Brief presentation
An International Associate Laboratory (LIA – Laboratoire International Associé) has been approved between the LBBE-UMR5558 and the Laboratório de Bioinformática of the LNCC/MCT, Brazil, managed by Dr Ana Tereza Vasconcelos. The LIA is called Laboratory InteRnational of research in bIOformatics (acronym LIRIO) and was officially created from January 1st, 2012 for a duration of 4 years with possibility of asking for a renewal once, which was granted. The project will then now last until the end of 2019. LIRIO is coordinated on the Brazilian side by Ana Tereza Vasconcelos, and on the French side by Marie-France Sagot. The activities of LIRIO cover research, teaching and also involve the bioinformatics platforms on both sides.
Research themes
The research conducted in the LIA concerns putting together all the activities currently conducted by each team separately or that each team involved in the LIA has already planned to do, but also new research that the synergy between the two teams will enable to address in future. This research concentrates on two main axes, one strongly concerned with the host-parasite relationship and the second with micro-environmental genomics and systems biology. Both address complex systems by a broad variety of experimental, bioinformatic and algorithmic approaches that reflect the complementarity of the two teams involved (biology including experimental part for the Brazilian team, algorithmics for the French one) while bioinformatics is a common language between the two.
Participants
The participants to the CNRS LIA Lirio are:
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On the French side, current members:
- Marie-France SAGOT: Senior Researcher Inria.
- Vincent LACROIX: Associate Professor UCBL.
- Arnaud MARY: Associate Professor UCBL.
- Blerina SINAIMERI: Junior Researcher Inria.
- Alain VIARI: Senior Researcher Inria.
- Cristina VIEIRA: Full Professor UCBL.
- Mariana GALVÃO FERRARINI: PhD in Bioinformatics and Biostatistics (Nov/2012-Nov/2015 funded by ERC AdG Sisyphe then FP7 KBBE BacHBerry project and FRM Inria).
- Leandro ISHI SOARES DE LIMA: PhD in Computational Biology (Fev/2015-Jan/2018 Ciência Sem Fronteira funding).
- Alice JULIEN-LAFERRIÈRE: PhD in Computational Biology (Dec/2013-Nov/2016 FP7 KBBE BacHBerry project).
- Carol MORTAGA: PhD in Computational Biology (Sept/2016-Aug/2019 funded by Conicyt).
- Henri Taneli PUSA: PhD in Computational Biology (Sept/2015-Aug/2018 H2020 ITN project).
- Martin WANNAGAT: PhD in Computational Biology (Nov/2013-Nov/2016 funded by ERC AdG Sisyphe then FP7 KBBE BacHBerry project).
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On the Brazilian side, current members:
- Ana Tereza RIBEIRO DE VASCONCELOS: Senior Researcher LNCC.
- Marisa NICOLAS: Junior Researcher LNCC.
- Luciane CIAPINA: Junior Researcher LNCC.
- Kary OCAÑA: Junior Researcher LNCC.
- Guilherme LOSS: Post-Doc LNCC.
- Rafael GUEDES: Post-Doc LNCC.
- Fabiola MARQUES: Post-Doc LNCC.
- Mauro DEFREITAS ORTIZ: Post-Doc LNCC.
- Maria Cristina MOTTA: Associate Professor, Federal University of Rio de Janeiro (UFRJ).
- Arnaldo ZAHA: Full Professor, Federal University of Rio Grande do Sul (UFRGS).
Additionally, two other researchers participate actively in the LIA Lirio. These are:
Associated projects
INRIA-FAPERJ RAMPA
Coordinators: (Brazil) Ana Tereza Vasconcelos, LNCC; (France) Marie-France Sagot
Main other participant: Maria Cristina Motta, Federal University of Rio de Janeiro (UFRJ)
Duration: 2011-2013
Brief description
Protozoa of the Trypanosomatidae family comprise a large number of species, some of which are agents of important illnesses such as leishmaniasis, Chagas’ disease and African trypanosomiasis. A small number of trypanosomatids have been described containing bacterium symbionts in the cytoplasm, known as endosymbionts. Angomonas deanei and Strigomonas culicis are examples of such species. The endosymbiont supplies the host trypanosomatid with essential nutrients which account for less stringent growth requirements. Both the protozoan and the bacterium maintain intensive metabolic exchanges resulting in an interesting model to study the co-evolution of metabolisms. This intricate dialog between the protozoan and the bacterium includes not only the metabolic point view, but also regulation and cell cycle, among others. This is thus also a special model to study cellular evolution. The aim of the project is to computationally and experimentally start studying this dialog.
CAPES-COFECUB Microbial Ecosystem of Swines
Coordinators: (Brazil) Ana Tereza Vasconcelos, LNCC; (France) Marie-France Sagot
Main other participant: Arnaldo Zaha, Federal University of Rio Grande do Sul (UFRGS)
Duration: 2013-2014, renewed for the period 2015-2016
Brief description
This project proposes to experimentally and mathematically explore the biodiversity of the bacterial organisms living in the respiratory tract of swines, many of which are pathogenic. Among these, Mycoplasma hyopneumoniae, Actinobacillus pleuropneumoniae, Actinobacillus suis, Streptococcus suis, Bordetella bronchiseptica, Pasteurella multocida, Mycoplasma flocculare and Mycoplasma hyorhinis are the most studied. However, the microbiome of the swine respiratory tract remains largely unknown, and possibly many more unidentified species live in this part of the organism and may influence decisively the infection process of the bacteria that are pathogenic.
Important aspects to be analyzed are the potential relationship of the metabolic pathways and regulatory systems of the bacterial species living in the respiratory tract. Both metabolism and gene expression regulation can be integrated. Transcription and translation are indeed processes that require energy and precursors, such as nucleotides and amino acids, which are made available by the capacity of metabolic pathways to produce them. On the other hand, transcription and translation exert demands on some metabolic network functions and thus limit others. It is important to point out that mycoplasma is dependent on external sources for several precursors of its metabolism.
This project is highly pluridisciplinary and will involve equally important experimental (wet-lab / sequencing) and methodological parts, the latter requiring the de novo development of mathematical models and of algorithms to analyse the data.
