, additional work is required to shed light
onto the molecular mechanism by
which the RP complex modulates the
activity and substrate specificity of
CP. We have initiated the structural
characterization of the base subunits
Rpn10, 1 & 2 from Saccharomyces cerevisiae.
Also, to obtain information about the
interaction network between the lid
and the base our strategy includes
the co-expression of the base subunit
Rpn10 together with some of the lid
subunits. Heterologous expression and
co-expression of the different subunits
is being performed in Escherichia coli
with the aim of obtaining appropriate
proteins and complexes for crystallization assays.
11/7/11 10:55 AM
17-18 November 2011
Rodrigo Arroyo*, Guillermo Suñé*,
Andreas Zanzoni, Travis Stracker,
Montserrat Soler-López and Patrick
Aloy
IRB Barcelona (Barcelona, Spain).
*These
authors contributed equally to
this work
Abstract
Breast cancer (BC) is the most frequently diagnosed non-skin cancer in
women world-wide. Distinct morphological features and clinical behaviors
turn breast cancer to a very heterogeneous disease. As a consequence, new
approaches to unravel new mechanistic pathways underlying breast cancer need to be applied, and mapping
protein-protein interactions is crucial
to understand the disease and also the
players involved in it.
In order to identify and characterize
novel interactions between causative
and associated breast cancer genes,
we have applied a systematic and rigorous pipeline based on high-throughput interaction studies to generate a
BC protein interaction network (BCPIN). We have identified by HT-Y2H,
491 interactions between genes that
are known to be involved in the disease. Furthermore we also detected
108 novel interactions that could have
a relevant function in the disease due
to their interaction with key players in breast cancer. Finally we have
identified new potential genes to be
involved in DNA damage response.
In this work we show how a combination of interaction discovery experiments and the computational analyses
of diverse biological data can provide further evidence for potential
causative/associated genes related
to breast cancer disease, suggesting
novel hypotheses as to their molecular
functioning.
POSTER 6
In vitro generation of Ly6C+ CD11b+
cells and analysis of their role in vivo
during inflammation
Erika Barboza, Catalina Rincón, Isabella Hirako, Luis F.Santamaria-Babi,
Antonio Celada
IRB Barcelona (Barcelona, Spain)
Abstract
Circulating monocytes provide defense
against infections and also contribute
to autoimmune diseases. Two types of
blood monocytes were recently identified in mice. CD11b+ CCR2low Ly6C−
CX3CR1high phenotype, migrate to uninjured tissues and differentiate into
resident macrophages and dendritic
cells (DCs). In contrast, a distinct inflamed monocyte subset with a CD11b+
CCR2highLy6ChighCX3CR1low phenotype
infiltrates infected tissue and contributes to the development of inflammation.
The aim of this study is to demonstrate
2nd IRB Barcelona
PhD Student Symposium
POSTER 5
Charting the interactome network
associated to breast cancer reveals
novel genes involved in DNA damage
response
47
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PhD Student Symposium
Life in Motion: Dynamics of Molecules and Systems
48
the migration and inflammatory capacity of Ly-6C+CD11b+ cells generated in
vitro, in two in vivo models of inflammation.
We have optimized two different animal models to induce local inflammation in non-sensitizied, immunocompetent Balb/c mice. In the first model,
1-fluoro-2,4-dinitrobenzene
(DNFB)
was applied topically on the right
ear to create skin-homing conditions
(DNFB dermatitis model) . In this skin
model, net ear swelling was calculated
by weight subtraction between right
and left ear after 24h and 48h of cells
injection. In the second model, an injection of Notexin was applied into the
anterior tibialis (AT) on the right leg to
induce myoinjuy (Notexin model).
Finally 1x106 and 3x106 Ly6C+CD11b+
cells generated in vitro previously
were injected i.v in both animal models. Gene expression was measured by
a quantitative real time PCR, cell migration was seen trough IVIS images,
flow cytometry studies and histology
assays in both models.
DNFB dermatitis model: Net ear swelling depended on the number of cells
injected in animals treated with DNFB.
DNFB and Ly6C+CD11b+ cells injected
mice presented an increased weight in
relation to DNFB no-treated mice. IVIS
experiments with Ly6C+CD11b+ cells
demonstrated the presence of fluorescence only in the inflamed ear, even 3
days after i.v. injection.
Notexin model: muscle injury depended on the number of cells injected in
animals treated with Notexin. Notexin-treated and Ly6C+CD11b+ cells injected mice showed muscle injury. IVIS
experiments with Ly6C+CD11b+ cells
lifeinmotion_booklet.indd 48
demonstrated the presence of fluorescence only in the inflamed muscle,
even 3 days after i.v. injection. Histology clearly indicated the presence of
injected cells in the inflammed tissues.
Our data demonstrated that DNFB
dermatitis and Notexin animal models
are good tools to study the molecular
mechanisms involved in the migration
of circulating Ly-6C+CD11b+ cells in inflammation.
POSTER 7
Reelin-overexpression mouse model
(Tg1/Tg2)
Carles Bosch
IRB Barcelona (Barcelona, Spain)
Abstract
Reelin is a large secreted glycoprotein
that is widely studied in the embryonic development of layered structures of the brain. After birth, Reelin
undergoes an expression pattern shift
and is expressed by some interneurons in postnatal and adult brain. Its
function is not well known at these
stages, although recent studies point
to a role in the regulation of neuronal plasticity. Here we used a conditional CamKII-alpha promoter-driven
Reelin-overexpression mouse model
(Tg1/Tg2) to analyze the modulatory
activity of Reelin on the formation of
dendritic spines and synaptic connections in a cytoarchitectonically intact
adult brain. Combining intracellular
labeling in fixed tissue and electron
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17-18 November 2011
microscopy analyses, we found that
overexpression of Reelin does not affect the density of dendritic spines,
but it increases their complexity in the
hippocampus.
Moreover,immunocytochemical studies
revealed alterations in the expression
patterns of Synaptopodin, a protein
related to the spine apparatus. In
addition, the density and complexity of presynaptic terminals were also
increased in Tg1/Tg2 mice. Finally,
administration of doxycycline mostly
reverted the alterations found in the
Tg1/Tg2 mice. All together, our results
indicate that reelin overexpression
leads to an increase in hippocampal
connectivity, and thus point to Reelin
as a key player in adult neural connectivity.
decades. On-pathway or off-pathway
helical intermediates are speculated
to have a significant influence on Aβ fibril formation1. By tuning the helicity
with either cosolvents1, inhibitors4,
or mutations, it has been shown to be
able to both reinforce and prevent fibril formation.
Here, we report that the full-length alloforms of the Japanese mutant of Aβ,
E22Δ -Aβ, exhibit enhanced structure
and helicity at the monomeric level.
The E22Δ mutation2 shows aggregation
rates in in vitro experiments that are
up to 400 times faster than wild type
Aβ3. Based on our preliminary findings
and experimental results generated
by others, we suggest that increased
helicity may contribute to the faster
aggregation process of E22Δ-Aβ.
POSTER 8
Ensemble shifts in amyloidogenic
peptides: Putative influence of monomer helicity on aggregation rate for
the Japanese mutant of Alzheimer’s
amyloid-b protein
POSTER 9
Involvement of patched in cell migration during tracheal system development in Drosophila melanogaster
1Dep. of Biochemistry, University of
Zürich (Zürich, Switzerland); 2Dep. of
Chemistry, University of Zagreb (Zagreb, Croatia)
Abstract
The mechanism of amyloid aggregation - the formation of β-sheet-rich
assemblies - has been a subject of extensive research during the past few
1IRB
Barcelona (Barcelona, Spain);
Molecular Biology Institute of
Barcelona (Barcelona, Spain)
2The
Abstract
Drosophila tracheal and nervous systems are models largely used to study
cellular migration and pathfinding
in morphogenesis and their common
characteristics and properties suggest
the existence of shared mechanisms
and interactions between them. Our
2nd IRB Barcelona
PhD Student Symposium
A. Burcul1,2, A. Magno1, A. Caflisch1, A.
Vitalis1
Elisenda Butí1,2, Duarte Mesquita1, Andreu Casali1 and Sofia J. Araújo1,2
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PhD Student Symposium
Life in Motion: Dynamics of Molecules and Systems
50
main project proposes investigating
possible common mechanisms between nervous and tracheal system
development. We started analysing
the tracheal phenotypes of a mutant
collection identified via its nervous
system phenotypes. This study may
identify not only factors involved in
the development of both systems, but
also processes where each of these
systems influences on the development of the other.
The D130 allele has been previously
mapped and sequenced and identified
as patched (ptc), which is involved in
an important pathway in development
of both invertebrates and vertebrates
- the Hedgehog (Hh) pathway. We are
currently analyzing the tracheal phenotype of the ptc mutant embryos to
further clarify the involvement of ptc
in tracheal development. We are particularly interested in the involvement
of ptc in cell migration and differentiation. So far we have observed that
the allele ptcD130 acts a genetic null,
doesn’t get internalized and is necessary for the migration of the ganglionic
branches. The overactivation of the Hh
pathway in the tracheal cells implies
a non-autonomous role in ganglionic
branch migration/extension.
However, rescue experiments suggest
Ptc receptor could have an autonomous effect in tracheal migration/
extension. These and other results
suggest that Ptc could have an independent role of Hh in tracheal system
development.
POSTER 10
Unveiling a new mechanism of regu-
lifeinmotion_booklet.indd 50
lation of angiogenesis through translational regulation by the CPEB family of proteins
Calderone V1, Gallego J2, Garcia-Pras
E2, Bosch J2, Fernandez M2, Mendez R1
1IRB
Barcelona (Barcelona, Spain);
Unit, Institute of Biomedical
Research (IDIBAPS), CIBERehd, Hospital Clinic (Barcelona, Spain)
2Liver
Abstract
Gene expression is regulated at multiple levels, including the translation of
mRNAs into proteins. The translational
control of stored mRNAs represents
and efficient way to rapidly increase
the cellular concentrations of proteins, regulate the homeostasis and
modulate transient and permanent
changes in cell biology.
One of the best characterized mechanisms of translational regulation involves changes in the poly (A) tail
length, mediated by the CPEB (Cytoplasmic Polyadenylation Element Binding protein) family of proteins. CPEB
regulates the translation of CPE containing mRNAs in germ cells, fibroblast
and neurons, driving both meiotic and
mitotic progression and modulating
the synaptic plasticity. Moreover, one
of the CPEB members, CPEB4, has
been found to drive pancreatic ductal
adenocarcinoma and glioblastoma development, where CPEB4 regulates tPA
mRNA translation, the production and
the vascularization of the tumor.
The aim of this study is to assess the
role of CPEB1 and CPEB4 in angiogenesis, through the translational regula-
11/7/11 10:55 AM
tion of the pro-angiogenic factors such
as vascular endothelial growth factor
(VEGF). Using portal vein hypertension model, we observed a correlation
between the activation of CPEB1, synthesis of CPEB4 and the, nuclear and
cytoplasmic processing of the VEGF
mRNA with its consequent translational activation. To better define the
mechanistic relevance of these correlations, we have implemented an
in vitro model of tubulogenesis using
the murine endothelial cell line H5V.
In this model we found that CPEB1 and
CPEB4 sequentially, and coordinated
through a positive translational feed
back loop, regulate alternative nuclear and cytoplasmic polyadenylation of
VEGF mRNA, which in turn are essential for the synthesis of VEGF and the
formation of endothelial tubular structures. Thus unveiling a new mechanism
of regulation of angiogenesis through
translational regulation by the CPEB
family of proteins.
POSTER 11
Structural conformation, kinetics of
aggregation
Giulio Chiesa
IRB Barcelona (Barcelona, Spain)
Abstract
Spinal Bulbar Muscular Atrophy (SBMA),
also known as Kennedy disease, is a
rare X-linked neurodegenerative disease. It affects motor neurons, determining a progressive weakness and
atrophy of limb and facial muscles,
leading to a reduction of motion capability. This disease is associated to
a mutation of the gene coding for the
Androgen Receptor (AR), in a sequence
that codes for polyglutamine tract,
making this disease fall into the category of the polyglutamine diseases,
together with Huntington Disease.
The pathogenic variant of the protein
is known to induce, in neuron motor
cells, the formation of aggregates that
contain primarily the Androgen Receptor. These aggregates have been associated to the neuron death.
Conversely, the nature of the structural characteristics of the aggregates
that probably are causing the motor
neuron death and, potentially, the
SBMA is still not clear. It is known that
a prominent role is played by the surrounding chains of the polyglutamine
tract, even if it is not known at the
atomic level which kind of behavior
they assume and how the aggregation is triggered. There are some evidence in literature that there might
be involved a third molecular species,
named oligomer, formed by the association of few Androgen Receptor
proteins, even if they have not been
seen, yet, and probably the toxicity
might be associated to these transient
species.
The aim of this work is to shed light
on the structural conformation of the
surrounding of the polyglutamine tract
and of the aggregate at the molecular
level, studying the kinetics of aggregation in vitro and in neuronal cells, to
design a realistic and evidence-based
model of its aggregation dynamics.
2nd IRB Barcelona
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17-18 November 2011
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Life in Motion: Dynamics of Molecules and Systems
POSTER 12
The protein expression pattern of
CD133+ colon cancer cells indicates
activation of the Wnt pathway and
potential alteration of splicing mechanisms
C. Corbo1,2, S. Orrù3,4, M. Gemei1,2, R.
Di Noto1,5, P. Mirabelli1, M. Ruoppolo1,5, L. Del Vecchio1,5, F. Salvatore1,5
2nd IRB Barcelona International
PhD Student Symposium
1CEINGE, Biotecnologie Avanzate scarl
(Naples, Italy); 2SEMM, European
School of Molecular Medicine (Naples,
Italy); 3Fondazione SDN-IRCCS (Naples, Italy); 4Facoltà di Scienze Motorie, Università di Napoli “Parthenope”
(Naples, Italy); 5Dipartimento di Biochimica e Biotecnologie Mediche, Università di Napoli “Federico II” (Naples,
Italy)
Abstract
Cancer stem cells (CSCs) theory represents a breakthrough in cancer research. CSCs are able to self-propagate
in vitro, they divide asymmetrically
and are tumorigenic. These cells can
initiate tumor formation, elude treatment and allow tumor reformation
after initial successful treatment. We
have characterized the protein expression pattern of CSCs in an attempt to
identify specific intracellular pathways
in this sub-population of tumor cells.
Specifically, we studied colon CSCs
starting from two colon cancer cell
lines: CaCo-2 and HCT116. Putative
CSCs were separated from differentiated cancer cells by flow cytometry
using CD133 as stemness marker. Total
protein extracts of purified CD133+
cells were then compared to protein
extracts of control cells (CD133-) using
2D-DIGE methodology.
The protein spots found to be significantly differentially expressed in the
two sub-population of cells were analysed by mass spectrometry: 17 proteins were identified for HCT116 and
30 for CaCo-2, some of which are involved in the Wnt/β-catenin pathway
that leads to activation of the transcription of genes responsible for cell
survival and proliferation. Interestingly, we also observed up-regulation
of the splicing factor SRp20, which is
a newly identified target gene of the
Wnt/β-catenin pathway (1).
SRp20 has also recently been shown to
play a critical role in cell proliferation
and tumor induction and maintenance
in various tumor types (2). To determine whether SRp20 accumulation is
a downstream effect of Wnt pathway
activation, we stimulated the pathway
and we observed SRp20 expression,
thus demonstrating a direct causeeffect relationship between Wnt pathway activation and the increased level
of SRp20.
In conclusion, our demonstration of activation of the Wnt pathway by CD133+
cells and of up-regulation of SRp20,
which is implicated in tumorigenesis,
raises the possibility of a sequential
series of molecular events occurring in
connection with this process.
POSTER 13
One b hairpin after the other: Folding mechanism of a transmembrane
52
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b-barrel protein
Mehdi Damaghi
ETH Zurich (Zurich, Switzerland)
Abstract
Despite their enormous relevance to
cellular vitality, the folding mechanisms of only a few transmembrane
proteins have been studied. From these
studies, only a handful of bstranded
membrane proteins were characterized. Current models describe that
transmembrane b barrels fold into the
lipid membrane in two major steps.
Firstly, the unfolded polypeptide interacts with the lipid surface where it
folds, tilts, and then inserts into the
membrane.
Consequently, it is thought that single
b strands and b hairpins form unstable units, and that b-barrel proteins
(pre-)fold prior to their insertion into
the cellular membrane. Experiments
studying the (un-)folding of membrane
proteins are conventionally carried
out by using thermal or chemical denaturation (detergent and/or exposed
to approximately 4–10m urea) which is
far a way from the nature.
Single-molecule force spectroscopy
(SMFS) represents a unique approach
to studying the refolding of membrane
proteins into the lipid membrane.[4]
SMFS is used to unfold and refold membrane proteins under conditions typical for their physiological environment
such as pH, electrolytes, temperature,
and, importantly in the absence of any
chemical denaturant or detergent.
Using SMFS, the mechanical unfold-
lifeinmotion_booklet.indd 53
ing and refolding of many different
water-soluble proteins have been investigated.Compared to the variety of
water-soluble proteins that were characterized, SMFS of membrane proteins
reveals much more detailed unfolding
and folding pathways.[4] To date, the
refolding of b-barrel membrane proteins into a lipid membrane has never
been addressed by SMFS.
Herein we report the application of
SMFS to unfold and refold the outer
membrane protein G (OmpG) from Escherichia coli. The structure of OmpG
comprises 14 b strands that form a
transmembrane b-barrel pore.In previous SMFS studies, we found that the b
barrel of OmpG unfolds via many intermediates. The main unfolding pathway
described the stepwise unfolding of
single b hairpins. This unfolding pathway was much more detailed than that
detected for the water-soluble b-barrel green fluorescent protein (GFP),
which mainly unfolds in one step when
a sufficiently high pulling force was
applied. In our refolding experiments,
OmpG that had been reconstituted in
native E. coli lipid membranes was
first imaged by AFM. Then, the AFM tip
was pushed onto the OmpG surface to
facilitate the nonspecific attachment
of the N terminus.
Withdrawal of the AFM tip stretched
the terminus and induced the unfolding
of OmpG. Force–distance (F–D) curves
recorded the force peaks that reflect
the unfolding steps of a single OmpG.
Each unfolding step represents that of
a b hairpin of the transmembrane b
barrel. To refold the partially unfolded
OmpG, we stopped withdrawal before
unfolding the last b hairpin VII. Then,
2nd IRB Barcelona
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Life in Motion: Dynamics of Molecules and Systems
we relaxed the unfolded polypeptide
by approaching the AFM tip close to
the membrane (ca. 5 nm).
After a given time to allow the
polypeptide to refold, the protein was
unfolded again to probe which structural regions refolded into the lipid
membrane. Our results suggest a fundamentally different folding mechanism for transmembrane b-barrel
proteins. In contrast to the two-stage
folding and insertion model of a transmembrane b barrel, we observe distinct folding steps for b hairpins.
POSTER 14
Chromatin dynamics throughout the
yeast cell cycle
Özgen Deniz1,2, Federica Battistini2,
Oscar Flores2, Montse Soler-Lòpez1,2,
Modesto Orozco1,2
2nd IRB Barcelona International
PhD Student Symposium
1Experimental
54
Bioinformatics Lab,
Joint Programme IRB Barcelona – BSC
(Barcelona, Spain); 2Molecular Modeling and Bioinformatics Group, IRB
Barcelona (Barcelona, Spain)
Abstract
The detailed positioning of nucleosomes is key to understand gene regulatory mechanism, since the packaging of DNA into nuclesosomes controls
DNA accessibility for processes like
transcription, repair and replication.
To maintain or alter this organization according to the cellular states,
nucleosomes are deposited, replaced
or exchanged. Here, we studied how
the nucleosome positioning pattern is
lifeinmotion_booklet.indd 54
affected by chromatin dynamics during DNA replication using synchronized
populations of Saccaromyces cerevisae.
