Raquel Silva

raquels@ipatimup.pt

RESEARCH ACTIVITIES AND INTERESTS

Molecular mechanisms involved in the evolution of genetic code alterations and adaptation of organisms to constitutive stress conditions.
Impact of proteome and genome instability in cell degeneration and aging.
Molecular evolution of proteins and metabolic pathways.

EDUCATION

2008 – present: Researcher, IPATIMUP.
2005 – 2008: Post-doctoral fellow, University of Aveiro. Project: mRNA mistranslation in yeast.
2005: PhD in Biology, University of Aveiro. Thesis: Molecular reconstruction of a genetic code alteration.
1999 – 2000: GABBA (Graduated Program in the Areas of Basic and Applied Biology), University of Porto.
1999 – Degree in Biology, University of Aveiro.

PUBLICATIONS

Gains, losses and changes of function after gene duplication: study of the metallothionein family.
Moleirinho A,Carneiro J,Matthiesen R,Silva RM,Amorim A,Azevedo L,
PLoS One.2011;6(4):e18487-.

Transcriptional profiling of azole-resistant Candida parapsilosis strains.
Silva AP,Miranda IM,Guida A,Synnott J,Rocha R,Silva R,Amorim A,Pina-Vaz C,Butler G,Rodrigues AG,
Antimicrob Agents Chemother.2011;55(7):3546-3556.

FKS2 mutations associated with decreased echinocandin susceptibility of Candida glabrata following anidulafungin therapy.
Costa-de-Oliveira S,Marcos M,Silva RM,Pinto E Silva,Rocha R,Amorim A,Goncalves RA,Pina-Vaz C,
Antimicrob Agents Chemother.2011;55(3):1312-1314.

The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation.
Silva RM,Duarte IC,Paredes JA,Lima-Costa T,Perrot M,Boucherie H,Goodfellow BJ,Gomes AC,Mateus DD,Moura GR,Santos MA,
PLoS One.2009;4(4):e5212-.

Codon-triplet context unveils unique features of the Candida albicans protein coding genome.
Moura GR,Lousado JP,Pinheiro M,Carreto L,Silva RM,Oliveira JL,Santos MA,
BMC Genomics.2007;8():444-.

Critical roles for a genetic code alteration in the evolution of the genus Candida.
Silva RM,Paredes JA,Moura GR,Manadas B,Lima-Costa T,Rocha R,Miranda I,Gomes AC,Koerkamp MJ,Perrot M,Holstege FC,Boucherie H,Santos MA,
EMBO J.2007;26(21):4555-4565.

A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans.
Gomes AC,Miranda I,Silva RM,Moura GR,Thomas B,Akoulitchev A,Santos MA.
Genome Biol.2007;8(10):206-.

Yeast proteome map (update 2006).
Perrot M,Guieysse-Peugeot AL,Massoni A,Espagne C,Claverol S,Silva RM,Jen� P,Santos M,Bonneu M,Boucherie H.
Proteomics.2007;7(7):1117-1120.

Evolution of the genetic code in yeasts.
Miranda I,Silva R,Santos MA
Yeast.2006;23(3):203-213.

Comparative context analysis of codon pairs on an ORFeome scale.
Moura G,Pinheiro M,Silva R,Miranda I,Afreixo V,Dias G,Freitas A,Oliveira JL,Santos MA.
Genome Biol.2005;6(3):58-.

Yeast as a model organism for studying the evolution of non-standard genetic codes.
Silva RM,Miranda I,Moura G,Santos MA,
Brief Funct Genomic Proteomic.2004;3(1):35-46.

PRIZES AND AWARDS

2005: Second best poster in MICRO-BIOTEC’05, area of genomics (Lidel Prize).
1998, 1999: Honour Scholarship, to students with exceptional results (University of Aveiro).
1998: Prize Prof. Egas Moniz, best student at the University of Aveiro (Governo Civil de Aveiro).
1997: Prize Dr. Vale Guimarães, best University student from Aveiro (Governo Civil de Aveiro).

RESEARCH PROJECTS

2010 – 2013 PTDC/BIA-PRO/099888/2008. Co-evolutionary study of NAD biochemical networks (Principal Investigator).
2010 – 2013 PTDC/AAC-AMB/104532/2008. AMPHIBIA - How will climate changes influence the viability of amphibian populations already stressed with anthropogenic contamination (consultant).
2005 – 2008: POCI/SAU-MMO/55476/2004. Impact of mRNA mistranslation on cell degeneration and evolution (member of team).
2005 – 2008: POCI/BIA-MIC/55466/2004. Unravelling the molecular basis of morphogenesis and mating triggered by a genetic code change in Candida albicans (member of team).
1997 – 1998: Praxis/2/2.1/DC&T/2291/95. EPANAFORA – educate to promote new attitudes towards the environment (member of team).

STAYS IN INTERNATIONAL LABORATORIES

Jun – Jul 2006: Sir William Dunn School of Pathology, University of Oxford, UK.
Oct – Dec 2003: Genomics Lab, University Medical Centre, Utrecht, The Netherlands (supported by an EMBO short-term fellowship).
Jan – Apr 2001 and Feb – Jul 2002: Institut de Biochimie et Génétique Cellulaires du CNRS, Bordeaux, France.
Jul 2000: Departamento de Microbiología II de la Facultad de Farmacia, Universidad Complutense de Madrid, Spain.

SELECTED ORAL COMMUNICATIONS

2011: Tales from a NAD world. CIIMAR invited seminar, Porto, Portugal.
2009: Evolution through proteome destabilization. 12th Portugaliae Genetica, Porto, Portugal.
2006: The role of mRNA mistranslation on cell degeneration and aging. XV National Congress of Biochemistry, Aveiro, Portugal.
2004: A proteomics approach to mRNA mistranslation in Saccharomyces cerevisiae. Congrès de la Societé Française d’Electrophorèse et d’Analyse Proteomique, Bordeaux, France.
2002: A functional genomics approach to the evolution of alternative genetic codes. XIII Congresso Nacional de Bioquímica, Lisboa, Portugal.