Centro de Engenharia Biológica (CEB)
Doctoral Program in Chemical and Biological Engineering (CEB)
Lucília Domingues

Phd Thesis

Designing synthetic-Ashbya cell factories (Concluded in 16/09/2019)

Publication and Meetings

Rui Silva is currently a Junior Researcher at the Centre of Biological Engineering (CEB) – University of Minho and the Associate Director at the Molecular Biotechnology Laboratory (LBM).

He holds a PhD degree in Chemical and Biological Engineering from the University of Minho (2019). His PhD research was focused on the development of microbial cell factories through metabolic engineering for the production of high-value chemicals using fermentation processes. This way, he systematically characterized a filamentous fungus (Ashbya gossypii) at physiological, cellular and molecular level and designed strategies for the valorization of industrial wastes. During his PhD, he performed a scientific mission at University of Salamanca (Spain). To date, he is author of seven publications in international peer-reviewed journals, three oral communications and six poster communications in scientific conferences.


Papers in international peer-reviewed journals (during DP_AEM )

·   Díaz-Fernández D, Aguiar TQ, Martín VI, Romaní A, Silva R, Domingues L, Revuelta JL, Jiménez A, 2019. Microbial lipids from industrial wastes using xylose-utilizing Ashbya gossypii strains. Bioresource Technology 293:122054.

·   Silva R, Aguiar TQ, Coelho E, Jiménez A, Revuelta JL, Domingues L, 2019. Metabolic engineering of Ashbya gossypii for deciphering the de novo biosynthesis of ?-lactones. Microbial Cell Factories 18:62.

·  Silva R*, Aguiar TQ*, Oliveira C, Domingues L, 2019. Physiological characterization of a pyrimidine auxotroph exposes link between uracil phosphoribosyltransferase regulation and riboflavin production in Ashbya gossypii. New Biotechnology  50:1-8. *Equal contributions.

·   Silva R, Aguiar TQ, Oliveira R, Domingues L, 2019. Light exposure during growth increases riboflavin production, ROS accumulation and DNA damage in Ashbya gossypii riboflavin-overproducing strains. FEMS Yeast Research 19:foy114.

·   Aguiar TQ, Silva R, Domingues L, 2017. New biotechnological applications for Ashbya gossypii: Challenges and perspectives. Bioengineered 8:309–15.


Other papers in international peer-reviewed journals

· Aguiar TQ*, Silva R*, Domingues L, 2015. Ashbya gossypii beyond industrial riboflavin production: a historical perspective and emerging biotechnological applications. Biotechnology Advances 33:1774–1786. *Equal contributions

·   Silva R*, Aguiar TQ*, Domingues L, 2015. Blockage of the pyrimidine biosynthetic pathway affects riboflavin production in Ashbya gossypii. Journal of Biotechnology 193:37–40. *Equal contributions.




Oral communications 

·   Silva R, Aguiar TQ, Domingues L, 2019. “Towards the valorization of crude glycerol to high-value chemicals by engineered Ashbya gossypii” 7thConference on Physiology of Yeasts and Filamentous Fungi (PYFF7) – Book of Abstracts, 67. Milan, Italy, June 24-27.

·   Silva R, Aguiar TQ, Oliveira R, Domingues L, 2017. “Ashbya gossypii riboflavin overproducing strains are highly susceptible to light-induced oxidative DNA damage” MICROBIOTEC’17 - Book of Abstracts, 61. Porto, Portugal, December 7-9.

·   Silva R, Aguiar TQ, Domingues L, 2016. “Engineering osmotic stress tolerance in the riboflavin producer Ashbya gossypii” BIOIBEROAMÉRICA 2016 - Book of Abstracts, 494. Salamanca, Spain, June 5-8.

Oral communications by invitation

·   Silva R, 2020. “Diversifying beyond Saccharomyces cerevisiae: the engineering potential of the filamentous fungus Ashbya gossypii for biomass-based products and energy” 1st Workshop of BBRI – Biomass and Bioenergy Research Infrastructure. Lisbon, Portugal, February 19.

·   Silva R, 2020. “The filamentous fungus Ashbya gossypii as an alternative cell factory” 8th Workshop of the Doctoral Program in Applied and Environmental Microbiology. Braga, Portugal, February 11.

Poster communications

·   Silva R, Coelho E, Aguiar TQ, Jiménez A, Revuelta JL, Domingues L, 2018. “Volatile compounds’ profiling and engineering of Ashbya gossypiistrains for de novo biosynthesis of lactones” Metabolic Engineering 12 – Book of Abstracts, 85. Munich, Germany, June 24-28.

·   Aguiar TQ, Silva R, Oliveira C, Domingues L, 2017. “Substrate inhibition of uracil phosphoribosyltransferase (UPRT) in distinct microbial species and its implications in the phenotype of uracil auxotrophs” MICROBIOTEC’17 - Book of Abstracts, 437. Porto, Portugal, December 7-9.

·   Silva R, Oliveira R, Aguiar TQ, Domingues L, 2017. “The Ashbya gossypii Comet Assay: measuring oxidative and non-oxidative damage in the DNA” 30 years Molecular Biology of Ashbya gossypii. Basel, Switzerland, April 28.

·   Silva R, Aguiar TQ, Domingues L, 2017. “Deciphering the uracil growth sensitivity of Ashbya gossypii pyrimidine auxotrophs” 30 years Molecular Biology of Ashbya gossypii. Basel, Switzerland, April 28.

·   Silva R, Aguiar TQ, Domingues L, 2016. “Why does uridine supplementation properly rescues the growth of Ashbya gossypii uracil auxotrophs, but not uracil?” XIX National Congress of Biochemistry. Guimarães, Portugal, December 8-10.

·   Silva R, Aguiar TQ, Domingues L, 2016. “Analysis of the sensitivity of different fungal species to uracil” PYFF6 - 6th Conference on Physiology of Yeast and Filamentous Fungi (Programme & Abstract Book). No. P96, 173. Lisbon, Portugal, July 11-14.

Visiting Researcher

Departamento de Microbiología y Genética, University of Salamanca – Salamanca, Portugal (May 2017 - July 2017)

Scientific short-term mission during the PhD: Construction of engineered strains for the de novo biosynthesis of lactones.


Communication Skills DP_AEM/Ana Salgado/AScience (course level 1), 2016. Braga, Portugal, September 30.

Communication Skills DP_AEM/Ana Salgado/AScience (course level 2), 2017. Braga, Portugal, February –  July.


PhD Thesis - Approved, with the final grade of Very Good.