Besides the global view of the chromatin dynamics, we have been analyzing
the nucleosome positioning patterns in
more detailed around the cell cycleregulated genes and certain important
genomics regions like centromeres and
replication origins.
POSTER 15
Structure and mechanism of V(D)J
recombinase
Marija Dramicanin
Spanish National Cancer Research
Center - CNIO (Madrid, Spain)
Abstract
V(D)J recombination is the specialized DNA rearrangement used by the
immune system to assemble the vast
repertoire of immunoglobulin and Tcell receptor genes. This DNA recombination process is initiated by a V(D)
J recombinase formed by the intimate
association of the RAG1 and RAG2 proteins. Mutations in RAG1/2 cause defects in lymphocyte maturation and
lead to immunodeficiencies (scid).
Moreover, failures in the control of
the recombinase activity have been
related to genome instability and the
development of lymphomas. Despite
the central role of RAG1/2 in the development of the immune system and
its implication in cancer, there is lack
of structural and functional knowledge
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POSTER 16
Understanding and predicting adverse drug reactions from biological
and chemical spaces
Miquel
Aloy1,2
Duran-Frigola1
and
Patrick
chemical and the biological spaces
seeking for regions that markedly correlate with adverse drug reactions
(ADRs). Given a collection of side effects and the drugs reported to cause
them, we gather (a) drugprotein interaction data and (b) the molecular
structural features of these drugs, in
order to elucidate individual perpetrators of each ADR.
For some side effects, we can propose
causative drug-protein interactions,
while for others we find small-molecule structures to be better carriers of
information. We then apply an aggregate scoring method, inspired in those
used in gene set enrichment analysis,
to discover sets of proteins and structural patterns related to each side effect.
Interestingly, our scoring method can
function as an ADR prediction tool
when applied backwards, by testing
the enrichment of the interactor proteins or the structural features of a
query molecule.
1IRB
Barcelona (Barcelona, Spain); 2Institució Catalana de Recerca i Estudis
Avançats - ICREA (Barcelona, Spain)
POSTER 17
A Smad action turnover switch operated by WW domain readers of a
phosphoserine code
Abstract
In pharmacology, it is key to identify
the mechanisms of drug action in order
to understand and infer adverse side
effects. Here, we see side effects as a
phenotypic signal in response to drug
treatment, and we aim at bridging the
gap between such responses and the
molecular basis of drug action.
To achieve so, we navigate both the
Albert Escobedo Pascual
lifeinmotion_booklet.indd 55
IRB Barcelona (Barcelona, Spain)
Abstract
When directed to the nucleus by
TGF‐β or BMP signals, Smad proteins
undergo cyclin-­‐dependent kinase
8/9 (CDK8/9) and Glycogen synthase
2nd IRB Barcelona
PhD Student Symposium
about the recombinase. This is mainly
due to the fact that these large and
multi-domain proteins are difficult to
obtain in soluble and active form.
Our goal is to divide the recombinase
in different domains that can be expressed separately for further purification and structural determination by
X-ray crystallography. We are tackling
the structural and functional characterization of the independent domains
of RAG1 and RAG2 from different
sources, human, mouse, chicken and
zebrafish. We are also working with
RAG-like proteins from sea urchin,
which are the only known RAG1-RAG2
gene pair identified outside the jawed
vertebrate lineage.
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2nd IRB Barcelona International
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kinase-­‐3(GSK3) Phosphorylations that
mediate the binding of YAP And Pin1
For transcriptional action, and of ubiquitin ligases Smurf1 And Nedd4L For
Smad destruction.
Here We demonstrate that there is an
order of events—Smad activation first
and destruction later—and that it is
controlled by a switch in the recognition of Smad phosphoserines by WW
Domains in their binding partners. In
The BMP pathway, Smad1 Phosphorylation by CDK8/9 Creates binding
sites for the WW domains of YAP, And
subsequent phosphorylation by GSK3
Switches off YAP Binding and adds
binding sites for Smurf1 WW domains.
Similarly, In the TGF-­‐β pathway,
Smad3 Phosphorylation by CDK8/9 Creates binding sites for Pin1 and GSK3,
Then adds sites to enhance Nedd4L
binding. Thus, A Smad Phosphoserine
code and a set of WW Domain code
readers provide an efficient solution
to the problem of couplingTGF‐β Signal delivery to turnover of the Smad
Signal transducers.
POSTER 18
Optical manipulation of vesicles and
organelles inside living cells
Arnau Farré, Carol López-Quesada,
Jordi Andilla, Estela Martín-Badosa,
Mario Montes-Usategui
Departament de Física Aplicada i Òptica, Universitat de Barcelona (Barcelona, Spain)
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lifeinmotion_booklet.indd 56
Abstract
Molecular and cellular biology have experienced in parallel a large boost during the past century. The joint advance
of the chemistry of life and the technological development of microscopy
has shed some light into questions
which remained unattainable, contributing with more specificity in the experiments that were carried out. Our
control on the chemical processes that
take place between molecules seems
currently endless.
However, biological phenomena involve a second less known aspect. Most
chemical processes in the cell are induced or catalyzed by mechanical actions, due to the deformation or the
polymerization of a certain protein,
for example. On the other hand, many
mechanical effects are triggered by
chemical reactions. Thus, we could assert that the proper growth of the cell
ultimately relies on two fundamental
pillars. The physical point of view has
been typically overlooked but represents the second actor of the story.
For instance, something as important
as order within the cell is foremost a
physical problem.
The underdevelopment of this part is
mainly due to the difficulty of the experiments. In recent years, several biophysical techniques have opened the
door to these problems. One of them
is optical tweezers. The technique is
based on the idea that light carries
momentum which can be transferred
to matter in order to exert small forces. The momentum from a single photon is too small to generate noticeable
forces, so one needs to use a large
light intensity. In practice, light is con-
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17-18 November 2011
filaments. The study of these proteins
inside living cells, however, has been
rather limited because of its complexity.
Here, we report the manipulation of
single organelles or vesicles inside living NG108 cells. By grabbing the vesicles within these cells we were able
to mechanically interact with these
active motor proteins. This contactless and harmless manipulation may
allow us to explore the presence of
other regulatory proteins involved in
the transport, which have not been
observed in the in vitro experiments
so far. We chose this kind of cells because of its massive transport, easily
observed without fluorescence.
POSTER 19
Nucleoid associated protein from
bacteria that discriminate between
horitzontally transferred genes and
core genes
Carles Fernández de Alba1,2, Carla
Solórzano3, Sonia Paytuby3, Cristina
Madrid3, Antonio Juarez3,4, Jesús
García1, Miquel Pons1,2
1IRB
Barcelona (Barcelona, Spain);
de Química Orgànica,
University of Barcelona (Barcelona,
Spain); 3Department of Microbiology,
University of Barcelona (Barcelona,
Spain); 4Institut de Bioenginyeria de
Catalunya (Barcelona, Spain)
2Departament
Abstract
Proteins of the Hha/YmoA family co-
2nd IRB Barcelona
PhD Student Symposium
centrated into a tiny spot by means
of an objective lens of a microscope.
Arthur Ashkin showed in the late 1980s
that in the focal spot of such lens the
energy density was large enough to
achieve forces in the range of 0.1-100
pN (1 pN = 10-12 N), typical from the
molecular domain. More importantly,
the forces that one could exert were
attractive, so the focal point became
thus stable. The laser could be used
thereby to manipulate samples in the
order of 100 nm – 100 μm. In addition,
Ashkin himself showed some years
later that if the laser wavelength was
in the infrared, the trap could be used
inside living samples without causing
any damage.
This technique is typically implemented in a microscope. The laser is introduced through one of the epi-fluorescence ports and the same objective
that it is used for imaging purposes
focuses the laser onto the sample to
manipulate it. The technique is often
combined with other microscopy techniques, such as fluorescence.
Although optical tweezers have been
used for the study of many different
systems, it has found a special application in the intracellular transport. The
mechanics of proteins such as kinesin,
dynein or myosin has been extensively studied in experiments where
cytoskeletal filaments were cultured
in vitro over microscope slides. By
trapping latex microspheres attached
to the motors, different authors have
been able to determine the main features of molecular motors, such as
the maximum force they can exert
or the way they translocate along the
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regulate with H-NS the expression of
horizontally acquired genes in Enterobacteria. Systematic mutations of the
conserved acidic residues in Hha have
allowed the identification of D48 as an
essential residue for H-NS binding and
the involvement of E25. These results
define the binding interface between
Hha and H-NS that was previously undefined due to major conformational
changes in Hha upon binding. Mutations affecting H-NS binding resulted
in loss of regulation of sensitive genes
in vivo.
POSTER 20
Non - parametric nucleosome positioning with nucleR
2nd IRB Barcelona International
PhD Student Symposium
Oscar Flores1 and Modesto Orozco1,2,3
1IRB-BSC Joint Research Program on
Computational Biology, IRB Barcelona
(Barcelona, Spain); 2Department of
Biochemistry and Molecular Biology,
University of Barcelona (Barcelona,
Spain); 3Instituto Nacional de Bioinformática (Barcelona, Spain)
Abstract
Eukaryotic chromatin is organized in
nucleosomes, a structure with ~147
basepairs (bp) of DNA wrapped around
an octamer of histones (Jiang and Pugh
2009). Nucleosomes affect the packaging and accessibility of DNA, thus
playing a crucial role in defining its
functionality (Jiang and Pugh 2009).
The development of high-throughput techniques, such as tiling arrays
(TA) and next generation sequencing
(NGS), coupled to Microccocal Nuclease (MNase) digestions has enabled the
study of nucleosome positioning at the
entire genome level for several organisms including humans (Jiang and Pugh
2009).
Some clear features emerged from
these studies, such as the presence of
well-positioned nucleosomes and their
depletion in regions surrounding transcription start sites (TSS; Jiang and
Pugh 2009). However, well-positioned
(phased across different cells) nucleosomes coexist with fuzzy (not-phased)
ones outside the TSS. This variability
makes nucleosome positioning complex, requiring therefore the development of algorithms to find the “mostprobable” nucleosomal configuration.
These approaches include, among others, Hidden Markov Models (HMM) (Lee
et al. 2007) and more complex artificial intelligence agents.
These methods are very powerful, but
the intrinsic assumptions and the level
of expertise of the modeler can significantly affect the results.
Here we present a new tool, nucleR
(Flores and Orozco 2011), integrated in
the open source, multiplatform R/Bioconductor framework. The approach
is based on a fast, non-parametric detection of all nucleosome dyads and
scoring of the calls. A good performance is achieved by filtering the noise
using Fast Fourier Transform (FFT). Algorithms presented here are suitable
for most TA and single or paired ended
NGS platforms but also can be applied
in similar peak-finding experiments as
in ChIP-Seq or ChIP-on-Chip.
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17-18 November 2011
Antonina E. Garanina1, Olga D. Belyaeva1, Olga A. Bercovich1, Valerij B.
Timoshin2, Valentina I. Larionova2
1St Petersburg Pavlov State Medical
University (St Petersburg, Russia); 2St
Petersburg Pediatric State Medical
Academy (St Petersburg, Russia)
Abstract
Resistin (RETN) an adipocytokin, predisposing to metabolic syndrome and
cardiovascular pathology. -180CG
RETN gene polymorphism (SNP) may
contribute to the development of
these conditions, but the publications
covering this problem are sparse. We
aimed to determine the frequency of
-180CG RETN gene SNP in patients with
abdominal obesity, and to study an effect of particular genotypes on serum
RETN level, lipid profile and on insulin
sensitivity
328 females, 130 males of 30-55 age
with abdominal obesity were examined. Waist circumference (WC) was
≥ 94 cm in males, ≥80 cm in females.
Control group included 119 children
and adolescents from Saint-Petersburg. Serum RETN, insulin levels and
lipid profiles were estimated by ELISA.
Genotyping was performed by PCRRFLP. Homa-IR was calculated as the
product of fasting insulin (μU/ml) and
glucose values (mmol/l) divided by
22.5.
No differences were revealed between
RETN levels among patients with vari-
lifeinmotion_booklet.indd 59
ous grades of obesity. RETN levels in
obese males and females were not
significantly different. C and G allele
frequency and СС, GG and СG genotype distribution did not differ between obesity and control groups. No
effects of the -180CG SNP were found
on glucose levels, BMI, WC, HOMA-IR
index. LDL levels were higher in -180C
carriers relative to those of CG and GG
genotypes (4,1±0,1 mmol/l, 3,8±0,1
mmol/, respectively; р<0,05). Positive
correlation was found between RETN
levels and BMI.
-180CG genotype distribution and allele frequencies were not different between patients with abdominal obesity
and children and adolescents. -180C
allele carriers demonstrated higher
LDL levels, relative to those of CG and
GG genotypes. RETN levels were positively correlated with BMI.
POSTER 22
Transmembrane Semaphorins during
adult synaptic remodeling and neuroglial interactions
Beatriz G. Armendáriz1, Ana Bribián2,
Fernando de Castro3, Eduardo Soriano1, Ferran Burgaya1
1IRB
Barcelona (Barcelona, Spain);
and Cellular Neurobiotechnology laboratory, Institute for Bioengineering of Catalonia - IBEC (Barcelona, Spain); 3Unidad de Neurología
Experimental, Hospital Nacional de
Parapléjicos (Toledo, Spain)
2Molecular
2nd IRB Barcelona
PhD Student Symposium
POSTER 21
-180 C/G Resistin gene polymorphism
in patients with abdominal obesity
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60
Abstract
Semaphorins constitute a large family
of soluble and transmembrane (TMB)
proteins, mainly involved in axon guidance cues (both repulsive and attractive) during neuronal development.
Nevertheless, some Semas (especially
transmembrane families) continue to
have high levels of expression in the
adult brain. This fact points to a possible role of TMB Semas in plasticity.
A commonly used model of synaptic
remodeling is the kainic acid, inducedstatus epilepticus (KA-SE), in which
the treatment of mice with convulsive
dosis of kainic acid leads to epileptic
seizures and death of some neuronal
populations. Several days later, granular and pyramidal neurites grow and
form new synapses. We have seen by
In Situ Hybridization that some TMB
Semas, such as Sema6B, Sema6C and
Sema4F, change their expression patterns in response to this synaptic remodeling: The expression of these proteins is reduced in hippocampus and
other brain areas immediately after
KA-SE injection, and increases after
some days.
This transient disappearance of repulsive cues could afford for the pathological neosynaptogenesis described
in epilepsy. Our ISH data have been
confirmed by Immunocytochemistry
when specific antibodies were available, and seen that some Semas are
also expressed in glial cells, suggesting
additional functions related to neuronglia interactions in the nervous system
for TMB Semaphorins.
Based on these data, we hypothesized
that Transmembrane Semaphorins
might have an important role in syn-
lifeinmotion_booklet.indd 60
aptic plasticity, since these molecules
are expressed in areas that suffer
synaptic remodeling and alter their
expression after kainate injections.
We are currently investigating the molecular pathways used by TMB Semas
to transduce repulsive signaling.
POSTER 23
Additional factors governing the passage of peptides across the bloodbrain barrier by passive diffusion
B. Guixer1,2, M. Malakoutikhah1,2, M.
Teixidó1,2 and E. Giralt1,2
1IRB
Barcelona (Barcelona, Spain);
de Barcelona (Barcelona,
Spain)
2Universitat
Abstract
One of the main challenges in drug delivery is to overcome the blood-brain
barrier (BBB). Intense research effort
has been devoted to the transport of
pharmaceutical agents into the brain.
After some years working with peptides that cross the BBB by passive
diffusion#2, (where physicochemical
properties of molecules play a crucial
role), we envisaged some characteristics that may be relevant for this
transport and that are usually overlooked. We performed several experiments to address these aspects. For
this purpose, we checked the flexibility, halogenation and stereochemistry
of peptides using a Parallel Artificial
Membrane Permeability Assay (PAMPA). As a case study, we chose Ac- (NMePhe)n-CONH2 (n: 2-4), previously
described to be potential BBB shuttles
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(by passive diffusion transport).
First, we studied flexibility by comparing linear Ac-NMePhe-NMePhe-CONH2
versus its analogous diketopiperazine#.
Diketopiperazine N-MePhe-N-MePhe is
one order of magnitude of permeability higher than its linear Ac-N-MePheN-MePhe-CONH2 counterpart. Next, we
examined the effect of chlorination
on both the lipophilicity and PAMPA
permeability of the peptides (Ac-(NMePhe)n-CONH2 family). Third, we
focused on the stereochemistry of Ac(N-MePhe)4-CONH2 by synthesizing and
testing a library of all diastereomers.
A correlation between homochirality
and permeability was found, as well as
enantiomeric discrimination, although
this parameter was not predictable
between enantiomeric couples.
To sum up, we consider these findings
of special relevance for the optimization of the pharmacokinetic properties
of a hit compound. These overlooked
aspects of peptides may also be critical for the effectiveness of compounds
and should be taken into account as
new tools to achieve molecules with a
greater capacity to overcome the BBB.
POSTER 24
The role of the cerebellum, hypothalamus and GABA during vestibular
compensation following unilateral
labyrinthectomy in rats
L. Hambardzumyan, V. Sarkisian
L. Orbeli Institute of Physiology, NAS
of Armenia (Yerevan, Armenia)
lifeinmotion_booklet.indd 61
Abstract
The crucial role of processes mediated by GABA receptors in neurons of
the lateral vestibular nucleus (LVN) of
Deiters’, as one of the mechanisms
for implementing vestibular compensation (VC) for the recovery of functions after unilateral labyrinthectomy
(UL) was established. It should be
noted that the mechanisms of inhibitory regulation of neuronal activity of
the vestibular system in health and in
the VC occurred with participation of
the cerebellum, while non cerebellar
pathways are essential in restoring of
the stability visual orientation during
movement.
We investigated manifestations of the
post stimulus excitatory and inhibitory activity of the Deiters’ neurons
in response to high-frequency stimulation (HFS) of I-V lobules of the cerebellar cortex. Post stimulus activity
was appeared in the form of tetanic
potentiation (TP) and depression (TD),
followed by post tetanic potentiation
(PTP) and depression (PTD). On-line
registration of the neuronal activity
was based on a program providing for
selection of spikes by amplitude discrimination. For selected comparable groups of neuronal spiking similar
complex averaged PETH (post event
time histogram), as well as cumulative
and frequency histograms were constructed.
In Deiters’ neurons to HFS of the cerebellar anterior cortex were predominantly revealed TD in intact rats, more
pronounced at 100 Hz. On 3d day after
the UL, even to stimulation of the cerebellum by 50 Hz frequency observed
TD in Deiters’ neurons similar to those
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62
in intact rats at 100 Hz, but as a rule
twice better expressed and accompanied by PTD and PTP. At 9th day
after the UL in conjunction with the
administration of proline-rich peptide
(PRP-1) depression in both intact and
damaged sides is not fully reached the
level of norm and was relatively greater on the affected side. The increased
depressive effects at 9th day after the
UL may not be assumed without the
protective effects of PRP-1.
The presence in LVN neurons almost
equally excitatory and depressive effects, realizing by HFS of hypothalamic
paraventricular and supraoptic nuclei
at 3d day after the UL, in contrast to
the cerebellar effect, indicate their
regulatory impact. Moreover, when
HFS of both hypothalamic nuclei TP at
LVN level, in pathology and the norm
is actually was the same, in contrast
to depression, which in the pathology was more pronounced than in the
norm, indicating the greater expression of the hypothalamic depression
compared with cerebellar effects. The
inhibitory protection of LVN neurons
during UL is suspected. In conclusion,
it is possible that in respect of autonomous and motor manifestations of the
multiple functioning of the vestibular
complex, the mentioned hypothalamic
regulation predominantly forms inhibitory output of the cerebellar cortex at
the level of LVN.
