organisation - the Instituto Gulbenkian de Ciência

QUANTITATIVE
ORGANISM BIOLOGY
Jorge Carneiro Principal Investigator
PhD in Biomedicine, Universidade do Porto, 1997
Post-doctoral Fellow, Theoretical Biology and Bioinformatics,
University of Utrecht, NL
Coordinator of the Estudos Avançados de Oeiras
Director PhD Programme in Computational Biology
Principal Investigator at the IGC since 1998
link to external website
We are broadly interested in the mechanisms underlying organismal properties
(namely immunological tolerance, body form and sensorimotor coordination)
and in creating quantitative modelling frameworks that bridge between the biochemical
micro-dynamics of individual cells and the supracellular collective behaviour.
In immunology, we study the cell population dynamics and homeostasis
involved in the interplay between health, autoimmunity and cancer; and search
for methods to measure repertoire diversity and structure. In cell biology, we
study stochastic gene expression and epigenetic regulation focusing on several
instances of monoallelic gene expression (e.g. antigen-receptor and cytokine
genes). We are also interested in understanding cellular form and motility, and
collective tissue dynamics. We are creating new simulation methods and tools
for rigorous comparison of simulation results with live-imaging data.
BIOINSTBOTS:
FROM BIO-INSPIRED TO INSTITUTIONAL-INSPIRED COLLECTIVE ROBOTICS
The main inspiration for collective robotics modelling, analysis and design originated
from the biology of social insects. Despite the success of swarm robotics
in relatively simple applications, there is no systematic method to design individual
behaviours at the micro level, including their interaction-based actions,
in order to obtain a desired collective behaviour at the macro level. In fact,
the emergent nature of the collective behaviour is a principle that precludes
goal- or performance-oriented design. We seek to study and formalise laws
that govern collective systems with the aim of synthesising systems of relatively
simple robots that display complex behaviour. In order to achieve this goal,
we study both biological systems and social systems. From biology, we focus
on cell populations. A single cell is relatively simple when compared with a cell
population, a cellular tissue or an organism. While from sociology, we focus on
institutional economics. Our objective is to bring together theories, ideas and
inspiration from institutional economics and cell biology under a common formal
framework for large robot populations modelling and analysis.
GROUP MEMBERS
Danesh Tarapore (Post-doc)
Thiago Guzella (PhD student) (co-supervised by Vasco Barreto))
Tiago Macedo (PhD student)
Tom Weber (PhD student)
Pedro Silva (Masters student) (left in September)
COLLABORATORS
Alberto Darszon (Instituto de Biotecnologia, UNAM, Cuernavaca, Mexico)
Gabriel Corkidi (Instituto de Biotecnologia, UNAM, Cuernavaca, Mexico)
Michal Or-Guil (Research Center ImmunoSciences (RCIS),
Humboldt University, Berlin, Germany)
Carmen Molina-Paris and Grant Lythe (Department of Mathematics.
University of Leeds, UK)
Pedro Lima (Institute of Systems and Robotics. IST/UTL, Portugal)
Anders Lyhne Christensen (Instituto de Telecomunicações
& Instituto Universitário de Lisboa (ISCTE-IUL), Portugal)
FUNDING
Fundação para a Ciência e a Tecnologia, (FCT), Portugal
Conacyt - Consejo Nacional de Ciencia y Tecnología, Mexico
For detailed quantitative simulations of cell populations and tissues that can be
rigorously formalised and validated by comparison with the natural system, we
focused on two cases studies:
1. CD4 T cell population dynamics;
2. Spatial pattern formation and dynamics in cell aggregates and tissues.
We redeployed T cells dynamics within a multiagent robotic system showing
that the collective dynamics brings forth a classification of environmental objects
according to some proto “self-nonself” categorisation that was not prescribed
to the individual agents.
MORPHODYNAMIC MODELLING AND IMAGING OF SEA URCHIN SPERMATOZOA
SWIMMING AND CHEMOTAXIS
Flagella and cilia are structurally conserved, present in many cell types and are
fundamental for many biological processes. Multiple diseases, including disruption
of left-right body asymmetry, result from ciliar protein mutations. Flagellar
driven sperm motility is crucial for gamete encounter and fertilisation. The objective
of this collaborative project with the group of Alberto Darszon from the
Institute for Biotechnology, UNAM (Cuernavaca, Mexico) is to gain insight into
sea urchin spermatozoa flagellar morphodynamics, making use of state of the
art imaging techniques and mathematical modelling. We search to understand
how molecular signals produced by the egg regulate intracellular [Ca2+] and flagellar
beating to guide spermatozoon towards the egg in the 3D world. We aim
to develop morphodynamical models of sperm cells and deploy these models
for quantitative image analysis.
IGC ANNUAL REPORT ‘11
RESEARCH GROUPS
28