organisation - the Instituto Gulbenkian de Ciência

COLLECTIVE
DYNAMICS
Gabriela Gomes Principal Investigator
PhD in Mathematics, University of Warwick, UK, 1993
Post-doctoral Researcher, Mathematics Institute, University of Warwick
Wellcome Trust Research Training Fellow in Mathematical Biology, Department of Biological Sciences, University of Warwick
Principal Investigator at the IGC since 2002
We study collective phenomena, such as self-organisation, criticality, and pattern
formation, arising from spatial and temporal constraints in physical and
biological systems, with a current focus on infectious disease ecology and evolution.
The central theme of our research derives from a conceptual model of
partial immunity whose collective outcome - the reinfection threshold - underlies
a phenomenological transition in epidemic dynamics, with practical implications
ranging from extreme geographical variability in the effect of vaccination
programmes to destabilised transmission favouring polymorphism in antigenically
diverse pathogens. We are interested in refining concepts and methodologies
by performing specific experiments in the laboratory and in natural
populations.
MOLECULAR EPIDEMIOLOGY OF MYCOBACTERIUM TUBERCULOSIS IN PORTUGAL:
IMPLEMENTING AND ANALYSING A DATABASE
We propose to genotype all the strains from sputum of smear positive pulmonary
tuberculosis cases with recent methods based on the variability of mycobacterial
interspersed repetitive units (MIRU) and variable number tandem
repeats (VNTR). A database that includes mycobacterial genotype and clinical
and demographic information about patients will be implemented, constituting
a valuable resource for molecular epidemiology studies, transmission models
and applied research on mycobacterial evolution and pathogenesis.
A total of 2286 isolates of M. tuberculosis DNA were genotyped for 90 SNPs.
About 300 strains were genotyped in the first year and 743 strains were genotyped
during the second year. In the last period of the project, 1239 more samples
were included. Increasing the number of genotyped strains is our immediate
goal and will allow us to infer on the genetic diversity of M. tuberculosis
circulating in the Portuguese population.
EXPLORING PATHOGEN DIVERSITY IN DISEASE EPIDEMIOLOGY
AND VACCINE RESEARCH
Viruses, bacteria and parasitic pathogens have evolved multiple strategies to
evade innate and acquired immune responses, facilitating transmission, allowing
the establishment of persistent and recurrent infections, and often hampering
the development of effective vaccines. Antigenic variation of immune
response targets is one such pathogen strategy that can only be confronted
with the support of a highly specialised research programme combining basic
and applied research. This is the theme of this project. The team integrates basic
research in infection, population genetics, and mathematical epidemiology,
with a range of practical aspects of experimental design from the laboratory
to the field. The overall research strategy is to unravel the molecular bases and
epidemiological significance of immunity in order to guide vaccine design and
deployment.
GROUP MEMBERS
João Sollari Lopes (Post-doc, started in April)
Ana Isabel Franco (Post-doc, started in September)
Cátia Bandeiras (Trainee, started in December)
Delphine Pessoa (Trainee)
Bruno Ceña (Trainee)
Caetano Souto Maior Mendes (Trainee, started in October)
COLLABORATORS
José Pereira-Leal (IGC, Portugal)
Isabel Marques (IGC, Portugal)
Carlos Penha-Gonçalves (IGC, Portugal)
Lounes Chikhi (IGC, Portugal)
Ana Godinho (IGC, Portugal)
Anabela Miranda
(INSA - Instituto Nacional de Saúde Dr. Ricardo Jorge, Portugal)
Ana Abecasis (CMDT-IHMT - Instituto de Higiene e Medicina Tropical,
Portugal)
Diogo Pinheiro (ISEG - Instituto Superior de Economia e Gestão, Portugal)
Raquel Sá-Leão (ITQB - Instituto de Tecnologia Química e Biológica,
Portugal)
Cláudia Codeço (Fundação Oswaldo Cruz, Brazil)
Alessandro Vespignani (Institute for Scientific Interchange, Italy)
Lewi Stone (Tel Aviv University, Israel)
Dirk Brockmann (Max Planck Institute Gottingen, Germany)
Ronald Smallenburg (Grote Griepmeting, The Netherlands)
John Edmunds (London School of Hygiene and Tropical Medicine, UK)
Olof Nyrén (Swedish Institute for Infectious Disease Control, Sweden)
Marc van Ranst (Rega Institute for Medical Research, Belgium)
Shlomo Havlin (Bar Ilan University, Israel)
Stefano Merler (Fondazione Bruno Kessler, Italy)
Daniele Miorandi (Center for Research and Telecommunication
Experimentation for NETworked communities, Italy)
Mário Silva (Faculdade de Ciências, Universidade de Lisboa, Portugal)
Natalia Mantilla (Universidad Nacional Autónoma de México, México)
Glória Teixeira (Universidade Federal da Bahia, Brazil)
FUNDING
Fundação para a Ciência e a Tecnologia (FCT), Portugal
Framework Programme 7, European Commission
We compared key parameters underlying pneumococcal transmission in Portuguese
and Finnish day care centres using a continuous-time event history model
in a Bayesian framework. We developed mathematical and statistical models to
elucidate the design of novel pre-clinical and clinical trials to assess intervention
efficacy both in the laboratory and in the field. The new designs are being
refined using Drosophila-Wolbachia as an experimental system.
EPIWORK - DEVELOPING THE FRAMEWORK FOR AN EPIDEMIC FORECAST
INFRASTRUCTURE
In recent years a huge flow of quantitative social, demographic and behavioural
data is becoming available, spurring the quest for innovative technologies that
can improve the traditional disease-surveillance systems, providing faster and
better localised detection capabilities and resulting in a broad practical impact.
IGC ANNUAL REPORT ‘11
RESEARCH GROUPS
40