In conditions of UL activity of Deiters’ neurons to HFS of cerebellum was
characterized by depression and inhibition with conjucation to tetanic effects also post tetanic manifestations
of activity, indicating the compensatory activation of inhibitory processes
lifeinmotion_booklet.indd 62
in pathology. In some systems during
development of the nervous system
GABA acts as a trophic factor that influences proliferation, migration, differentiation, maturation of synapses
and cell death. Predominantly inhibitory changes in neuronal activity of
Deiter’s nucleus from the cerebellum
confirm the importance of GABA receptors as regulators both in norm and
in pathology.
POSTER 25
Nonlinear dimensionality reduction
for accelerated molecular dynamics
calculations
Behrooz Hashemian, Daniel Millan,
Carlos Braga, Marino Arroyo
Universitat Politecnica de Catalunya
(Barcelona, Spain)
Abstract
Free energy is the central thermodynamic function in biological systems
as it provides the relevant thermodynamic forces that drive structural
processes for biomacromolecules.
Molecular Dynamics (MD) simulations
allow the calculation of these properties in a potentially precise manner. Notwithstanding, extracting such
thermodynamic information from a MD
simulation is often a very challenging
process described by the presence of
a large conguration space with many
metastable basins. A spate of methods
has been proposed to overcome this
diulty either by enhancing the sampling of the phase space, or by focus-
11/7/11 10:55 AM
ing instead on the transition paths between specific conformations. A family
of successful methods relies on a judicious identification of the reaction
coordinates along which the chemical
transformation takes place, and applies an appropriate bias along them
to overcome the energy barriers. The
unambiguous identification of the relevant reaction coordinates for a given
chemical process is often not immediately apparent.
We propose a method that automatically identifies low dimensional nonlinear reaction co-ordinates on the basis
of MD trajectories or other ensembles
characterizing the large deviation flexibility of the molecule. These datadriven (as opposed to insight-driven)
reaction coordinates provide a mechanistic description of the conformational transitions, and are the basis of
accelerated MD.
POSTER 26
Unusual mechanical properties of a
four-helix bundle
Heidarsson PO1, Valpapuram I2, Camilloni C3, Tiana G3, Poulsen FM1, and
Cecconi C4
1University
of Copenhagen (Copenhagen, Denmark); 2University of Modena
and Reggio Emilia (Modena, Italy);
3University of Milano (Milano, Italy);
4CNR-Institute Nanoscience S3 (Modena, Italy)
Abstract
Single-molecule force spectroscopy
has proven to be an effective method
to study protein folding. Using optical
tweezers it is possible to mechanically unfold and refold single protein
molecules through a defined reaction
coordinate, namely the end-to-end
distance. From these experiments
both kinetic and thermodynamic information can be derived as well as distances to the transition state along the
reaction coordinate.
We used optical tweezers and molecular dynamics simulations to study
the (un)folding processes of the fourhelix bundle acyl-CoA binding protein
(ACBP). ACBP unfolds in a two-state
manner that is largely independent
of pulling speed. We determined (un)
folding force and dwell time distributions through force-ramp and forcejump experiments respectively. Both
methods show consistently that single
ACBP molecules are highly compliant
to force, with an unfolding transition state that is extended by ~ 5 nm
from the native state. MD simulations
confirmed the unusual position of the
transition state along the reaction coordinate and showed how the unfolding process starts with the disruption
of tertiary contacts between helix 1
and the rest of the protein, followed
by disruption of helix1’s secondary
structure. Then helix 4 starts loosing
both secondary and tertiary contacts.
In the transition state structure, the
secondary contacts in helix 4 and the
structure of helix 2-helix 3 are still
formed. Remarkably, this structure
closely resembles that of the transi-
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tion state observed in bulk studies.
POSTER 27
The application of gauge symmetry
and soliton theory to folded protein
Shuangwei Hu
2nd IRB Barcelona International
PhD Student Symposium
Laboratoire de Mathématiques et Physique Théorique, Université de Tours
(Tours, France)
Abstract
Protein structure is organized hierarchically from the primary aminoacid
sequence, to regular -helices and
-strands at the secondary level,and
finally to the tertiary compact shape.
In the cell, the newly synthesized
polypeptide chain of a protein undergoes a spontaneous collapse to the
proper tertiary structure, in order to
perform its specific function. After
more than fifty years of scientific inquiry on this classic problem of protein
folding, a solution is slowly rising on
the horizon.
We have recently developed a novel
approach to further investigate protein folding, by means of the general
concepts of gauge invariance, soliton
and universality. The gauge structure
emerges in the Frenet equation which
is utilized to describe the shape of
protein backbone. The gauge invariance principle in quantum field theory
leads us an effective energy functional
for a protein, which had been found to
catch the universal properties of folded proteins in their collapse phase,
characterized by the scaling law of
gyration radius on the tertiary level of
protein structure. We have uncovered
the existence of wide universality on
the secondary level of protein structure, in terms of soliton theory.
The synthesis of the gauge-invariant
energy functional with the discrete
Frenet equation leads to a kink soliton
solution, which is identified as the
helix-loop-helix motif in protein. The
parameters that characterize a particular protein fold are all global on
the secondary level, going beyond all
the details and complexities of amino
acids and their interactions. The mainchain folding of entire proteins is then
built by assembling multiple solitons.
We present the intimate connection
between our model and a generalized
nonlinear Schrödinger equation and
use it to speed up the simulation.
The modeling of a number of biologically active proteins reproduces the
native structure with experimental
accuracy. The success of our approach
works in line with the discovery obtained in template-based prediction
methods and structural classification schemes that there is a limited
number of native state folds, in their
simple modular nature.
However, compared with the weakness
of discretized search space in template-based prediction methods, the
advantage of present soliton model
is to serve for a functional methodology of building the super-secondary
structure in a continuous space, thus
providing fundamental flexibility to
analyse the entire chain of a long protein. We believe that the our work will
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POSTER 28
Role of flotillins in the trafficking and
processing of the Alzheimer Amyloid
Precursor Protein
Bincy Anu John, Antje Banning, Ritva
Tikkanen
Institute of Biochemistry, Medical Faculty, Justus Leibig-University Giessen
(Giessen, Germany)
Abstract
Flotillins are highly conserved, ubiquitous proteins which are associated
with cholesterol enriched membrane
microdomains, known as rafts. The two
members of the flotillin protein family
have been recently recognized to regulate the cellular metabolism of the
Alzheimer Amyloid precursor Protein
(APP). Flotillin-1 was shown to directly
bind to the cytoplasmic tail of APP and
to be associated with the β-secretase
BACE-1, whereas Flotillin-2 downregulation results in altered endocytosis
and reduced amyloidogenic processing of APP. In addition, flotillins accumulate in the cortex of Alzheimer´s
Disease (AD) patients. Amyloidogenic
lifeinmotion_booklet.indd 65
processing has been implicated to take
place in lipid rafts, and the activities of both enzymes responsible for
the amyloidogenic processing of APP,
BACE-1 and γ-secretase, are concentrated in lipid rafts. So far, it has only
been shown that APP directly interacts
with flotillin-1. Our preliminary results
implicate that the APP cytoplasmic tail
directly interacts with both flotillin-1
and flotillin-2. Additionally, the substitution of the Tyrosine residues in the
cytoplasmic domain of APP previously
shown to reside in the canonical transport/endocytic signals and affecting
the cellular trafficking (Y653, Y682,
Y687) resulted in reduced interaction
with flotillins. Our laboratory has recently developed a mouse line genetically ablated for the flotillin-2 gene.
We found that the expression of APP in
the brain of flotillin-2 knockout mice
was reduced as compared to the wild
type siblings. Therefore, these results
support the hypothesis that flotillins
play a significant role in the processing
and/or trafficking of APP.
POSTER 29
Structure-driven development of
antiviral compounds against human
enterovirus
Zuzanna Kaczmarska1,2, Michael Goldflam1, Lionel Costenaro1,2, Ernest Giralt1, Miquel Coll1,2
1IRB
Barcelona (Barcelona, Spain); 2Institute de Biologia Molecular de Barcelona - CSIC (Barcelona, Spain)
2nd IRB Barcelona
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open doors to new ways of the future
research on the protein folding problem. The model we develop forms a
solid basis to start and will be easily
extended to include the amino acid
specific interaction so that it can describe the dynamics of proteins, with
the goal to finally address issues such
as the mechanism of protein folding
and misfolding.
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Abstract
Picornaviridae are among the most
diverse and well known viral families
that include many important pathogens of humans and animals. They
are small, icosahedral ss+RNA viruses,
causing a variety of diseases ranging
from mild to fatal infections. Vaccines
are available for PV, HAV and FMDV viruses, but no effective prophylaxis is
implemented for other picornaviruses.
So far, anti-viral research has focused
on the capsid, whereas inhibitors targeting non-structural proteins (i.e.
proteases, helicases, polymerases)
have remained largely unaddressed.
Our project – within the European consortium Silver – is focused on searching
for novel antiviral compounds against
human enteroviruses (HEV) via fragment screening methods.
The use of STD-NMR as primary screening technique enables an efficient
identification of fragment hits which
can be profiled in a more detailed way
using X-ray crystallography. Co-crystallization/soaking of the most successful
STD hits with the protein target is carried out to obtain their 3D structures.
The structural data provided by NMR
and crystallography techniques allows
identifying the close contacts between
the fragment and the target protein,
helps to infer the requirements underlying the association, and suggests
novel ligands by both fragment-growth
and fragment-linking strategies. Results obtained so far with an enterovirus 3C protease as a target will be
presented.
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POSTER 30
Epigenetic regulation in pre-eclampsia
Asmita Kulkarni1, Vinita Khot1, Preeti
Chavan-Gautam1, Savita Mehendale2,
Hemlata Yadav1, Sadhana Joshi1
1Interactive
Research School for
Health Affairs, Bharati Vidyapeeth
University (Pune, India); 2Bharati
Medical College and Hospital, Bharati
Vidyapeeth University (Pune, India)
Abstract
Epigenetics refers to the study of mitotically (and potentially mieotically)
heritable changes in gene expression
that are not caused by changes in DNA
sequence. Chromatin remodeling (DNA
methylation and Histone modification)
regulates several biological processes
affecting embryonic development.
Epidemiological studies suggest that
adverse influences during fetal life increase the risk of developing disease in
adult life also referred to as ‘developmental origins of health and disease’
(DOHAD). Epigenetic regulation of key
genes involved in adult disease is currently considered to be the underlying
mechanism for fetal programming. Maternal nutrition is an important determinant of one carbon metabolism that
lies at the heart of intrauterine epigenetic programming.
Preeclampsia is a pregnancy complication is the world’s leading cause of
fetal and maternal morbidity and mortality, stems from shallow trophoblast
invasion leading to incomplete vascular remodeling that impairs uteropla-
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systolic (p<0.01) and diastolic (p<0.05)
blood pressure was seen in the term
pre-eclamptic group while there was
no association with birth outcome.
The study for the first time provides
evidence for altered global DNA methylation patterns in pre-eclamptic placentas and its association with blood
pressure. It is possible that increased
homocysteine levels may be related to
increased methylation in pre-eclampsia. Further, studies on larger sample
size may prove helpful in understanding the association between homocysteine and global DNA methylation in
pre-eclamptic women. Further studies
need to examine the epigenetic changes occurring at the gene specific level
for angiogenic and anti-angiogenic
factors in pre-eclampsia and may provide valuable insights into pathways
likely to be epigenetically regulated.
Understanding all these mechanisms
may help in understanding pathways
associated with adverse pregnancy
outcomes.
POSTER 31
Study of the conformational dynamics of prolyl oligopeptidase
Lopez, Abraham
IRB Barcelona (Barcelona, Spain)
Abstract
Prolyl Oligopeptidase (POP) is a big
citosolic protease with a high molecular weight (80 KDa). Its function is to
hydrolyze post-proline bonds in short
peptides. Structurally (1), this mono-
2nd IRB Barcelona
PhD Student Symposium
cental blood flow. It ffects approximately 5-8% of all pregnancies and
increases the risk of preterm birth and
intra uterine growth retardation The
placenta performs the vital functions
of exchange of oxygen, nutrients, antibodies, hormones, and waste products
between the mother and fetus; hence
plays a direct role in fetal programming. Thus altered maternal nutrition
may influence epigenetic patterns in
the placenta thereby affecting birth
outcome.
Our earlier studies in pre-eclamptic
women have shown increased oxidative stress, increased homocysteine
and reduced polyunsaturated fatty
acids levels especially docosahexaenoic acid (DHA) as a one of the factors responsible for pre-eclampsia.
Membrane phospholipids are major
methyl group acceptors and reduced
DHA levels may result in diversion of
methyl groups towards DNA ultimately
resulting in DNA methylation as we
have recently described in one carbon metabolic pathway. Recently, it
has also been shown that angiogenic
factors are involved in blood pressure
modulation in pregnancy.
In the present study we investigated
the global DNA methylation levels in
placentas of pre-eclamptic women
(i.e. women delivering at term and
those delivering preterm) and their
associations with maternal blood pressure and birth outcome. Increased
homocysteine and global DNA methylation levels were seen in the preeclamptic group (term and preterm
PE) as compared to the normotensive
group (p<0.05).A positive association
between global DNA methylation and
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68
meric enzyme is formed by two welldefined main domains: the catalytic
domain, an a-b hydrolase domain, and
the structural domain, constituted by
a seven-bladed b-propeller. The fringe
between these two domains is flexible and allows some conformational
freedom. This probably gives an equilibrium between two main conformers, the open and the closed form.
Different evidences suggest that this
equilibrium may be related with the
enzymatic activity. Moreover, the role
of the inhibitors should displace this
equilibrium towards the closed form,
thus affecting the dynamic properties
of the system.
The elucidation of the biological function of POP has been a parallel work
together with the finding of new POP
inhibitors. This protease shows a high
concentration in the central nervous system tissues, thus suggesting
a certain role in the cognitive processes. First hypothesis were in contradiction with the cytosolic location
of POP. More recent studies point the
POP function in the regulation of the
inositol triphosphate pathway, which
agrees with the intracellular location.
In the other hand, different research
lines suggest a key role of in proteinprotein interactions, independently
from its catalytic activity.
POSTER 32
High-speed tracking of organelles in
living cells: resolving molecular motor stepping events
Carol López-Quesada, Estela Martín
Badosa and Mario Montes-Usategui
lifeinmotion_booklet.indd 68
Universitat de Barcelona (Barcelona,
Spain)
Abstract
Intracellular transport constitutes a
fundamental mechanism in many cellular processes, which is required for
the proper cell functioning and development. Molecular motors are the specialized molecular machines that govern vesicle trafficking in living cells.
In most cases, molecular motors are
constituted by one tail domain that
serves as a linker between the motor
protein and the displaced cargo, and
two domains (heads) or binding sites
which are the responsible for the characteristic motion of molecular motors.
These domains, by converting the energy from the hydrolysis of the ATP, detach and reattach alternatively from
the cytoskeletal filaments that serve
as a track.
Certainly, motor proteins actively displace cellular components in a stepwise mode with a fixed step size, in the
nanometer scale, along the network of
the cytoskeletal filaments. Because of
its importance, molecular motors have
been extensively studied in vitro.
However, in vivo experiments may provide valuable information of the molecular machinery in the real and more
complex environment. In particular,
the translocation of the center of mass
of driven cargos can be used to study
the individual motor dynamics and also
explore how motors work cooperatively in organelle transport.
In this work, we present the high-speed
tracking of motor-driven organelles
which is addressed to detect the step-
11/7/11 10:55 AM
wise motion of different cargos. In living cells, where physiological ATP concentration is high (1-10mM), molecular
motors act at higher speeds and then,
micro-second acquisition rates are
required. This implies the need for
a highly sensitive and fast device to
record the motion of the displaced organelles. We employed a high speed,
back illuminated, electron multiplying
CCD camera (EM-CCD, Ixon-860, Andor Technologies) which combines the
capability of detecting single photons
with the ability to reduce the readout
noise below the detection limit.
POSTER 33
Selection of regulator oligonucleotide aptamers of STAT5 protein involved in leukemias
Claire Loussouarn, Emilie Stephan‐
Queffeulou,
Séverine
Padiolleau‐
Lefèvre, Alain Friboulet, Bérangère
Avalle
University of Technology of Compiegne CNRS (Compiegne Cedex, France)
Abstract
Whether solid cancers or leukemia
are the result of abnormal cell proliferation in healthy tissue this abnormal
proliferation is due to intracellular
protein over expression or protein excessive activation led by an oncogenic
event. Still today, it is absolutely necessary to find new therapeutic molecules targeting specifically this kind
of proteins.
In this context, STAT5 (Signal Transducers and Activators of Transcription)
appears as a particularly useful target
because it is constitutively activated
in many human cancers. In fact, its
involvement in leukemogenesis has
been demonstrated by the use of its
constitutively activated mutated form
in mice. In this case, mice mutants
where affected by precocious leukemias. STAT proteins factors are activated by different ligands belonging
to cytokine, hormone or growth factor
families. STAT proteins control fundamental cellular processes, including
survival, proliferation and differentiation by modulating the expression of
specific target genes. These factors
belong to the JAK/STAT signaling pathway, which is activated by a ligand
dependent activation of a particular
class of receptor associated tyrosine
kinases.
To struggle against tumorigenesis,
JAK/STAT signaling pathway can be
inhibited at different levels. The aim
is to target specifically STAT5 factors.
As STAT5s involve at different steps of
the JAK/STAT pathway, they can be
inhibited at different levels: Whether
when STAT monomers are latent in the
cytoplasm during its phosphorylating
process its dimerization its translocation into the nucleus or also its DNA
binding. Our project consists in an in
vitro selection of single strand oligonucleotides (aptamers) able to inhibit
specifically STAT5 proteins to prevent
cancer cell proliferation. The aim is to
disrupt JAK/STAT pathway while being
the most effective to restore healthy
signal transduction.
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The headlight method of this project
is being the SELEX (systematic evolution of ligand by exponential enrichment) method, which makes possible
the selection of specific 3D structured
ligands with high affinity for target
proteins.
POSTER 34
The role of noise and microRNAstranscription factors “network motifs” in the onset and progression of
rare, complex inherited tumor predisposing disorder: the multiple endocrine neoplasia type 1 as a model
Ettore Luzi, Francesca Marini, Alberto
Falchetti and Maria Luisa Brandi
2nd IRB Barcelona International
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University of Florence (Florence, Italy)
A basic notion of modern system biology is that biological functions are
performed by groups of genes that act
in an synergic and interdependent way
(network). These complex networks
[(Gene Regulatory Network-(GNR)]
can be divided into simpler regulatory patterns called network motifs,
composed by three or four interacting
components that are able to perform
elementary signal processing functions. Network motifs can be divided
into two categories: feedback and
feedforward loops.
We have now evidence that microRNAtranscription factors are recurrent
network motifs that enhance the robustness of gene regulation in mammalian genome by buffering the impact of
noise on gene expression. Many human
genetic diseases result from loss-offunction germline mutations in one of
the two homologous gene loci. These
are often referred to as autosomal
dominant diseases because of frequent
phenotypic dominance of the mutated
allele over the wildtype allele during
transmission along generations.
There are presently two prevailing
theories explaining the autosomal
dominant expression of these diseases.
One explanation originates from the
Knudson two-hit theory of hereditary
cancers, where loss of heterozygosity
or occurrence of somatic mutations
impairs the function of the wild-type
copy. While these somatic second hits
may be sufficient for stable disease
states, it is often difficult to determine
if their occurrence necessarily marks
the initiation of disease progression.
A more direct consequence of a heterozygous genetic background is haploinsufficiency, referring to a lack of sufficient gene function due to reduced
wild-type gene copy number; however,
haploinsufficiency can involve a variety of additional mechanisms, such as
noise in gene expression or protein levels, injury and second hit mutations in
other genes. These stochastic factors
are likely to contribute to the characteristics of variable time of onset and
incomplete penetrance of many autosomal dominant diseases.
