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.
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.
PARTICIPATION IN 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).
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).
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.
PUBLICATIONS
Moleirinho A, Carneiro J, Matthiesen R, Silva RM, Amorim A, Azevedo L (2011).
Gains, losses and changes of function after gene duplication: study of the metallothionein family.
PloS one 6: e18487. doi: 10.1371/journal.pone.0018487.
Silva AP, Miranda IM, Guida A, Synnott J, Rocha R, Silva R, Amorim A, Pina-Vaz C, Butler G, Rodrigues AG (2011).
Transcriptional profiling of azole-resistant Candida parapsilosis strains.
Antimicrobial agents and chemotherapy 55: 3546-56. doi: 10.1128/AAC.01127-10
Costa-de-Oliveira S, Marcos Miranda I, Silva RM, Pinto E Silva A, Rocha R, Amorim A, Gonçalves Rodrigues A, Pina-Vaz C (2011).
FKS2 mutations associated with decreased echinocandin susceptibility of Candida glabrata following anidulafungin therapy.
Antimicrobial agents and chemotherapy 55: 1312-4. doi: 10.1128/AAC.00589-10
Silva RM, Pereira F, Carneiro J, Sobral O, Ribeiro R, Amorim A, Soares AMVM, Lopes I (2010).
Microevolution in a Natural Population of Daphnia longispina Exposed to Acid Mine Drainage.
Interdisciplinary Studies on Environmental Chemistry — Biological Responses to Contaminants 3: 213–218.
Silva RM, Duarte ICN, Paredes JA, Lima-Costa T, Perrot M, et al. (2009).
The Yeast PNC1 Longevity Gene Is Up-Regulated by mRNA Mistranslation.
PLoS ONE 4(4): e5212. doi:10.1371/journal.pone.0005212
Silva RM, Paredes JA, Moura GR, Manadas B, Lima-Costa T, Rocha R, Miranda I, Gomes AC, Koerkamp MJG, Perrot M, Holstege FCP, Boucherie H, Santos MAS (2008).
Genetic Code Alteration Plays a Critical Role in the Evolution of Candida Genes - Quantitative Analysis of Single Amino Acid Changes using a 4000 QTRAP® system.
Applied Biosystems Technical note 115TN10-01.
Silva RM, Paredes JA, Moura GR, Manadas B, Lima-Costa T, Rocha R, Miranda I, Gomes AC, Koerkamp MJG, Perrot M, Holstege FCP, Boucherie H, Santos MAS (2007).
Critical roles for a genetic code alteration in the evolution of the genus Candida.
EMBO J. 26 (21): 4555-4565.
Gomes AC, Miranda I, Silva RM, Moura GR, Thomas B, Akoulitchev A, Santos MAS (2007).
A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans.
Genome Biology 8 (10): R206.
Moura GR, Lousado JP, Pinheiro M, Carreto L, Silva RM, Oliveira JL, Santos MAS (2007).
Codon-triplet context unveils unique features of the Candida albicans protein coding genome.
BMC Genomics 8: 444.
Perrot M, Guiyesse-Peugeot A, Massoni A, Espagne C, Claverol S, Silva RM, Jenö P, Santos MAS, Bonneu M, Boucherie H (2007).
Yeast proteome map (update 2006).
Proteomics 7 (7): 1117-1120.
Miranda I, Silva RM, Santos MAS (2006).
Evolution of the genetic code in yeasts.
Yeast 23: 203-213.
Moura G, Pinheiro M, Silva RM, Miranda I, Afreixo V, Dias G, Freitas A, Oliveira JL, Santos MAS (2005).
Comparative context analysis of codon pairs on an ORFeome scale.
Genome Biology. 6 (3): R28.
Silva RM, Miranda I, Moura G, Santos MAS (2004).
Yeast as a model organism for studying the evolution of non-standard genetic codes.
Briefings in Functional Genomics and Proteomics. 3 (1): 35-46.
Silva RM, Gomes AC, Santos JM, Perrot M, Boucherie H, Santos MAS (2003).
On the engineering of a genetic code change in yeast.
Yeast 20 (S1):S151.
Santos JM, Silva RM, Santos MAS (2001).
The global impact of ambiguous mRNA decoding on gene expression.
Europ. J. Biochem. 268 (S1):46.
Santos JM, Silva RM, Domingues P, Amado F, Santos MAS (2001).
Genómica Funcional em Aveiro.
Boletim de Biotecnologia 68:13-18.
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