MEN 1 is a rare hereditary cancer
syndrome characterized by a variety
of endocrine and nonendocrine neoplasms and lesions. Multiple endocrine
neoplasia type 1 (MEN1) syndrome is
characterized by tumours of the par-
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POSTER 35
Action of the hypothalamic prolinerich peptide and cobra venom during
vestibular compensation following
unilateral labyrinthectomy
L.Manukyan, L., V.Sarkisian
L.Orbeli Institute of Physiology, NAS
of Armenia (Yerevan, Armenia)
Abstract
Still remains quite actual the problem
and uncovered mechanisms of the vestibular compensation (VC), following
unilateral labyrinthectomy (UL). The
hypothalamic proline-rich peptide
(PRP-1) and cobra venom Naja Naja
Oxiana (NOX) action on Deiters’ lateral
vestibular nucleus (LVN) neurons upon
dynamics of recovery after UL was carried out. Early and late tetanic, - post
tetanic potentiation and depression
of neurons to bilateral high frequency
stimulation of hypothalamic supraoptic and paraventricualar nuclei was
studied. The analysis of spike activity by on-line selection and software
package was produced. The complex
averaged peri event time and frequency histograms were constructed.
The increasing of inhibitory and excitatory reactions of Deiters’ neurons at
early stage of VC following PRP-1 and
NOX injection reaching the norm at
late stage was revealed. Moreover, the
shifts of post stimulus activation are
relatively more expressive when high
frequency stimulation by 100Hz.
In histochemical study revealing of
the activity of Са2+-dependent acidic
phosphatase (AP) was carried out. In
UL animals’ data with application of
PRP-1 indicated on of progressing delay of central chromatolysis of Deiters’
neurons, leading to deep neurodegenerative pattern of cellular shade, up
to its total disappearance was shown.
In the whole the ferment activity pre-
2nd IRB Barcelona
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athyroids, of the neuroendocrine cells
of the gastro entero pancreatic tract,
and of the anterior pituitary. MEN1
gene, a tumour suppressor gene, encodes menin protein. Loss of heterozygosity at 11q13 is typical of MEN1
tumours in agreement with the Knudson’s two-hit hypothesis.
In silico analysis with Target Scan, Miranda and Pictar-Vert softwares for the
prediction of miRNA targets indicated
miR-24-1 as capable to bind to the
3’UTR of MEN1 mRNA. We investigated
this possibility by analysis of miR-24-1
expression profiles performed in parathyroid adenomas tissues from MEN1
gene mutation carriers, in their sporadic non-MEN1 counterparts and in
normal tissues. Interestingly, the MEN1
tumorigenesis seems to be under the
control of a “negative feedback loop”
between miR-24-1 and menin protein
that mimicks the second hit of Knudson’s hypothesis and that could buffer
the effect of the stocastic factors that
contribute to the onset and progression of this disease. The functional
significance of this regulatory in MEN1
tumorigenesis, is the basis of for opening future developments of RNA-based
strategies in the in vivo control of tumorigenesis in MEN1 carriers.
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served during 19 days after UL and
PRP-1 exerts on LVN neurons of injured
side more favorable influence. On
intact side PRP-1 lead to the gain of
phosphorylation, which is more typical
for neurons surviving deep stress. Morphological data concerning the NOX
application let to assume that in some
large neurons take place delay of deep
metabolic disorders resulting in total
degeneration.
The morphological picture indicates
that under the NOX action a hyper activation is observed but it may be assumed that abrupt intensification of
ferment activity probably also promote
the purification of affected nerve tissue and tendency to adaptation. Thus,
the protective effect of NOX venom
after UL is obvious. However effects
are quite expressive and often exceed
the norm level which indicates their
abnormal expression. Without diminishing the significance of NOX venom
of exogenous nature, one should convince of natural and successful effect
of PRP-1 – a true endogenous biological
modulator.
POSTER 36
uPAR regulates vascular smooth muscle cells senescence by interfering
with Telomeric Repeat Binding Factor 2 (TRF2) proteasomal degradation
Hodjat M, Durnler I, and Kiyan Y1
Nephrology Department, Vascular Biology Research Group, Hannover Medical School (Hannover, Germany)
Abstract
Urokinase plasminogen activator receptor (uPAR) has been known for
regulation of cell migration, invasion
and proliferation. Recent data have
also shown involvement of uPAR in
cell cycle and senescence regulation
in cancer cells. However, molecular mechanisms of uPAR interference
with these processes are not thoroughly addressed. We studied role of
uPAR in vascular smooth muscle cells
(VSMC) senescence using Doxorubicin
(Dx)-induced senescence model. The
anthracycline Dx is widely used in
chemotherapy against Wide range of
cancers. However, Dx application and
dosage are limited due to injmy to
non-targeted tissues.
Induction of cell senescence by low
doses of Dx might be one of mechanisms of late Dx toxicity. We found
that in human VSMC Dx induces senescent response. Interestingly, uPARsi
prevented Dx-induced senescence.
We further observed that DX­induced
senescence in VSMC is mediated by
ubiquitination and degradation of
Telomeric Repeat Binding Factor 2
(TRF2). TRF2 belongs to the telomerecapping protein-complex shelterin and
prevents activation of factors triggering DNA-damage response (DDR) from
unaappad lalamaras that may laad ra
cellular saaasaanaa.
Al the same time DDR factors (such
as ATM, Chk-2) were activated in specific nuclear foci in uPARsi VSMC. Our
results showed that the activity of
Proteasomal 20s as well as ubiquitination of TRF2 was increased after Dx
treatment; however uPARSi resulted in
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reduction of proteasomal activity. We
concluded that decreased proteasomal
degradation of TRF2 might be caused
by impaired proteasomal activity in
uPARsi cells and uPAR may involve in
regulatory mechanism of the proteasome system during senescence.
POSTER 37
Measuring stall forces of molecular
motors in living cells with optical
tweezers
J. Mas, A. Farré, C. López-Quesada, X.
Fernández, E. Martín-Badosa, M. Montes-Usategui
Facultat de Física, Universitat de Barcelona (Barcelona, Spain)
Abstract
Processive molecular motors are the
main responsibles for the directed
transport of organelles within the
cell cytoplasm. Molecular motors can
be studied from the physical point of
view in order to establish their characteristic velocities and forces. This parameters depend on the motor type,
and the number of collaborating molecular motors carrying simultaneously
any specific organelle within the cell
cytoplasm. One important physical
parameter is the stall force, which is
the maximum pulling force that a motor can hold without detaching from
its microtubule or actin filament. This
parameter might be important for
describing different transport mechanisms, specially in those situations
where different molecular motors
lifeinmotion_booklet.indd 73
might be competing (e.g. possible tugof-war between kinesin and dynein for
moving an organelle along a microtubule).
Stall forces of different molecular
motors are widely studied in the literature, where experimental in vitro
studies use spherical microbeads as artificial cargoes, isolating the molecular motor under controlled conditions.
However, molecular motors naturally
operate in a more complex environment where several local conditions
might significantly contribute to their
actual performance. For example, cytoplasmic dynein motor operation can
be substantially modified by the presence of specific proteins.
Although in vitro experiments might
be progressively complicated, in vivo
sutides (i.e. in a living cell) of molecular motor forces would be necessary for validating the previous in
vitro measurements, and improve our
knowledge on cellular transport mechanisms. However, few studies exist in
living cells due to the historical lack of
a simple reliable technique for measuring physical forces into the cells.
Optical tweezers (OT) consist of a
highly focused laser beam capable of
trapping small objects (typically from
100nm to 10um) and measuring physical forces acting on the trapped object
(from 0.1 to 100pN). Force measurements in OT traditionally require the
calibration of the trap stiffness for
each specific trapped object and medium. The standard calibration method requires a purely viscous medium
and a spherical trapped bead, thus it
cannot be applied in more complex
situations.
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Here we present the direct measurement of light momentum changes in
single-beam optical tweezers as a suitable technique for measuring forces
inside living cells, where few alternatives exist. The valuable advantages
of this method for working in this
conditions are its robustness (system
force calibration remains constant regardless of the trapped object shape,
refractive index or surrounding medium), and its compatibility with advanced microscopy.
We will present our measurements of
stalling events in living cells, where
different a organelles undergoing directed motion are trapped on-the-fly
with a laser, revealing in real time
the pulling force of the molecular
motors that are carrying the trapped
organelle. Since every specific motor type (myosin, kinesin, dynein) has
a characteristic stall force, further
statistical analysis of several traffic
events should let us determine different physical behaviors (stall force,
velocity, direction...) which we could
possibly associate to different molecular motor kinds and different number
of collaborating molecular motors, improving our knowledge on the processes behind the intracellular transport.
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Poster Session B comprises all posters
(abstract numbers) from 38 to 74. You
should install you poster until Friday
18th of November, before 10 am the
latest, and you should remove it same
Friday 18th after the round table.
Please remember that the Friday’s
poster session will be divided in two
sections, one in the morning at 10.35
and the other in the afternoon at
14.10 and that poster authors should
be present on both sessions.
POSTER 38
Overexpression of the Activated
cdc42-associated tyrosine kinase
(Ack1) in neuronal cultures
Maria del Mar Masdeu1,2, Anna La
Torre1,2, Eduardo Soriano1,2 and Jesus
Mariano Ureña1
1Faculty
of Biology, Universitat de Barcelona (Barcelona, Spain); 2IRB Barcelona (Barcelona, Spain)
Abstract
Ack1 (Activated Cdc42-associated tyrosine kinase) is a cytoplasmatic tyrosine kinase highly expressed in the
brain, specially in areas where migration processes take place. Also it has
been observed that this strong expression of Ack1 is present during development and sustained throughout
adulthood. Furthermore, it has been
demonstrated that Ack1 is localized in
dendrites and postsynaptic regions and
that its expression is up-regulated by
an increase in neuronal activity (Ureña
et al, 2005).
Previous works have shown that Ack1
is phosphorylated upon stimuli with
growth factors and recruited to activated receptors. However Ack1 physiological functions are still very much
unknown, specially in the Nervous System. To unravel the functions of Ack1
in neuronal plasticity we have developed a lentiviral system to overexpress
Ack1 in neurons. Infection of primary
neurons with these lentiviruses and
analysis of the morphology of these
neurons show that Ack1 overexpression induces dendritic branching in
both cerebellar granular cells and in
neurons from mouse hippocampus.
Consistent with these data, we are
working on silencing Ack1 by shRNA
lentiviral system to check if silencing this protein there is a decrease
in the complexity of the arborization
patterns of dendrites. Together these
data suggest a role of Ack1 in the process of neurite maturation in neuronal
cells and as key regulator of neuronal
architecture.
POSTER 39
The Eutherian-specific Armcx gene
cluster encodes for mitochondrial
2nd IRB Barcelona
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Posters Session B
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proteins that regulate neuronal trafficking and interacts with the KHC/
Miro/Trak2 complex
Serena Mirra1, Guillermo LópezDoménech1, Román Serrat1, Salvatore D’Aniello2, Ildiko Somorjai2,
Alba Abad3, Nathalia Vitureira1, Elena
García-Arumí4, María Teresa Alonso5,
Macarena Rodriguez-Prados5, Ferran Burgaya1, Antoni Andreu4, Javier
García-Sancho5, Ramón Trullas3, Jordi
García-Fernàndez2 and Eduardo Soriano1
1IRB
Barcelona (Barcelona, Spain);
of Biology, and Institute of
Biomedicine - IBUB, University of Barcelona (Barcelona, Spain); 3Neurobiology Unit, Institut d’Investigacions
Biomèdiques de Barcelona - CSIC,
IDIBAPS (Barcelona, Spain); 4Institut
de Recerca del Hospital Vall D´Hebrón
(Barcelona, Spain); 5Instituto de Biología y Genética Molecular - IBGM,
Universidad de Valladolid & CISC (Valladolid, Spain)
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2Faculty
76
Abstract
Brain function and neural transmission
requires high energy consumption in
a neuronal activity-dependent manner. Appropriate energy production
and supply in neurons is controlled by
complex molecular mechanisms that
regulate mitochondrial trafficking and
distribution, including Kinesin motors
and several GTPases and adaptors such
as Mitofusins, Miro1-2 and Trak2.
Here we report evidence of a new
protein family that localizes to mitochondria and regulates mitochondrial
lifeinmotion_booklet.indd 76
dynamics and trafficking. This family
of proteins is encoded by an array of
armadillo repeat-containing genes located in the X chromosome. The Armcx
cluster is unique to Eutherian mammals and evolved from a single ancestor gene (Armc10) present since the
origin of vertebrates.
Here we show that Armcx genes and
Armc10 transcripts are highly expressed in the developing and adult
nervous system. Furthermore, we
demonstrate that Armcx3 expression
levels regulate mitochondrial trafficking in neurons and that Alex3 interacts
with the Kinesin/Miro/Trak2 complex
in a Ca2+-dependent manner. Our data
provide evidence of a new Eutherianspecific family of mitochondrial proteins that regulates mitochondrial dynamics and trafficking. On the basis of
our findings, we propose that these key
processes are differentially regulated
in the brain of higher vertebrates.
POSTER 40
tRNA modifications as novel modulators of genome structure and gene
expression
Eva Maria Novoa1, Mariana Pavon-Eternod2, Tao Pan2 and Lluís Ribas de Pouplana1,3
1IRB
Barcelona (Barcelona, Spain);
of Chicago (Chicago, USA);
3Catalan Institution for Research and
Advanced Studies - ICREA (Barcelona,
Spain)
2University
11/7/11 10:55 AM
Abstract
The principles that shape genome
structure and determine differences in
genome composition between species
are poorly understood.
Here we analyze the genomes of over
500 species in terms of their tRNA
gene populations and codon usage.
We identify two tRNA wobble base
modifications that contributed to the
extant codon usage biases between
Archaea, Bacteria and Eukarya. These
modifications increase the translation
efficiency of tRNAs and are caused
by kingdom-specific modification enzymes. We show that genome-wide
gene expression levels correlate with
the number of codons affected by
these modifications.
We also numerically and experimentally show that, contrary to prior
observations, genomic codon usage
and tRNA gene frequencies correlate
in Bacteria and Eukarya if these two
modifications are taken into account.
Presence or absence of these modifications explains patterns of gene expression observed in previous studies,
leading to the conclusion that translational efficiency has been an universal
parameter driving codon composition
in the genomes of all extant species.
POSTER 41
From venoms to BBB shuttles
B. Oller1, M. Teixidó1, E. Giralt1,2
1IRB
Barcelona (Barcelona, Spain);
of Barcelona (Barcelona
Spain)
2University
Abstract
The relevance of drug targeting to
the brain stems from the high number
ofpatients suffering from illnesses affecting the central nervous system
(CNS) such as Alzheimer’s and Parkinson’s diseases, depression, epilepsy,
migraine headache and stroke. The
urge to find effective cures is emphasized by the increasing life expectancy
associated with age-related neurodegenerative disorders. However, potentially efficient therapies still face the
challenge of reaching their targets
because they are unable to cross the
Blood-brain barrier (BBB).
Therefore, finding BBB shuttles can
greatly improve the efficacy of such
treatments. Natural products offer a
rich variety of scaffolds and, among
them, venoms have almost been unexploited as a source of new pharmaceuticals. Only a small number of the
known venom components is suspected to reach the brain by crossing the
BBB transcellularly. Yet, it is estimated
that there are several hundred thousands of venom constituents, many
neurotoxic, and only 1500 had been
sequenced by 2006. Hence, studying
the venoms that have been reported
to affect the CNS appears to be a novel
and promising approach to finding new
shuttles. Apamin, a potassium channel blocker from bee (Apis mellifera)
venom, is one of the few described
peptidic neurotoxins that has been
demonstrated to cross the BBB.
Although its toxic effect is clearly an
undesired characteristic, several nontoxic analogues have been described
in the literature. In this study, apamin
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has been synthesized manually using
Fmoc/tBu solid-phase peptide synthesis. After oxidation under air-oxygen
and purification, the correct mass has
been assessed by ESI and MALDI-TOF
MS and NMR experiments TOCSY and
NOESY have verified the proper folding. A PAMPA assay showed that the
permeability by passive diffusion of
apamin is negligible.
Therefore, the BBB permeability asserted in the literature must be due
to active transport, which is currently
being studied in a BBB in vitro cell
based model. Initially, two allegedly
non-toxic analogues were synthesized
using a microwave peptide synthesizer. One of them, had two alanines
in the positions 13 and 14 instead of
the native arginines. The other one
had the same modification and, in addition, the glutamines were removed
to further decrease the toxicity. However, both of the exhibited fairly low
water-solubility.
Therefore, a third analogue with ornithines instead of arginines, which had
been described in the literature, was
synthesized. All of them have been oxidized, purified and their permeability
is being studied in the cellular model.
Apart from the work with apamin, venom from the most dangerous Brazilian
spider Phoneutria nigriventer, that
has been reported to reach the CNS
without BBB inflammation, has been
obtained in order to perform permeability studies.
Some preliminary results have been
achieved, which have revealed that
concentrations up to 300µg of venom/
mL do not damage endothelial cells
but allow little permeation. Further
experiments are being performed to
contrast this data and elucidate the
transported compound/s. In conclusion, venoms could be regarded as a
promising source of new BBB shuttles;
the results obtained until now are
encouraging to some extent and currently further in vitro assays are being
performed to extend the scope of this
study.
POSTER 42
Elastic network model reveals how
oncogenic key residues in the EGFR
extracellular domain control equilibrium dynamics
Laura Orellana1,5 and Modesto Orozco1,2,3,4,5
1IRB
Barcelona (Barcelona, Spain);
Supercomputing Center
(Barcelona, Spain); 3University of
Barcelona (Barcelona, Spain); 4Parc
Científic de Barcelona (Barcelona,
Spain); 5Faculty of Physics, University
of Barcelona (Barcelona , Spain)
2Barcelona
Abstract
The epidermal growth factor receptor
(EGFR) family is the prototype of protein tyrosine kinase receptors, which
are key regulators of cellular growth
and differentiation. In the presence of
EGF and other ligands, the EGFR extracellular domain undergoes a dramatic
conformational change from a closed,
autoinhibited monomer to an active,
open form, which is able to dimer-
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POSTER 43
Tube maturation via function of two
lifeinmotion_booklet.indd 79
genes: Blimp-1 and pri
Ozturk, Arzu1,2; Araujo, Sofia1,2; Casanova, Jordi1,2
1IRB
Barcelona (Barcelona, Spain);
Molecular Biology Institute of
Barcelona (Barcelona, Spain)
2The
Abstract
In the animal kingdom, there are many
examples of tubular organ systems
like the mammalian lungs and vascular system. Drosophila melanogaster
tracheal system is a comparatively
simple system to study tubular organ
development. By investigating the role
of the genes required for proper development of the tracheal system we
aim to understand mechanisms giving
rise to a functional tracheal tree. We
are investigating the role of two genes
functioning in the late embryonic tracheal development: Blimp-1 (B-lymphocyte-inducing maturation protein)
and pri (polished rice – also known as
tarsalless (tal)).
Both genes are expressed in Drosophila tracheal cells during embryonic development. In the absence
of either of them the tracheal tubes
do not expand properly. It was also
shown that the taenidial folds, which
give mechanical strength to tracheal
tubes, are not properly formed in both
Blimp-1 and pri mutants. In order to
understand the exact role of Blimp-1
and pri in tracheal development, the
mutant phenotypes are characterized
using known markers for tracheal development; CBP (chitin binding probe),
vermiform (verm) and piopio (pio).
2nd IRB Barcelona
PhD Student Symposium
ize and selfphosphorylate triggering a
complex signaling cascade.
In the deadly brain tumor glioblastoma
multiforme, there have been found
multiple point missense mutations in
the extracellular sensing domain, associated with an increased activity,
and presumably, a constitutively open
conformation.
Here we explore the near equilibrium
dynamics of the EGFR ectodomain using an elastic network model, which
suggests that the entire structure
behaves like a global spring with an
intrinsic tendency to open, that it is
repressed by strategic contacts. We
developed a simple local perturbation
algorithm, designed to detect regions
critical for the conformational dynamics. The hot spots found are mainly
network hubs at interdomain contact
regions, in many cases involving mutations in both interacting surfaces.
Overall, the results show that although
protein motion is mainly encoded in
the global structure, minimal changes in critical points can have a large
dynamical impact, which can explain
the deleterious effects of many singlepoint pathological mutations. Furthermore, the surprising correlations found
with oncogenic mutations provide a
strong evidence that at least some
proteins explore a highly harmonical
energy landscape near equilibrium,
and that this intrinsic structure encoded dynamics can be regulated by
specific interfacial contacts conserved
during evolution.
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The presence of luminal chitin was
confirmed via CBP, in Blimp-1 and primutants. And the expression analysis of both verm and pio in Blimp-1
and primutants resulted in no difference when compared to the wt. The
insect hormone ecdysone has been
already shown to regulate the expression of Blimp-1 during embryonic development With the aim of revealing
upstream factors controlling pri expression, its expression pattern was
analyzed in the absence of ecdysone
synthesis (shade mutant). And the results of the analysis revealed that in
the absence of ecdysone, pri is not expressed. Thus the expression pattern
of pri is regulated by ecdysone as in
the case of Blimp-1. The similarities
observed in both Blimp-1 and primutants and their regulation of expression by the same molecule, ecdysone,
suggest cooperative functioning of
those genes in the regulation of tube
maturation.
80
POSTER 44
Regulation of cancer cell viability by
p38 MAPK
L. Pereira1,2, I. Dolado1, A. Swat1 and
A.R. Nebreda1,2,3
1CNIO - Spanish National Cancer Research Center (Madrid, Spain); 2IRB
Barcelona (Barcelona, Spain); 3ICREA
- Institució Catalana de Recerca i Estudis Advançats (Barcelona, Spain)
Abstract
p38α MAPK plays an important tumor
lifeinmotion_booklet.indd 80
suppressor role, which is mainly mediated by its pro-apoptotic and antiproliferative activities. A key function
of p38α to inhibit tumor initiation involves the induction of apoptosis upon
detection of high levels of ROS in cells
that are undergoing malignant transformation.
Interestingly, human cancer cell lines
containing high levels of basal ROS
are able to uncouple p38α activation, which results in hyperactivation
of the JNK pathway. We have found
that these cancer cells are sensitized
to apoptotic death induced by chemotherapeutic agents. This hypersensitivity to apoptosis can be reduced by
treatment with either JNK inhibitors
or antioxidants, suggesting the implication of ROS-mediated upregulation of the JNK pathway. Accordingly,
inhibition of p38α in human cancer
cells where p38α is fully functional,
increases intracellular ROS levels and
JNK activity making them more sensitive to apoptosis. Taken together, our
results indicate that impairment of
the p38 MAPK pathway allows ROS accumulation, compromising the viability of cancer cells due to JNK pathway
hyperactivation. Our results also illustrate how the combination of p38α inhibitors with chemotherapeutic agents
could be potentially exploited for cancer therapy.
POSTER 45
GC-dependent selection on stop codons determines their usage in bacterial genomes
Inna S. Povolotskaya1, Fyodor A. Kon-
11/7/11 10:55 AM
drashov1,2, Peter K. Vlasov1
1Centre
celona
Spain)
for Genomic Regulation (BarSpain); 2ICREA (Barcelona,
Abstract
Translation termination is a crucial
step in protein synthesis and is usually initiated by three stop codons,
encoded as TAA, TGA and TAG. These
three stop codons are thought to be
functionally equivalent in the broad
sense of effective translation termination. Additional functions, such as coding for extra amino acids, effects only
a tiny fraction of all codons (Lobanov
2010), and different stop codons can
be interchanged (Vakhrusheva 2011,
Isaacs 2011) or even lost (Barrell 1979,
Yamao 1985, Turanov 2009) without
obvious functional consequences.
Thus, at present there is broad consensus that three stop codons are functionally equivalent and interchanging
stop codon is not expected to have
functional or selective consequences.
In that case substitutions between different stop codon should be neutral,
such that the rate of evolution between stop codon should be broadly
equivalent to the synonymous rate of
evolution and the frequency of the
stop codon usage should be governed
by similar selective and mutational
forces that govern nucleotide usage in
synonymous sites.
The hypothesis of selective equivalence of stop codons has not been
rigorously tested, however, contrary
to the general expectations there are
data that suggest that stop codons may
lifeinmotion_booklet.indd 81
not be entirely synonymous. Firstly,
translation termination efficiency in
some contexts is stop codon dependent (Poole 1995, Pavlov 1998). Second,
TAG and TGA stop codons frequency in
bacterial genomes with different GCcontents is strikingly different (Wong
2008), such that TGA usage increases
with genomic GC-content while TAG is
GC-content independent. We studied
stop codon usage and evolution in bacterial genomes to gain an understanding of whether or not stop codons are
used indiscriminately without any fitness costs. We compared rates of stop
codon evolution to the rate of synonymous evolution and apply a simple
population genetics model formulated
by Bulmer (1991) to the frequency of
stop codon usage and G-content in
bacterial genomes.
This theoretical framework assumes
that two substitutions rarely segregate
at the same time, which fits well to
stop codon evolution given the relative
rarity of stop codons. In this model we
use guanine frequency in two fold synonymous sites instead of GC-content
of the genome as an independent variable. Two rates of mutation G->A and
A->G are an explicit part of the model
of stop codon evolution and exactly
the same mutations are found in G<>A
two-fold synonymous sites, making it
possible to model G-content while using the same mutation rates. We also
consider finesses of every allele to be
different, with the selection S1 shaping
G-content of the genome and selection
S2 acting on TAG.
The observed frequencies of stop codons in bacterial genomes can be explained only if stop codons are not
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selectively equivalent, with weak negative selection acting on TAG codons
for G-content >16% and very weakly
positive selection for this stop codon
when G-content <16%. For biologically
plausible rates of mutations we show
that, in bacteria, TAG stop codon is
universally associated with lower fitness, with TAA being the optimal stop
codon for G-content < 16% while for Gcontent > 16% TGA has a higher fitness
than TAG.
POSTER 46
Phenol metabolisms in yeasts: identification and evolutionary analysis
of genes involved in gentisate and
3-oxoapidate pathways in Candida
parapsilosis
Leszek P. Pryszcz1, Jozef Nosek2, Toni
Gabaldon1
1Centre
2nd IRB Barcelona International
PhD Student Symposium
for Genomic Regulation (Barcelona, Spain); 2Faculty of Natural
Sciences, Comenius University (Bratislava, Slovakia)
82
Abstract
Candida parapsilosis is an emerging
fungal human pathogen. It is able to
degrade various hydroxy derivatives of
benzenes and benzoates through two
pathways: gentisate and 3-oxoapidate.
However, genes involved in these pathways remain unknown. We analyzed
transcriptomes (RNAseq) of Candida
parapsilosis cultivated on three carbon sources: glucose, 3- and 4-hydroxybenzoate.
Among highly up-regulated genes, we
lifeinmotion_booklet.indd 82
identified seven possibly coding for
enzymes that are involved in these
pathways. Recently, some of these
were confirmed. We proposed transcription factors regulating switch of
metabolism from glucose to hydroxy
benzoates.
Moreover, we identified putative membrane transporters required to import
3- and 4-hydroxybenzoate. Subsequently, the evolutionary history of
gentisate and 3-oxoapidate pathways
in yeasts was analyzed. We didn’t find
any evidence of horizontal gene transfer.
Complete pathways were found only
in 5 out of the 25 sequenced Saccharomycotina species. Among these,
Pichia stipitis is known to metabolize
phenols. The remaining four, Candida
parapsilosis and another three Candida species recently sequenced by us,
are emerging human pathogens. This
suggests, gentisate and 3-oxoapidate
pathways may play important role in
pathogenesis.
POSTER 47
Modeling of the regulation of microtubule dynamic instability by row of
associated proteins
Pydiura N.A., Dr. Karpov P.A., Prof.
Blume Ya.B.
Institute of Food Biotechnology and
Genomics NASU (Кyiv, Ukraine)
Abstract
Plant microtubules (MTs) represented
by α- and β-tubulin heterodimers con-
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lifeinmotion_booklet.indd 83
lar modeling and docking, we consequently packed tubulin heterodimers,
constructing 13 associated protofilaments, forming site by site a hollow
cylinder of the microtubule.
By homology and ab-initio modeling we
managed construction of spatial models of A. thaliana homologues, based
on mammalian +end tracking protein
EB1 (MAP1), katanin, kinesin and TOG
domain of MOR1 which were used as
templates. We have compared the refined models with the initial templates
and investigate differences in structural organization and biochemical
properties. Additionally, we have carried out the protein-protein docking
of the both reconstructed A. thaliana
and the mammalian templates with
the models of tubulin complexes.
So, constructed 3-D models gave us
possibility to investigate molecular
mechanisms of the dynamic microtubule instability regulation in plant and
animal cells.
POSTER 48
Distinguishing the folding dynamics
of proteins at single molecule level
Ravishankar Ramanathan and Victor
Muñoz
Centro de Investigaciones Biológicas,
Spanish Research Council (Madrid,
Spain)
Abstract
Proteins are biological nano-machines
that self-assemble into their functional states with particular dynamics de-
2nd IRB Barcelona
PhD Student Symposium
trol the row of fundamental cell processes such as cell division, growth,
transport etc. For the construction of
functional MT structures, the lengths
of individual MTs must be precisely
regulated.
This ensured by MT controlled growth
and shrinkage – the phenomenon of
“dynamic instability”. Being a target of biotechnology, the processes
of plant MT organization are studied
in detail. Plant cells lack centrioles
that organize MTs in the cytoplasm of
animal cells. Instead, animals, cortical
MT nucleation sites in plant cells have
diffuse localization. Although, animal
MT structures differ from plants, the
processes of dynamic instability should
be regulated in the similar manner.
These processes are regulated by MT
associated proteins (MAPs): stabilizing
by MAP65, EB1 and WVD2, and destabilizing by MAP215, katanin and kinesin-13. In present study we compare
molecular processes of MT elongation
and regulation of MT dynamic instability in plant and animal (mammalian)
cells.
Using Modeller9v8 we develop homology models of Arabidopsis thaliana α- / β-tubulin heterodimer and
γ-tubulin. X-ray PDB-structures of Bos
taurus, 1Z2B, 1FFX and 3DU7, were
used as homology modeling templates
for α- and β-tubulins (79%, 80%, and
78% identity respectively), and human
3CB2 for γ-tubulin (71% identity), respectively. These models were evaluated by the ligand-protein docking
with dinitroaniline and phosphoroamide herbicides and were found consistent with our experimental data. With
the help of the in silico macromolecu-
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Life in Motion: Dynamics of Molecules and Systems
84
fined by the nature of their sequences
and the physical conditions. Dynamics of this assembly process called as
folding is differentiated for different
proteins by the thermodynamic barriers that separate their unfolded and
native conformations.
Many small proteins have high barriers
(2-state) while an increasing number
of proteins are being characterized
to be having medium to zero barriers
(1-state or Downhill) for folding. Single molecule Förster Resonance Energy
Transfer (smFRET) is the experimental
technique of choice to probe this conformational dynamics for a given protein at the molecular level.
Here, we develop a methodology for
analysis of smFRET experimental data
to identify and distinguish the underlying conformational fluctuations producing the observed trajectories. We
perform stochastic simulations of protein folding scenarios with different
barriers (high, medium and downhill)
using a one-dimensional free energy
surface model and generate probability distributions of conformational
states. Then we simulate smFRET
trajectories by adding Poissoniannoise of photon arrivals and calibrate
their time-scales to be similar for all
the scenarios. We perform extensive
analysis to quantitatively estimate the
differences between these trajectories and to distinguish the underlying
scenarios.
POSTER 49
Eukaryotic expression of a catalytic
antibody model to study catalytic
antibodies involved in autoimmune
lifeinmotion_booklet.indd 84
pathologies
Raouia Ben Naya, Adeline Guellier,
Bérangère Avalle, Alain Friboulet,
Séverine Padiolleau-Lefèvre
University of Technology of Compiegne-CNRS (Compiegne Cedex, France)
Abstract
In 1946, Pauling postulated that antibodies could present an enzymatic
activity. The first catalytic antibodies (abzymes) were produced in 1986.
From 1989, catalytic antibodies were
found in sera issued from several different health statuses (safe, pathological and auto-immune). Since then
and the breakthrough of antibody
engineering, abzymes appear to be
revolutionary tools to perform studies
at the interface between chemistry,
biochemistry, biology and immunology.
Nevertheless, the metabolic role of
catalytic antibodies remains unclear.
Consequently, the development of
expression systems allowing to come
closer to physiological conditions constitute an important challenge. This
will lead to consider potential therapeutic applications. Our goal is to develop a relevant expression system for
the production of a model catalytic
antibody. Mammalian cells become a
favorable system for the production
of recombinant proteins because they
are able to retain the original protein
folding, assembly and post translational modifications.
Our laboratory has previously elicited several catalytic antibodies by
exploiting idiotypic network, and derived fragments were obtained by
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POSTER 50
Development of skeletal patterning
in the vertebrate limb bud
Jelena Raspopovic
Centre for Genomic Regulation (Barcelona, Spain)
Abstract
Skeletal patterning in the vertebrate
limb bud has long been a model system
to study how undifferentiated cells
obtain their positional information
during development. While positional
information driven by morphogen gradients has been largely accepted to
explain digit patterning and identity,
the new era of conditional mutants
and computational simulations show
that another mechanism could be responsible: a self-organizing Turing type
mechnanism. Nevertheless these kind
of mechanism still lack of molecular
evidence in the limb.
To approach this problem we have first
described, in spatio-temporal resolution, the expression of the earliest
marker of chondrogenesis ,Sox9, using
whole mount in situ hybridization on
mouse embryos and Optical projection
tomography. In parallel we have analyzed the expression pattern of genes
of the Tgfb family, proposed previously
as candidate genes for a self-organizing mechanism of the skeletal patterning. We found a spatial correlation between Sox9 and BMP genes, that can
be explained by a Turing-type model.
Currently we are analyzing Bmp protein distribution and signaling to describe the system in more detail.
POSTER 51
The EAGR box: a Mycoplasma exclusive domain implicated in protein-protein interactions with components of mycoplasmas terminal
organelle
Ratera M., Calisto BM., Martinelli L.,
Broto A., Pinyol J., and Fita I.
2nd IRB Barcelona
PhD Student Symposium
using recombinant DNA technology.
Among them, the IgG 9G4H9 displays a
beta-lactamase activity. The scFv (single chain Fragment variable) derived
from 9G4H9 was cloned. Its catalytic
mechanism was largely studied and
its active site was identified by sitedirected mutagenesis.
Moreover, beta-lactamase is not intrinsically present in mammalian systems.
All this makes 9G4H9 a relevant model
for the development of a new expression system of catalytic antibodies.
We have cloned the scFv 9G4H9 in an
eukaryotic vector and transformed
HEK293T cells. The results suggest that
the scFv 9G4H9 is secreted in the culture medium in quantities comparable
to the periplasmic prokaryotic system
previously described. The functionality of the catalytic antibody is currently tested by ELISA using a suicide
inhibitor and by fluorescence using
the Fluorocillin as substrate. The first
results obtained are promising. This
approach will be applied to the whole
antibody 9G4H9 and to other catalytic
antibodies involved in pathologies.
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2nd IRB Barcelona International
PhD Student Symposium
The Molecular Biology Institute of Barcelona (Barcelona, Spain)
Abstract
Mycoplasma genitalium is a motile,
self-replicating human pathogen that
often presents an asymmetrical pearlike shape due to a characteristic
membrane protrusion composed by a
complex cytoskeleton, the terminal
organelle. This complex structure is
considered to be the scaffold for mycoplasmas adherence to host cells and
gliding motility. To date, up to 12 distinct proteins have been localized into
the terminal organelle and interaction
between them result in the formation
of the supra-molecular structures observed in the mycoplasmas terminal
organelles.
A well conserved domain, Enriched in
Aromatic and Glycine Residues (EAGR)
box, is found in single or multiple copies in many proteins of the terminal
organelle of motile mycoplasmas and
there is no evidence for the presence
of this domain in other prokaryotic or
eukaryotic organisms. Cells bearing a
deletion of the EAGR box in the terminal organelle cytadherence-associated
proteins MG312 and MG386 revealed
that these mutant cells present severe
mobile handicap.
The EAGR box crystal structure solved
to 2.9 Å resolution by the Single-wavelength Anomalous Dispersion (SAD)
method of the M. genitalium MG200
protein revealed that the domain
presents an essentially new fold with
some peculiar features, such as its
plasticity and the presence and organi-
zation of the intra- and inter-subunits
symmetry axes which result in the unbalance of interactions, that suggest a
role for the EAGR box in protein-protein interactions. In order to detect
the expected interactions predicted to
exist between EAGR boxes and other
cytadherence-associated proteins of
the terminal organelle we have characterized possible binary complexes
by NMR.
POSTER 52
Screening for posttranslational regulators of somitogenesis in zebrafish
Sandra Richter and Andrew C. Oates
Max Planck Institute of Molecular Cell
Biology and Genetics (Dresden, Germany)
Abstract
Skeletal muscles, vertebrae and dermis arise during vertebrate embryonic
development from somites. A molecular oscillator termed the segmentation clock is thought to govern the
precise and rhythmic generation of
new somites. The segmentation clock
is comprised of several transcription
and signaling factors whose gene expression oscillates through negative
feedback loops. However, very little
is known about how the oscillations
are generated and how their period is
regulated. Previous work has focused
on the role of transcriptional regulation, but posttranslational regulation also plays a significant role. For
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POSTER 53
In vitro cellular senescence as a tool
to study the effects of aging in macrophages
Rodríguez-Ruiz J, Youssif C, Lloberas J,
Comalada M1 and Celada A
IRB Barcelona (Barcelona, Spain)
Abstract
Macrophages play a key role in the immune response destroying pathogens
directly or releasing mediators which
can activate other cells. However,
macrophages from aged mice present
defects in their functional activities
due to the aging process that alter the
immune response. Cellular senescence
is characterized by a permanent cell
cycle arrest and is produced after continuous replication of a cell. The accumulation of senescent cells seems
to be involved in and is responsible for
the induction of aging. In the present
study we have considered whether
the functions of long-lasting cultures
of macrophages from young mice resembles to the functions found in senescent cells responsible for the aging
patterns previously described.
We used bone-marrow derived macrophages from 6-8 weeks old Balb/c mice
cultured in vitro for 7 (normal culture)
and 21 (senescent culture) days. Macrophages from 21 days cultures were
positive for two different senescence
markers: telomere shortening and high
β-galactosidase activity (determined
by a specific pH-dependent staining).
Macrophage senescence was correlat-
2nd IRB Barcelona
PhD Student Symposium
example, in order to synchronize the
genetic oscillations of neighboring
cells, the Notch receptor is proteolytically cleaved at the plasma membrane
(Huppert et al., 2005). Additionally,
oscillating Hes/Her proteins are destabilized by multiple ubiquitination (Hirata, 2002) and inhibition of ERK phosphorylation blocks somite formation in
chick (Delfini et al., 2005).
We will investigate the role of different kinases and phosphatases during
zebrafish (Danio rerio) somitogenesis
in vivo using an image-based, highthroughput small molecule screen. So
as not to interfere with early embryonic development, zebrafish embryos
will only be treated with kinase and
phosphatase inhibitors during segmentation. Afterwards, the embryos will
be fixed for in-situ hybridization to
visualize somite boundaries and analyzed for possible segmentation defects. The desired outcomes include
changes in somite length or number
or somite boundary defects in an otherwise normally developing embryo.
Interesting candidates will be further
characterized regarding their function
during somitogenesis. The relevant
small molecules should be powerful
and flexible tools for the further study
of somitogenesis.
Ultimately, the goal of this work is
to precisely describe the function of
specific phosphorylation targets in the
segmentation clock and the interplay
with other already known factors during somitogenesis.
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2nd IRB Barcelona International
PhD Student Symposium
ed with a reduced proliferation (measured by 3H-thymidine incorporation) in
response to specific growth factors (MCSF and GM-CSF) due to an increase of
cells in the G1 phase of the cell cycle
(measured by flow cytometry) and in
the p21/p27 expression.
In addition, an increased LPS-induced
pro-inflammatory cytokine expression (tnfα, Il-1β) and a reduced IA/
IE expression induced by IFN-g were
observed in senescent macrophages.
Finally, an increase in ROS production
(measured by flow cytometry) and a
reduction of STAT-5 phosphorylation
induced by GM-CSF was also observed
in senescent macrophages, which correlate with that observed in macrophages from aged mice as we previously demonstrated. Gene and protein
expression analysis were evaluated
by quantitative-PCR and western blot
or flow cytometry, respectively. Our
results demonstrate that cellular senescence induced in long-lasting macrophage cultures may be a good tool
to evaluate the altered macrophage
functions during the aging process.
POSTER 54
Identification of huntingtin aggregation modifiers
Eugenia Rojas-Puente, Angeli Möller
and Erich Wanker
Max Delbrueck Center for Molecular
Medicine - MDC (Berlin, Germany)
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Abstract
Huntingtinton’s disease is an autosomal dominant inherited disease
that leads to neurodegeneration. Its
causative gene, huntingtin, encodes
a protein containing between 6-35
glutamine residues in its N-terminal
domain. This protein becomes pathogenic upon expansion of the glutamine
rich tract (≥36 residues), aggregating
in cells, leading to synaptic and neuronal dysfunction and ultimately disease. In this project, I investigated 28
proteins, which were characterized as
potential modifiers of huntingtin (HTT)
aggregation. This prediction was based
on earlier yeast 2 hybrid screening,
siRNA experiments and computational
analysis.
The ability of the 28 candidate proteins to enhance or suppress HTT aggregation was tested in FRET and BiFC
assays, in which fluorescent aggregates
are formed following overexpression
of the mutant HTT. The study identified 8 consistent modifiers of mutant
HTT aggregation; 7 suppressors and 1
enhancer. In general the proteins were
involved in transcription regulation,
RNA splicing and the ubiquitin-proteasome system, processes well known to
regulate protein aggregation.
POSTER 55
Reelin delays amyloid aggregation
dynamics and rescue Alzheimer’s
disease mice from cognitive impairments
Rossi D, Pujadas L, Carulla N, Teixeira
CM, Andrés R, Parcerisas A, Giralt E,
Soriano E
11/7/11 10:55 AM
17-18 November 2011
Reelin is an extracellular matrix glycoprotein essential for neurodevelopment and controlling neurogenesis,
dendritic morphology and synaptic
plasticity in adult brain. Recent studies suggest a possible involvement of
Reelin into Alzheimer’s disease (AD)
pathology. To unravel a possible causal
or protective role for Reelin into AD,
we first performed in vitro assays of
amyloid aggregation, showing that
Reelin makes part of Aβ42 fibrils and
induces a dose-dependent delay in the
amyloid aggregation dynamics.
We then generated Reelin overexpressing mice in an AD background (TgRln/
J20) and analysed amyloid plaque load
at different ages, finding that Reelin
overexpression decreases the plaque
amount in hippocampus and cortex.
Finally, behavioural tests show that
Reelin overexpression rescues J20 AD
mice from cognitive impairments, as
asseessed by Novel Object Recognition
test. All together these data suggest a
possible neuroprotective role for Reelin into AD.
POSTER 56
Tramtrack is genetically upstream of
genes controlling tracheal tube size
in Drosophila
Barbara Rotstein1, David Molnar2, Boris
Adryan2, Marta Llimargas1
1Institut de Biologia Molecular de
Barcelona - CSIC (Barcelona, Spain);
2Cambridge Systems Biology Centre &
Department of Genetics, University of
Cambridge (Cambridge, UK)
Abstract
The Drosophila transcription factor
Tramtrack (Ttk) is involved in a wide
range of developmental decisions,
ranging from early embryonic patterning to differentiation processes in
organogenesis. Given the wide spectrum of functions and pleiotropic effects that hinder a comprehensive
characterisation, many of the tissue
specific functions of this transcription
factor are only poorly understood. We
recently discovered multiple roles of
Ttk in the development of the tracheal
system on the morphogenetic level.
Here, we sought to identify some of the
underlying genetic components that
are responsible for the tracheal phenotypes of Ttk mutants. We therefore
profiled gene expression changes after
Ttk loss- and gain-of-function in whole
embryos and cell populations enriched
for tracheal cells. The analysis of the
transcriptomes revealed widespread
changes in gene expression.
Interestingly, one of the most prominent gene classes that showed significant opposing responses to loss- and
gain-of-function was annotated with
functions in chitin metabolism, along
with additional genes that are linked
to cellular responses, which are impaired in ttk mutants. The expression
changes of these genes were validated by quantitative real-time PCR and
further functional analysis of these
candidate genes and other genes also
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expected to control tracheal tube size
revealed at least a partial explanation
of Ttk’s role in tube size regulation.
The computational analysis of our
tissue-specific gene expression data
highlighted the sensitivity of the approach and revealed an interesting set
of novel putatively tracheal genes.
POSTER 57
Protein-Protein and RNA-Protein
complexes by solution NMR
Constanze Schelhorn1, Lidia Ruiz1 and
Maria J. Macias1,2
1IRB
2nd IRB Barcelona International
PhD Student Symposium
Barcelona (Barcelona, Spain); 2Institució Catalana de Recerca i Estudis
Avançats - ICREA (Barcelona, Spain)
Abstract
Smad ubiquitination regulatory factor 2 (Smurf2) is an ubiquitin ligase
that participates in degradation of
TGF-β receptors. In addition to a C2
and a HECT domain, Smurf proteins
contain multiple WW domains, which
are named for two highly conserved
trytophan residues. The consistent
secondary structure of WW-domains
is a single three-stranded β-sheet.
One conserved tryptophan lies on one
side of the sheet in the hydrophobic
core and is required for domain stability, the second tryptophan lies on the
opposite side of the sheet in a targetbinding pocket.
Generally WW-domains recognize a
PPXY sequence known as PY-motif.
In human Smurf2 WW1 domain a mu-
tation of a conserved Tyrosine to a
Glutamine, which forms part of the
binding pocket, occurs. Upon this mutation binding of the conserved PY-motif regions in Smads is inhibited. One
specific goal is to spot a target motif
for the WW1 domain, which is likely to
be a proline-rich sequence.
The RNA recognition motif (RRM) is the
most abundant RNA-binding motif in
higher vertebrates. RRMs are reported
to recognize not only RNA/DNA but to
interact also with further proteins.
Here we focus on the RRMs of the Cytoplasmic Polyadenylation Element
Binding (CPEB) proteins. This family
of proteins mediates many biological
processes such as germ-cell development, synaptic plasticity and cellular
senescence.
Furthermore, CPEB regulates polyadenylation-induced translational control.
The CPEB family is constituted by four
members, which can form a varying
number of isoforms due to alternative
splicing. Independently of the single
CPEB protein, isoform or organism, all
proteins of the CPEB family are characterized by the presence of two RNA
Recognition Motifs (RRM) located in
the carboxy terminal regionand followed by a highly conserved zinc finger
domain. The binding platform of CPEB
Proteins is the Cytoplasmic Polyadenylation Element, a U-rich sequence in
the 3’-region of mRNA. It was reported
that only the tandem of the two RRM
domains is able to show binding to the
CPE.
We plan to perform a screening of
small molecules as potential binders
of the RRM domains of CPEB and test
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POSTER 58
Migration of mesodermal cells depends on activity of the serum response factor
Benedikt Schwartz
Max-Planck Institutue for Molecular
Genetics (Berlin, Germany)
Abstract
With the onset of gastrulation at day
6.5 of mouse embryogenesis, epiblast
cells in the posterior tip of the embryo
ingress through the primitive streak
(PS), undergo an epithelial to mesenchymal transition (EMT), and migrate
away to differentiate into mesodermal cells. During the following days of
embryonic development, a continuous
generation of new mesodermal cells
is essential for the extension of the
anterior-posterior body axis. Mouse
mutants deficient for the transcription
factor Srf (Serum Response Factor)
have a severe gastrulation defect and
do not form any detectable mesodermal cells (S. Arsenian et al., 1998).
Srf is a versatile factor that can regulate various cellular processes such
lifeinmotion_booklet.indd 91
as differentiation, proliferation and
migration. However, the role of Srf
during mesoderm generation and axis
extension is unknown. For analysis, we
generated conditional knock out (KO)
embryos that specifically lack Srf in
the PS and nascent mesoderm.
These embryos display an axis truncation, revealing that Srf is essential for
axis extension. Differential gene expression profiles of caudal ends from
conditional Srf KO embryos as well as
ChIP-seq analysis revealed that the
majority of direct Srf target genes in
the PS and nascent mesoderm encode
proteins that are associated with cell
migration. Ex vivo migration assays
and immunofluorescence staining of
mutant embryos confirmed a cell migration defect in Srf deficient mesoderm, confirming recent findings that
link cell migration to axis extension.
POSTER 59
Nek9 is a Plk1-activated kinase that
controls prophase centrosome separation through Nek6/7 and the mitotic kinesin Eg5
M Teresa Bertran1, Sara Sdelci1, Laura Regué1, Joseph Avruch2, Carme
Caelles1,3 and Joan Roig1
1IRB
BArcelona (Barcelona, Spain);
General Hospital and
Department of Medicine, Harvard
Medical School (Boston, USA); 3Department of Biochemistry and Molecular Biology - Pharmacy, Universitat de
Barcelona (Barcelona, Spain)
2Massachusetts
2nd IRB Barcelona
PhD Student Symposium
their ability to modulate and to inhibit
RNA-protein interactions in vitro by
applying NMR based titrations. A special focus will be devoted to studying
the impact of the different protein
isoforms on target recognition. The
most promising ligand candidates will
be selected for the structural characterization in complex with either RNA
or CPEB proteins.
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PhD Student Symposium
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92
Abstract
The NIMA-family protein kinases Nek9
and the highly similar Nek6 and Nek7
form a signaling module activated during mitosis and required for normal
mitotic spindle assembly. The module
upstream kinase, Nek9 (also known as
Nercc1), is activated at centrosomes
during prophase through a mechanism that involves phosphorylation,
although the molecular details of this
have remained elusive. We have identified the Polo-family kinase Plk1 as
Nek9 direct activator and propose a
multi-step activation mechanism for
Nek9 that involves phosphorylation by
CDK1 resulting in Plk1 binding to Nek9
followed by Nek9 phosphorylation and
activation by Plk1.
Our results provide a basis to understand the temporal and spatial pattern
of Nek9 activation, integrate signaling
through the NIMA-family with that of
CDK1 and Plk1, and suggest new ways
through which these two major mitotic
kinases could control the organization
and function of the mitotic machinery. In this regard we show how downstream of CDK1 and Plk1, Nek9, Nek6
and Nek7 are crucial for centrosome
separation during prophase as well as
how this process is controlled by Plk1
through the activation of Nek9 and ultimately the phosphorylation of the mitotic kinesin Eg5 at Ser1033, a Nek6/7
site that together with the CDK1 site
Thr926 is necessary for the accumulation of Eg5 at centrosomes and subsequent centrosome separation. Failure
to phosphorylate Eg5[Ser1033] results
in longer prometaphases showing the
importance of prophase centrosome
separation for a timely mitosis.
lifeinmotion_booklet.indd 92
POSTER 60
CPEB at the mitotic spindle: regulating localized translation to ensure
proper cell division and chromosome
segregation
Carolina Segura Morales
IRB Barcelona (Barcelona, Spain)
Abstract
Generation of asymmetry, such as
body-plan determination in the embryo or synaptic plasticity in neurons, requires the synthesis of specific proteins only at particular times
and places. In order to preclude the
ectopic expression of these proteins,
their mRNAs need to be transported
in a repressed state until they reach
their final destination. For this, those
transcripts bear specific elements,
usually in their 3’UTR, which are recognized by RNA binding proteins that
recruit the machinery responsible for
the localization, repression or activation of these RNAs in the correct time
and space.
CPEB (cytoplasmic polyadenylation element binding protein) is able to bind
RNAs containing the cytoplasmic polyadenylation element (CPE). This protein
has a dual function in the translational
regulation of CPE containing-maternal
RNAs driving meiotic progression in
Xenopus oocytes. First, CPEB maintains the RNAs in a repressed state
by recruiting a “repression complex”
that will shorten the poly(A) tail and
preclude the association with the ribosome. This CPEB-mediated complex
associates with microtubules in the
11/7/11 10:55 AM
17-18 November 2011
POSTER 61
Structural reorganizations within
amyloid-beta protein aggregation
lifeinmotion_booklet.indd 93
Bernat Serra1, Ernest Giralt1,2, Natàlia
Carulla1
1IRB
Barcelona (Barcelona, Spain);
de Química Orgànica,
Universitat de Barcelona (Barcelona,
Spain)
2Department
Abstract
Aggregation of the amyloid-beta protein (Aβ) is linked to the aetiology of
Alzheimer’s disease (AD). Monomeric
Aβ protein molecules self-aggregate
into transient oligomeric species that
further associate to form the characteristic amyloid fibrils. Among the
different aggregation states, the species that best correlate with the neurodegeneration observed in AD are
oligomeric intermediates. Due to its
heterogeneous and dynamic nature,
these species have been difficult to
characterize with common biophysical
techniques. In order to gain structural
information on these aggregates we
use a pulse- labeled hydrogen/deuterium exchange strategy.
This experiment is based on the solvent accessibility of hydrogen amides.
With this approach we are able to
identify the most protected regions in
a given aggregation state, thus yielding information related to the degree
of structure of the different Aβ aggregates. These experiments provide
relevant structural information on the
species populated during fibril formation and are important to identify validated therapeutic targets for AD.
2nd IRB Barcelona
PhD Student Symposium
animal pole of the oocyte and later in
the meiotic spindle. Then, after progesterone stimulation, CPEB is phosphorylated by Aurora A, which induces
the replacement of the “repression
complex” by the “activation complex” promoting the elongation of the
poly(A) tail and translation.
We have recently showed that CPEB is
also involved in the progression of the
cell cycle of somatic cells, as the depletion of CPEB reduces cell proliferation by affecting the polyadenylation
state of hundreds of mRNAs during the
cell cycle.
Here we show that CPEB is indeed
controlling the translation of CPE-containing mRNAs at the mitotic spindle,
recruiting the repression and the activation complexes. Moreover, depletion
of CPEB leads to mitotic abnormalities
and errors in chromosome segregation
in differentiated cells. To obtain a genome wide picture of the mRNAs whose
CPEB-mediated local translation at the
spindle mediate the assembly and stabilization of the mitotic spindle, we
have obtained a highly pure fraction
of spindles and sequenced the associated transcripts to, then, identify the
CPE-containing 3’ UTRs. Altogether
our results suggest that, indeed, local
translation at the spindle is required
for correct microtubule dynamics and
chromosome segregation. A possible
function for CPEB generating protein
synthesis gradients within the spindle
will be discussed.
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POSTER 62
Aß aggregation modulated by biomimetic membrane particles
Montserrat Serra Batiste1, Ernest Giralt1,2, Natàlia Carulla1
1IRB
Barcelona (Barcelona, Spain);
de Química Orgànica,
Universitat de Barcelona (Barcelona,
Spain)
2nd IRB Barcelona International
PhD Student Symposium
2Department
Abstract
Alzheimer Disease (AD) is a senile dementia that has been associated with
misfolding and aggregation of the
amyloid-ß (Aß) protein. Monomeric Aß
molecules aggregate into oligomeric
species that grow and reorganize into
characteristic amyloid fibrils. Recently, it has been postulated that the
key toxic moiety of AD are soluble Aß
oligomers (Walsh 2002, Nature). Thus,
these species have become the target
of most scientists studying AD at the
molecular level.
Since most of the Aß oligomer toxicity processes occur at the membrane
level, we are testing the hypothesis
that biomimetic membrane particles
can be used to stabilize Aß oligomers.
Our approach comprises the use of
Aß40 and Aß42 proteins and the detergent dodecylphosphocholine, DPC, as
a membrane mimetic.
The strategy that we are following
consists on studying these proteins
at two different Aß to micelle ratios.
A first one, at low micelle concentration, where more than one Aß protein
molecule is forced to share a micelle,
94
lifeinmotion_booklet.indd 94
increasing the probability of protein
oligomerization. A second one, at high
micelle concentration, where stoichiometrically one Aß protein molecule
can interact with a micelle, favoring
the stabilization of Aß as monomeric
species. We are studying these systems
using nuclear magnetic resonance
(NMR) and circular dichroism (CD).
The structural information obtained
from these studies will contribute to
structurally characterize an important
target in AD, the Aß oligomers as well
as to obtain insights into the molecular
mechanisms of Aß oligomer formation.
POSTER 63
DNA repair and prostate cancer progression: a putative new role for NBN
gene
Joana R. Silva1,4, Ana Teixeira1,5, Francisco P. Lobo2, Rui M. Medeiros1,3,4,5
1Portuguese Institute of OncologyPorto (Porto; Portugal); 2Portuguese
Institute of Oncology (Porto, Portugal); 3CEBIMED, Faculty of Health Sciences of Fernando Pessoa University
(Porto, Portugal); 4LPCC, Research Department-Portuguese League Against
Cancer - NRNorte (Porto,Portugal);
5ICBAS, Abel Salazar Institute for the
Biomedical Sciences, University of
Porto (Porto, Portugal)
Abstract
DNA repair defects may increase genomic instability and result in tumor
development. However, it remains
unclear the function of NBN, a gene
11/7/11 10:55 AM
17-18 November 2011
POSTER 64
Critical assessment of paramagnetic
relaxation enhancement for ensemble calculation of disordered states
Jordi Silvestre-Ryan, Santi EstebanMartín, and Xavier Salvatella
IRB Barcelona (Barcelona, Spain)
Abstract
In NMR spectroscopy, paramagnetic
relaxation enhancement (PRE) can be
used to probe transiently formed longrange contacts in macromolecular
structures. This is particularly powerful for the structural characterization
of intrinsically disordered and unfolded proteins. Here we assess the structural information encoded in PRE data,
and its use in describing ensemble representations of disordered states.
We seek to determine both the optimal number of PRE labels for structural determination as well as their capabilities in reproducing contact regions
and contact populations. We first constructed several ensembles of a model
protein with a variety of imposed tertiary contacts, and then attempted to
reproduce the ensembles through simulations restrained by theoretical PRE
intensities. Almost universally, the PRE
data is able to recapture the contacts
of the synthetic ensembles provided
that one PRE label is placed every 1020 residues.
However, the degeneracy inherent in
ensemble-averaged PRE data, compounded by the radius to the minus
sixth dependency, makes it difficult to
distinguish between contact distances
and populations. As a consequence,
while the contacts themselves remain
visible, their populations are largely
determined by the size of the simulated ensemble.
2nd IRB Barcelona
PhD Student Symposium
involved in this defense mechanism.
In this study, we aimed to explore the
role of this gene in prostate cancer
progression, by studying its mRNA expression and analyzing a putative genetic polymorphism.
NBN
8360G>C
polymorphism
(rs1805794) was characterized in a
series of 425 patients diagnosed with
prostate cancer, using PCR-RFLP. The
NBN mRNA expression was further
evaluated by Real-Time PCR
We found that individuals carriers of
NBN 8360GG genotype present an almost two fold increased risk for advanced prostate disease (OR = 1,90; IC
= 1,29 – 2,80; p = 0,001). In addition,
this was confirmed by age adjusted logistic regression analysis (OR = 1,87; IC
= 1,26 – 2,79; p = 0,002 for GG genotype carriers). Furthermore, high tumor grade (OR = 3,02; IC = 2,32 – 3,92;
p = < 0,001) and high serum PSA (OR
= 6,48; IC = 4,48 – 9,38; p = < 0,001)
were consistently associated to advanced disease. Regarding NBN mRNA
expression, we did not found any association with the different outcomes
nor genotypes (p = 0,926; p = 0,894,
respectively).
Our results suggest for the first time
that NBN 8360GG genotype appears
to be associated with a higher risk for
advanced prostate cancer, thus suggesting a possible new role for NBN in
prostate cancer progression.
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POSTER 65
The knockdown of the maternal glucocorticoid receptor mRNA affects
transcript contents and development
in zebrafish embryos
Tatjana Skobo
2nd IRB Barcelona International
PhD Student Symposium
University of Padova (Padova, Italy)
96
Abstract
My PhD project is an extension and
consolidation of a previous research in
our lab, showing a double epigenetic
influence by two maternal factors on
zebrafish development. The first is
the ooplasmic content of the stress
hormone cortisol taken up from the
maternal circulation and deposited in
the lipophilic matrix of the yolk. The
second is its cognate receptor, named
glucocorticoid receptor (gr), whose
transcript is the most abundant among
maternal transcripts for steroid hormones in ovulated oocytes. Morpholino
knockdown of maternal gr mRNA was
associated with severe cranio-facial
and caudal malformations in embryos
and larvae, while 150 highly expressed
transcripts were up- or down regulated
at 5 hpf, as determinate by pangenomic expression microarray.
The aim of my study is to monitor by
semi-quantitative RT-PCR and/or qRTPCR and whole mount in situ hybridization a number of maternal and/or
zygotic transcripts targeted by gr at
different developmental stages under three experimental conditions,
namely egg enrichment with cortisol,
morpholino gr knockdown and gr gain
of function with zebrafish full length gr
lifeinmotion_booklet.indd 96
mRNA. Special attention will be paid
to the expression of genes controlling
the formation and streaming migration
of neural crest cells to check whether
the observed cranio-facial deformities
are due to their sensitivity to gr deficiency.
POSTER 66
Investigation of ribosomal protein S6
kinase interaction with novel partner
TDRD7
Oleksandr Skorokhod1, Ivan Nemazanyy, Ganna Panasyuk, Valeriy Filonenko
and Ivan Gout2
1Institute of Molecular Biology and Genetics (Kyiv, Ukraine); 2University College London (London, UK)
Abstract
Ribosomal protein S6 kinases (S6Ks)
belongs to the AGC family of Ser/
Thr kinases and are implicated in the
regulation of cell size, growth and metabolism. Mammalian cells express two
forms of the kinase, S6K1 and S6K2
(known as S6Kα and S6Kβ, respectively). Ribosomal S6 kinase 1 (S6K1)
is an important player in cellular PI3K/
mTOR signalling network involved in
proteins translation and cytosceleton
rearangements.
Our recent yeast two hybrid screening
using S6K1 as bait allowed us to identify a novel binding partner of S6K1–
TDRD7 (Trap)[1]. TDRD7 is a scffold
protein with unknown function, previously identified in complexes with
proteins which regulate cytoskeleton
11/7/11 10:55 AM
17-18 November 2011
POSTER 67
Effects of insulin-like growth factor I
abuse on human lymphocytes
lifeinmotion_booklet.indd 97
Spaziani S1,2, Imperlini E3,4, Mancini A1,
Martone D1, Orrù S1,2,3 and Buono P1,3,4
1DISIST Università di Napoli (Naples,
Italy); 2CEINGE Biotecnologie avanzate
s.c.a.r.l. (Naples, Italy); 3Fondazione
SDN, IRCCS (Naples, Italy); 4DBBM,
Università di Napoli “Federico II” (Naples, Italy)
Abstract
Insulin-like growth factor-I (IGF-I) is a
peptide hormone produced by the liver
in response to growth hormone action.
The main effect of IGF-I is an increase
in protein and DNA synthesis, besides
it stimulates the cell proliferation of
muscle tissue and the production of
red blood cells, hence an increased
resistance. IGF-I is included in the
World Anti-Doping Agency (WADA) list
of banned drugs for athletes. Tests on
healthy volunteers fail to detect clinically significant differences between
treatment groups and controls, due
to amount of hormone used, certainly
lower than the doses taken by abusers.
In vitro IGF-I stimulates proliferation
of transformed neoplastic cell clones
and the growth of pre-existing tumor
tissues. Moreover, a positive correlation was observed between circulating
IGF-I concentrations and the incidence
of prostate and breast cancers.
Although data are available about
IGF-I signal transduction, relatively
little is known about how IGF-I abuse
changes protein expression. Previously, we studied the androgen receptor
signaling induced by supraphysiological doses of dihydrotestosterone on
lymphocytes by means of differential
2nd IRB Barcelona
PhD Student Symposium
dynamics, mRNA transport and protein
translation apparatus.
To confirm and investigate the role of
S6K1-TDRD7 interaction we conduct
more detailed studies of this proteins
interplay. The bioinformational analysis of TDRD7 primary structure allowed
us to determine several functional
domains within TDRD7 and possible
S6K1 sites of phosphorylation on this
protein. At the next step six different fragments of TDRD7 were cloned,
ovexpresed and purified from bacteria cells. These recombinant proteins
were used in a set of pull-down experiments with full-length S6K1. Direct
interaction between C-terminal tudor
domain of TDRD7 and S6K1 has been
shown. This interaction were further
confirmed in Far-Western blot on recombinant S6K1 and TDRD7 fragments.
Also, purified domains of TDRD7 were
used as antigens for mouse immunizations and generation of monoclonal
antibodies[2]. The generated antibodies were used for studying S6K1/TDRD7
interaction in mammalian cells in vivo.
We succeed to detect an interraction
between TDRD7 and S6K1, but not with
S6K2 in reaction of co-immunoprecipitation in HEK293 and rat brain lysates.
Also, we have found that S6K1 phosphorylate 3 from 6 fragments of TDRD7
in the in vitro kinase reaction, which
indicate that S6K1-TDRD7 interaction
has some physiological role, which
need further investigation.
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Life in Motion: Dynamics of Molecules and Systems
proteomic analysis; so the treatment
altered cell motility and exerted a
prosurvival effect.2 Now, in order to
highlight cellular pathways sensitive to
supraphysiological treatment of IGF-1,
we investigated the protein expression
profile of human primary lymphocytes
by using the 2D DIGE technology. In response to IGF stimulation, 28 protein
spots increased at least two-fold and
12 protein spots decreased at least
two-fold in the treated cells compared
to un-stimulated cells. IGF-I sensitive-proteins, identified using mass
spectrometry procedures coupled to
bioinformatic tools, will be further
investigated as health risk factors for
IGF-I abusers.
POSTER 68
Rational design of inhibitors of APE-1
2nd IRB Barcelona International
PhD Student Symposium
Maria Tintoré1, Sandrea M. Francis2,
Ruben Gil3, Antonio Morreale3, Angel
R. Ortiz3, Federico M. Ruiz4 and Carme
Fábrega1
98
1IRB
Barcelona (Barcelona, Spain);
of Biomedicine of Valencia
- IBV-CSIC (Valencia, Spain); 3Bioinformatics Unit, CBMSO - CSIC-UAM (Madrid, Spain); 4Chemical and Physical
Biology CIB - CSIC (Madrid, Spain)
2Institute
Abstract
Chemotherapy still constitutes the
major pharmacologic approach against
cancer. However, the biochemical repair systems of the cancer cell machinery respond, trying to mitigate
the cellular damage induced by these
lifeinmotion_booklet.indd 98
agents. As a result, the clinical efficacy of chemotherapeutic agents is
often limited. Several advances in the
molecular biology of cancer have identified key pathways involved in the
DNA repair of the damage induced by
chemotherapeutic agents. Between all
the mechanisms, we can highlight the
base excision repair (BER) pathway.
Apurinic/apyrimidinic endonuclease
(APE-1) is one of the crucial enzymes
in this mechanism.
Due to its activity, further studies have
been focused in the development of
inhibitors for APE-1 enzyme. Here, we
report the employment of docking and
virtual screening techniques based in
the crystallographic models to search
for compounds that can act as APE-1
inhibitors. The discovered compounds
have shown to be active in vitro assays, with activities between low and
medium micro-molar range. Currently,
we are undertaking in vivo assays in
order to determine their cytotoxicity
and their effects in cancer cell survival. At the same time, we are in the
process of solving the crystallographic
structure of the complexes formed by
APE-1 and each one of the active compounds in order to optimize their affinity for the target.
POSTER 69
Understanding the antagonist mechanism of Peroxisome ProliferatorActivated Receptor gamma
Nadine Utz
IRB Barcelona (Barcelona, Spain)
11/7/11 10:55 AM
17-18 November 2011
lifeinmotion_booklet.indd 99
PPAR-g. This knowledge might help to
develop new medications for so widespread illnesses like diabetes or obesity with less side effects then found
for current used pharmaceuticals, i.e.
thiazolidinediones.
POSTER 70
Macrophages and DNA repair
Valverde-Estrella Lorena,
Jorge and Celada Antonio
Lloberas
IRB Barcelona (Barcelona, Spain)
Abstract
Aicardi-Goutières syndrome (AGS) is a
genetically determined encephalopathy and is associated with a perturbation of type-I interferon metabolism.
Recent molecular advances have revealed that AGS can be caused by biallelic mutations in at least 5 genes
encoding TREX1, the 3 subunits of
RNaseH2 and SAMHD1. Evidences show
that the nucleases defective in AGS
are involved in removing endogenously
produced nucleic acid species, and
that a failure of this removal results
in activation of the immune system.
(Crow et al. 2006 and 2009)
SAMHD1 (SAM domain HD domain-containing protein 1) is a protein that is
encoded by the samhd1 gene in humans. This gene (located on chromosome 20 in humans and chromosome 2
in mice) might play a role in the regulation of the innate immune response,
even is still unknown.
TREX1 is a homodimeric protein which
cleaves ssDNA in 3’->5’ direction.
2nd IRB Barcelona
PhD Student Symposium
Abstract
Peroxisome proliferator-activated receptor gamma (PPAR-g) is a nuclear
receptor that regulates many cellular
functions including adipocyte differentiation, fatty acid oxidation, glucose
metabolism and inflammatory gene expression. Current available insulin sensitizing drugs used in the treatment of
diabetes T2 activate PPAR-g (agonists),
but are associated with severe side effects. In contrast to agonists, PPAR-g
antagonists reduce obesity and have
also beneficial effects on insulin sensitivity. These data therefore lead to the
concept that weak agonists and even
antagonists of PPAR-g, could represent
the next generation of PPAR-g modulators with therapeutic potential.
Although many structures of PPAR-g
bound to different ligands were solved,
little is so far known about the mode
of action of agonists and especially of
antagonists. In this work we present a
comparison of the dynamic behaviour
between the agonist Farglitazar and
a related antagonist bound to PPARg, each in the presence and absence
of the coactivator SRC-1. Massive molecular dynamics (MD) simulations of
an agonist and an antagonist bound to
the ligand binding domain of PPAR-g,
each in the presence and absence of
the coactivator, have been carried out
under physiological conditions.
Additional Umbrella Sampling was carried out to study the effect caused by
the antagonist to the binding of the
coactivator SRC-1. The results of the
simulations of PPAR-g-agonist/antagonist indicate that due to an allosteric
mechanism the antagonist prevent the
forming of the active holo structure of
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2nd IRB Barcelona International
PhD Student Symposium
RNaseH2 is a heterotrimeric protein
which removes RNA from DNA-RNA
hybrids. Loss of one of these proteins
causes Aicardi-Goutières syndrome
The objective of this work is to study
rnaseh2 and samhd1 cellular and tissue expression and its role in macrophages during activation. Moreover,
we want to characterize samhd1 gene
during the pro-inflammatory response
and further study samhd1 promoter.
samhd1 is also induced by pro-inflammatory stimuli whereas rnaseh2
(neither of three subunits) is not well
induced. Furthermore, we have observed that using macrophages from
STAT1-/- mouse, the induction of samhd1 by IFNγ is abolished, indicating
that induction of samhd1 by IFNγ is
through STAT1 pathway.
With this work we can conclude that
samhd1 as well as trex1 are exonucleases that mutations that are associated with AGS and are induced by proinflammatory stimuli whereas rnaseh2
is not induced by pro-inflammatory either anti-inflammatory cytokines.
100
POSTER 71
Kinetics in signal transduction
pathways involving promiscuous
oligomerizing receptors can be determined by receptor specificity: Apoptosis induction by TRAIL
Almer M. van der Sloot2, Eva Szegezdi1,
Devalingam Mahalingam1, Robbert H.
Cool3, Inés G. Muñoz5, Guillermo Montoya4, Wim J. Quax3, Steven de Jong5,
Afshin Samali1 and Luis Serrano2,6
1School
of Natural Sciences, National
lifeinmotion_booklet.indd 100
University of Ireland (Galway, Ireland); 2EMBL/CRG Systems Biology
Research Unit, Centre for Genomic
Regulation-CRG (Barcelona, Spain);
3University of Groningen (Groningen,
Netherlands); 4Spanish National Cancer Research Centre (Madrid, Spain);
5University Medical Center Groningen (Groningen, Netherlands); 6ICREA
(Barcelona, Spain)
Abstract
We show by computer modeling that
kinetics and outcome of signal transduction in case of hetero-oligomerizing receptors of a promiscuous ligand largely depend on the relative
amounts of its receptors. Promiscuous
ligands can trigger the formation of
non-productive receptor complexes,
which slows down the formation of active receptor complexes and thus can
block signal transduction.
Our model predicts that increasing the
receptor-specificity of the ligand without changing its binding parameters
should result in faster receptor activation and enhanced signaling. We experimentally validated this hypothesis
using the cytokine Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand
(TRAIL) and its four membrane-bound
receptors as an example. Bypassing ligand-induced receptor heterooligomerization by receptor-selective
TRAIL variants enhanced the kinetics
of receptor activation and augmented
apoptosis.
Our results suggest that control of
signaling pathways by promiscuous
ligands could result in apparent slow
biological kinetics and blocking signal
11/7/11 10:55 AM
transmission. By modulating the relative amount of the different receptors
for the ligand, signaling processes like
apoptosis can be accelerated or decelerated and even inhibited. It also implies that more effective treatments
using proteins therapeutics could be
achieved simply by altering specificity.
POSTER 72
Manipulation of biological samples
with optical tweezers: thermal effects
I. Verdeny, A-S. Fontaine, A. Farré, M.
Montes-Usategui, E. Martín-Badosa
Departament de Física Aplicada i Òptica,, Universitat de Barcelona (Barcelona, Spain)
Abstract
The optical tweezers technique has
significantly evolved in the last decades, thus, opening up new research
horizons and creating a wide range of
innovative applications, both in the
physical and biological fields. Optical
tweezers use a highly focused laser
beam to trap and manipulate microscopic neutral objects and, therefore,
a high-magnification and high-numerical-aperture microscope objective
is required. This technique presents
distinct advantages such as non-contact force for cell manipulation, force
resolution as accurate as 0.1 pN and
the ability to work in liquid medium
environments.
Even though the main feature of this
technique is the manipulation of liv-
lifeinmotion_booklet.indd 101
ing samples with supposedly minimal
effects at certain conditions (continuous-wave, near-infrared laser beams),
the response of living matter to the
interaction with laser light is still
not clear. There are previous studies
evaluating the cell response to laser
irradiation with optical tweezers1-4
and several parameters (laser power,
irradiation time, wavelength...) have
been tested in various types of cells
and organisms. Different cell functions
(cloning efficiency, ability to grow,
motility…) and reactions (viability, apoptosis and stress response) have been
used to assess damage.
Photothermal and photochemical processes primarily due to laser absorption
seem to be the major detrimental
causes. Thermal damage induced by
heating of the sample can trigger the
cellular stress response or heat shock
response, which is the earliest defense
mechanism of cells when subjected to
physiologically relevant changes in the
environment.
However, an increase on the heat
stress can lead to the activation of apoptosis or even necrosis. The main purpose of this work is to quantify the local temperature increase in the focus
of the optical trap and subsequently
evaluate the thermal damage upon a
specific kind of cells as a testing sample (NG108 cells) by an apoptosis/viability study.
POSTER 73
Who is who in the dynamics of Aβ fibrils
Sílvia Vilaprinyó-Pascual1, Ernest Gi-
2nd IRB Barcelona
PhD Student Symposium
17-18 November 2011
101
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Life in Motion: Dynamics of Molecules and Systems
ralt1,2, Natàlia Carulla1
2nd IRB Barcelona International
PhD Student Symposium
1IRB Barcelona (Barcelona, Spain);
2Departament de Química Orgànica,
Universitat de Barcelona (Barcelona,
Spain)
102
Abstract
The process of amyloid-β protein (Aβ)
aggregation is inherent to the origin
and progression of Alzheimer’s disease
(AD). Aβ aggregation involves different species that exist in complex equilibrium, ranging from low molecular
weight aggregates, such as dimers, to
amyloid fibrils. Soluble Aβ oligomers,
intermediates in this process, confer
synaptic dysfunction, whereas the
large insoluble deposits of Aβ amyloid
fibrils, the end product of aggregation,
are a potential reservoir of Aβ oligomers.
To characterize the kinetics of interconversion between different species
during Aβ aggregation, we monitored
H/D exchange in Aβ fibrils using electrospray ionization mass spectrometry
(ESI-MS), and demonstrated that Aβ
amyloid fibrils are not static but dynamic entities. The molecules comprising the fibrils are continuously dissociating and re-associating, resulting
in a molecular recycling within the
fibril population.
To further understand the implications
of this process in the neurotoxicity of
Aβ fibrils, we want to elucidate the nature of the recycling species. InsulinDegrading Enzyme (IDE) is a monomeric
Aβ degrading agent aimed at obtaining
insights into the recycling behavior
for Aβ40 and Aβ42 fibrils. Since IDE is
lifeinmotion_booklet.indd 102
known to only proteolyze monomeric
Aβ molecules, its addition in Aβ fibrils
supernatants makes it possible to determine whether the recycling species
are oligomeric or monomeric.
POSTER 74
GM-CSF protects macrophages to
DNA damage
Youssif C, Sebastian C, Comalada M
and Celada A
IRB Barcelona (Barcelona, Spain)
Abstract
Macrophages perform critical functions during the immune response.
Macrophages proliferate in response
to specific growth factors, including
Macrophage Colony-Stimulating Factor
(M-CSF), Granulocyte-Macrophage Colony-Stimulating Factor (GM-CSF) and
Interleukin-3 (IL-3). Like all eukaryotic
cells, macrophages can be exposed to
different DNA damaging agents, which
might alter the crucial functions of
these phagocytes. GM-CSF protects
bone marrow cells from the apoptosis
induced by DNA damaging agents.
DNA damage was induced using Etoposide (50µM), a Topoisomerase II inhibitor that causes double-strand breaks.
As a cellular model, we used primary
cultures of bone marrow derived
macrophages and we compared their
response to DNA damage in the presence of GM-CSF and M-CSF. Performing
viability assays by crystal violet technique, we observed less susceptibility
to apoptosis in macrophages growing
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2nd IRB Barcelona
PhD Student Symposium
in the presence of GM-CSF compared
to M-CSF.
Moreover, GM-CSF led to a faster recovery of the DNA damage induced by
Etoposide than M-CSF, measured by
the phosphorylation of H2AX. Comparing the DNA damage checkpoint
proteins, we further observed that
under basal conditions, the basal expression of 53BP1 (p53 binding protein
1, a protein proposed to function as a
transcriptional coactivator of the p53
tumor suppressor) was higher in M-CSF
growing macrophages, as well as NBS1
expression and phosphorylation.
In accordance, we also observed a lower phosphorylation and faster recovery
of p53, when damage was induced in
macrophages growing in the presence
of GM-CSF compared to M-CSF. Taken
together, these data indicate, that
GM-CSF-growing macrophages show a
lower activation of DNA damage checkpoint proteins and a faster recovery of
the DNA damage induced compared to
M-CSF-growing macrophages, leading
to the observed protective effect of
GM-CSF on macrophages.
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PhD Student Symposium
Participants
Maria Adell
IBMB-IRB
mamcri@ibmb.cisc.es
Francisco Barriga
IRB Barcelona
francisco.barriga@irbbarcelona.org
Suvi Aivio
IRB Barcelona
suvi.aivio@irbbarcelona.org
Adrian Baumann,
IRB Barcelona
adrian.baumann@irbbarcelona.org
Elias Akoury
MPI for Biophysical Chemistry
elak@nmr.mpibpc.mpg.de
Najate Benhra
IRB Barcelona
najate.benhra@irbbarcelona.org
Hadeel Al-Rawaf
University of Oxford
hadeel37@gmail.com
M. Teresa Bertran
IRB Barcelona
teresa.bertran@irbbarclona.org
Olga Alster
Nencki Institute of Experimental Biology
o.alster@nencki.gov.pl
Carles Bosch
IRB Barcelona
carles.bosch@irbbarcelona.org
Juliana Amodio
IRB Barcelona
juliana.amodio@irbbarcelona.org
Laura Boulan
IRB Barcelona
laura.boulan@irbbarcelona.org
Vaishnavi Ananthanarayanan
MPI for Molecular Cell Biology and Genetics
ananthan@mpi-cbg.de
Michal Breker
The Weizmann Institute of Science
michal.breker@weizmann.ac.il
David Aparicio
IBMB-IRB
daacri@ibmb.csic.es
Antonija Burcul
University of Zurich
burculantonija@gmail.com
Rodrigo Arroyo
IRB Barcelona
rodrigo.arroyo@irbbarcelona.org
Elisenda Buti
IRB Barcelona
elisenda.buti@irbbarcelona.org
Erika Barboza
IRB Barcelona
erika.barbosa@irbbarcelona.org
Joao Miguel Calado
Instituto de Medicina Molecular
joaofreire@fm.ul.pt
Pablo José Barrecheguren
IRB Barcelona
bendril@hotmail.com
Joaquim Calbó
IRB Barcelona
joaquim.calbo@irbbarcelona.org
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Vittorio Calderone
IRB Barcelona
vittorio.calderone@irbbarcelona.org
Sean Doran
IRB Barcelona
sean.doran@irbbarcelona.org
Michela Candotti
IRB Barcelona
michela.candotti@irbbarcelona.org
Christopher Douse
Imperial College London
christopher.douse09@imperial.ac.uk
Vida de la Paz Castro
PCB
vdlpcastro@pcb.ub.es
Marija Dramicanin
CNIO
mdramicanin@cnio.es
Antonio Celada
IRB Barcelona
antonio.celada@irbbarcelona.org
Miquel Duran
IRB Barcelona
miquel.duran@irbbarcelona.org
Giulio Chiesa
IRB Barcelona
giulio.chiesa@irbbarcelona.org
Bahareh Eftekharzadeh
IRB Barcelona
bebiochem@googlemail.com
Miquel Coll
IRB Barcelona
miquel.coll@irbbarcelona.org
Susana Eibes
IRB Barcelona
susana.eibes@irbbarclona.org
Monica Comalada
IRB Barcelona
monica.comalada@irbbarcelona.org
Albert Escobedo
IRB Barcelona
albert.escobedo@irbbarcelona.org
Claudia Corbo
CEINGE
corbo@ceinge.unina.it
Arnau Farré
UB
arnau.farre@ub.edu
Tiago Cordeiro
IRB Barcelona
tiago.cordeiro@irbbarcelona.org
Carles Fernandez
IRB Barcelona
carles.fernandez@irbbarcelona.org
Sergi Cuartero
IRB Barcelona
sergi.cuartero@irbbarcelona.org
Ana Patricia Ferreira
IRB Barcelona
ana.ferreira@irbbarcelona.org
Mehdi Damaghi
ETH Zurich
mehdi.damaghi@bsse.ethz.ch
Kateryna Filippovych
University of Jyvaskyla
kafilipp@gmail.com
Ozgen Deniz
IRB Barcelona
ozgen.deniz@irbbarcelona.org
Oscar Flores
IRB Barcelona
oscar.flores@irbbarcelona.org
2nd IRB Barcelona
PhD Student Symposium
17-18 November 2011
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2nd IRB Barcelona International
PhD Student Symposium
Life in Motion: Dynamics of Molecules and Systems
Francisco Freixo
IRB Barcelona
francisco.freixo@irbbarcelona.org
Ivan Ivani
IRB Barcelona
ivan.ivani@irbbarcelona.org
Antonina Garanina
Pavlov Saint Petersburg State Medic. Univ.
a.garanina@yahoo.com
Bincy John
Justus Leibig University
bincyanujohn@gmail.com
Beatriz García
IRB Barcelona
beatriz.garcia@irbbarcelona.org
Zuzanna Kaczmarska
IRB Barcelona
zuzanna.kaczmarska@irbbarcelona.org
Josep Garcia
IRB Barcelona
josep.garcia@irbbarcelona.org
Vinita Khot
Interact. Research School for Health Affairs
vinita_fb@yahoo.co.in
Júlia García
IRB Barcelona
julia.garcia@irbbarcelona.org
Roberta Kiffin
IRB Barcelona
roberta.kiffin@irbbarcelona.org
Sylwia Gawrzak
IRB Barcelona
sylwia.gawrzak@irbbarcelona.org
Nicolas Lecland
IRB Barcelona
nicolas.lecland@irbbarcelona.org
Helena Gonzalez
IRB Barcelona
helena.gonzalez@irbbarcelona.org
Tiago Lopes
IRB Barcelona
Tiago.lopes@irbbarcelona.org
Bernat Guixer
IRB Barcelona
bernat.guixer@irbbarcelona.org
Abraham López
IRB Barcelona
abraham.lopez@irbbarcelona.org
Lilia Hambardzumyan
L.A. Orbeli Institute of Physiolog NAS RA
mlilia@bk.ru
Behrooz Hashemian
UPC
behrooz.hashemian@upc.edu
Carol López
UB
carol_lopez@ub.edu
Petur Heidarsson
University of Copenhagen
poh@bio.ku.dk
Jens Luders
IRB Barcelona
jens.luders@irbbarcelona.org
Shuangwei Hu
LMPT
hushuangwei@gmail.com
Ettore Luzi
Reg. Center on Endocrine Hereditary Tumors
eluzi@unifi.it
Claire Loussouarn
CNRS UMR
claire.loussouarn@utc.fr
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Mariano Maffei
IRB Barcelona
mariano.maffei@irbbarcelona.org
Raúl Mendez
IRB Barcelona
raul.mendez@irbbarcelona.org
Hodjat Mahshid
Hannover medical School
Hodjat.mahshid@mh-hannover.de
Laia Miret
IRB Barcelona
laia.miret@irbbarcelona.org
Tobias Maier
CRG
tobias.maier@crg.es
Serena Mirra
IRB Barcelona
serena.mirra@irbbarcelona.org
Carlos Maillo
IRB Barcelona
carlos.maillo@irbbarcelona.org
Elisa Montagni
IRB Barcelona
elisa.montagni@irbbarcelona.org
Larisa Manukyan
L.A. Orbeli Institute of Physiology NAS RA
larmanukyan@rambler.ru
Anna Montaner
IRB Barcelona
anna.montaner@irbbarcelona.org
Oriol Marimon
IRB Barcelona
oriol.marimon@irbbarcelona.org
Mariana Muzzopappa
IRB Barcelona
mariana.muzopappa@irbbarcelona.org
Marko Marjanovic
IRB Barcelona
marko.marjanovic@irbbarcelona.org
Luca Martinelli
IRB Barcelona
luca.martinelli@irbbarcelona.org
Eduard Noguera
IRB Barcelona
eduard.noguera@irbbarcelona.org
Eva Maria Novoa
IRB Barcelona
eva.novoa@irbbarcelona.org
Carlos Martínez
IRB Barcelona
carles.martinez-pons@irbbarcelona.org
Catarina de Oliveira
CRG
catarina.deoliveira@crg.cat
Josep Mas
UB
josep.mas@ub.edu
Benjamí Oller
IRB Barcelona
benjami.oller@irbbarcelona.org
Núria Masachs
IRB Barcelona
nuria.masachs@irbbarcelona.org
Laura Orellana
IRB Barcelona
laura.orellana@irbbarcelona.org
Maria del Mar Masdeu
IRB Barcelona
maria.masdeu@irbbarcelona.org
Arzu Ozturk
IRB Barcelona
arzu.arzuozturk@gmail.com
2nd IRB Barcelona
PhD Student Symposium
17-18 November 2011
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2nd IRB Barcelona International
PhD Student Symposium
Life in Motion: Dynamics of Molecules and Systems
Antoni Parcerisas
IRB Barcelona
antoni.parcerisas@irbbarcelona.org
Jelena Raspopovic
CRG
jelena.raspopovic@crg.eu
Lorena Pereira
IRB Barcelona
lorena.pereira@irbbarcelona.org
Ben Naya Raouia
CNRS UMR
raouia.ben-naya@utc.fr
Lidia Pérez
IRB Barcelona
lidia.perez@irbbarcelona.org
Mercè Ratera
IBMB/CSIC
merce.ratera@irbbarcelona.org
Daria Picchioni
IRB Barcelona
daria.picchioni@irbbarcelona.org
Carles Recasens
IRB Barcelona
carles.recasens@irbbarcelona.org
Simone Pieretti
IRB Barcelona
simone.pieretti@irbbarcelona.org
Katrin Rein
IRB Barcelona
katrin.rein@irbbarcelona.org
Inna Povolotskaya
CRG
inna.povolotskaya@crg.eu
Sandra Richter
MPI of Molecular Cell Biology and Genetics
sarichte@mpi-cbg.de
Leszek Piotr Pryszcz
CRG-Centre for Genomic Regulation
lpryszcz@crg.eu
Chiara De Rienzo
Università degli Studi di Firenze
bradypus986@gmail.com
Lluís Pujadas
IRB Barcelona
lluis.pujadas@irbbarcelona.org
Antoni Riera
IRB Barcelona
antoni.riera@irbbarcelona.org
Giuseppe Pulice
IRB Barcelona
giuseppe.pulice@irbbarcelona.org
Judith Rodriguez
IRB Barcelona
judith.rodriguez@irbbarcelona.org
Ximena Carolina Pulido
PCB
xppulido@pcb.ub.es
Eugenia Rojas
MDC Berlin-Buch
euge.rojas@gmail.com
Nikolay Pydiura
Inst. of Food Biotechnol. & Genomics NASU
pydiura@gmail.com
Oriol Ros
IRB Barcelona
oriol.ros@irbbarcelona.org
Ravishankar Ramanathan
CIB CSIC
ravi@cib.csic.es
Daniela Rossi
IRB Barcelona
daniela.rossi@irbbarcelona.org
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17-18 November 2011
Barbara Rotstein
IBMB-CSIC
brbbmc@ibmb.csic.es
Tatjana Skobo
University of Padova, Department of Biology
tatjana.skobo@bio.unipd.it
Lidia Ruiz
IRB Barcelona
lidia.ruiz@irbbarcelona.org
Oleksandr Skorokhod
Institute of Molecular Biology and Genetics
fiwinner@ukr.net
David Sala
IRB Barcelona
david.sala@irbbarcelona.org
Joana Silva
Instituto Português de Oncologia do Porto
joanafariasilva@gmail.com
Carlos Sanchez
IRB Barcelona
carlos.sanchez@irbbarcelona.org
Constanze Schelhorn
IRB Barcelona
constanze.braasch@irbbarcelona.org
Jordi Silvestre
IRB Barcelona
jordi.silvestre@irbbarcelona.org
Benedikt Schwartz
MPI for Molecular Genetics
bschwart@molgen.mpg.de
Montse Soler
IRB Barcelona
montse.soler@irbbarcelona.org
Sara Sdelci
IRB Barcelona
sara.sdelci@irbbarcelona.org
Sara Spaziani
University of Naples “Parthenope”
spaziani@ceinge.unina.it
Carolina Segura
IRB Barcelona
carolina.segura@irbbarcelona.org
Milos Tatarski
IRB Barcelona
milos.tatarski@irbbarcelona.org
Bernat Serra
IRB Barcelona
bernat.serra@irbbarcelona.org
Neus Teixidó
IRB Barcelona
neus.teixido@irbbarcelona.org
Montserrat Serra
IRB Barcelona
montserrat.serra@irbbarcelona.org
Roman Serrat
IRB Barcelona
roman.serrat@irbbarcelona.org
Giorgia Testoni
IRB Barcelona
giorgiat85@gmail.com
Maria Tintoré
IRB Barcelona
maria.tintore@irbbarcelona.org
Pedro Sfriso
IRB Barcelona
pedrosfriso@irbbarcelona.org
Johan Tisserand
IRB Barcelona
johan.tisserand@irbbarcelona.org
2nd IRB Barcelona
PhD Student Symposium
Christopher Sinadinos
IRB Barcelona
christopher.sinadinos@irbbarcelona.org
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Life in Motion: Dynamics of Molecules and Systems
Natalia Trempolec
IRB Barcelona
natalia.trempolec@irbbarcelona.org
Nadine Utz
IRB Barcelona
nadine.utz@irbbarcelona.org
Jordi Vallès
IRB Barcelona
jordi.valles@irbbarcelona.org
Lorena Valverde
IRB Barcelona
lorena.valverde@irbbarcelona.org
Almer Van der Sloot
CRG
almer.vandersloot@crg.es
Ione Verdeny
UB
ioneverdeny@ub.edu
Sílvia Vilaprinyó
IRB Barcelona
silvia.vilaprinyo@irbbarcelona.org
2nd IRB Barcelona International
PhD Student Symposium
Jessica Vitos
IRB Barcelona
jessicavitos@googlemail.com
Catrin Youssif
IRB Barcelona
catrin.youssif@irbbarcelona.org
Justyna Zaborowska
Univeristy of Oxford, Sir William Dunn
School of Pathology
justyna.zaborowska@path.ox.ac.uk
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Life in Motion: Dynamics of Molecules and Systems
Acknowledgements
2nd IRB Barcelona International
PhD Student Symposium
We are grateful to a number of people that supported us in the organization
of this symposium, from the early stages of conceiving the format to the
logistics of preparing and hosting such an event. In particular, we would like
to thank:
•
IRB Barcelona group leaders Joan J. Guinovart (IRB Barcelona
Director), Marco Milan (IRB Barcelona Programme Coordinator Cell
and Developmental Biology), Patrick Aloy (IRB Barcelona Laboratory
Structural Bioinformatics and Network Biology), Xavier Salvatella
(IRB Barcelona Laboratory of Molecular Biophysics) and Ernest Giralt
(IRB Barcelona Programme Coordinator Chemistry and Molecular
Pharmacology) for general advice on how to organize a scientific
meeting, and for their trust in our ability to independently plan this
symposium.
•
Patricia Nadal, Clara Caminal, Meritxell Gavaldà, Sarah Sherwood, Luca
Tancredi Barone, Tanya Yates, Jorge Dominguez, Sonia Saborit, the
IRB Barcelona Finance Department, in particular Alex Puerto, Maite
Navarro and Elisva de la Hoz, and the entire IRB Barcelona Purchasing
Department, headed by Yolanda Olmos, for helping us to find sponsors
for the event.
•
Marco Grillo (IRB Barcelona Laboratory Development and morphogenesis
in Drosophila) who contributed significantly in the earlier stages of
planning the symposium.
•
Daniel Carey, designer from Newcastle upon Tyne, UK, for the final
touch on design of the poster and covers for the booklet.
•
And last but not least, the IRB Barcelona Directorate for funding this
event.
The PhD Student Symposium Committee
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IRB Barcelona
The Institute for Research in Biomedicine (IRB
Barcelona) is an independent, non-profit research
centre engaged in basic and applied biomedical
science. Its ultimate aim is to improve the quality
of people’s lives by developing new applications for
the remarkable discoveries being made in the life
sciences.
IRB Barcelona was established in 2005 by the
Government of Catalonia (through the Ministry
of Innovation, Universities and Business and the
Ministry of Health), the University of Barcelona and
the Barcelona Science Park (PCB, Parc Científic de
Barcelona), and is led by Joan J Guinovart (Director)
and Joan Massagué (Adjunct Director). It has recently
been awarded a “Severo Ochoa Centre of Excellence” by the Spanish Ministry
of Science and Innovation.
Research is organised into five interdisciplinary programmes, which focus
on Cell and Developmental Biology, Structural and Computational Biology,
Molecular Medicine, Chemistry and Molecular Pharmacology, and Oncology.
In addition to the International PhD Student Symposium series, IRB Barcelona
also offers the ‘Barcelona BioMed’ series, including seminars, conferences,
forums, workshops and courses is a key component of IRB Barcelona’s
scientific training and outreach activities, and provides a unique opportunity
to bring the world of life sciences research to Barcelona and to bring the
outstanding life sciences research done here in Barcelona to the world.
2nd IRB Barcelona
PhD Student Symposium
The missions of IRB Barcelona are to promote multidisciplinary research
of excellence at the interface between biology, chemistry and medicine,
to foster collaborations with local, national and international research
institutes, to provide high-level training in the biomedical sciences to staff,
students and visitors, to promote innovation and technology transfer, and
to actively engage in an open dialogue with the public through a series of
outreach and education activities.
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Life in Motion: Dynamics of Molecules and Systems
Practical information
Institute for Research in Biomedicine (IRB Barcelona)
Conference Secretariat
c/o Barcelona Science Park
Baldiri Reixac 10
08028 Barcelona, Spain
Tel: +34 934034955
Fax: +34 934037114
www.irbbarcelona.org
2nd IRB Barcelona International
PhD Student Symposium
Aquarium
L’Aquàrium de Barcelona
Moll d’Espanya del Port Vell, s/n
08039 Barcelona
Tel: +34 932 21 74 74
www.aquariumbcn.com
Hotel Catalonia Ramblas
Contact: Miquel Grau
C/ Pelayo 28
08001 Barcelona
Tel: +34 933168400
Fax: +34 933168402
ramblas.reservas@hoteles-catalonia.es
www.hoteles-catalonia.com
Restaurant
FrescCo Medinaceli
Pl. Duc de Medinacelli, 2
08002 BarcelonaTel: +34 933 18 58 57
Taxi
Tel: +34 933033033 or +34 933070707
Emergency services
Tel: 112
114
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2nd IRB Barcelona
PhD Student Symposium
Notes
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PhD Student Symposium
Notes
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PhD Student Symposium
Notes
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PhD Student Symposium
Notes
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PhD Student Symposium
Notes
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Index of speakers
Vaishnavi Ananthanarayanan
32
Francisco Barriga
42
Mónica Bettencourt-Dias
12
Michal Breker
40
Julius Brennecke
16
Aaron Ciechanover
22
Tiago Cordeiro
39
Christopher H Douse
41
João Miguel Freire
38
Anne-Claude Gavin
18
Christian Griesinger
24
Piet Gros
26
Nicolas Lecland
36
Tobias Maier
35
Conly L Rieder
20
Erik Sahai
28
Sarah A Teichmann
14
Justyna Zaborowska
34
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