Patrícia
Apura
...
DP_AEM student
Instituto de Tecnologia Química e Biológica (ITQB)
Doctoral Program in Molecular Biosciences (ITQB)
2016-2020
Sandra Viegas
Patrícia
0
0

Phd Thesis

"Post-transcriptional control strategies in Synthetic Biology" - PD/BD/128034/2016 - Defense 21.12.2020

The revolution of genomics and growth of systems biology urged the creation of synthetic biology, an engineering discipline aiming at recreating and reprogramming cellular functions for industrial needs. There has been a large effort in synthetic biology to develop versatile and programmable genetic regulators that would enable the precise control of gene expression. Synthetic RNA components have emerged as a solution, offering a diverse range of programmable functions, including signal sensing, gene regulation and the modulation of molecular interactions. Owing to their compactness, structure and way of action, several types of RNA devices that act on DNA, RNA and protein have been characterized and applied in synthetic biology. RNA-based approaches are more ‘economical’ for the cell, since they are generally not translated. These RNA-based strategies act on a much shorter time scale than transcription-based ones and can be more efficient than protein-based mechanisms. In this PhD, we explored these RNA components as building blocks in the RNA synthetic biology field. The components were tested in two different model microorganisms, the widely studied and industrially used bacterium, Escherichia coli, and one of the most stress resistant and industrially promising bacteria, Pseudomonas putida. The RNA building blocks were thoroughly characterized as relevant and very promising molecular tools for the manipulation of gene expression.

Publication and Meetings

·     Apura, P., Gonçalves, L. G., Viegas, S. C., Arraiano, C. M., “The world of ribonucleases from pseudomonads: a short trip through the main features and singularities”. Microbial Technology, 2021 Aug, Online ahead of print.

·     Apura, P., de Lorenzo, V., Arraiano, C. M., Martínez-García*, E., and Viegas*, S. C., “Ribonucleases control distinct traits of Pseudomonas putida lifestyle”, Environmental Microbiology, (2021) 23(1), 174–189.

·     Apura, P., Saramago, M., Peregrina, A., Viegas, S. C., Carvalho, S. M., Saraiva, L. M., Arraiano, C. M., and Domingues, S., “Tailor-made sRNAs: a plasmid tool to control the expression of target mRNAs in Pseudomonas putida”, Plasmid, Volume 109, May 2020, 102503.

·     Apura, P., Domingues, S., Viegas, S. C., and Arraiano, C. M., “Reprogramming bacteria with RNA regulators”, Biochem Soc Trans. 2019 Oct 31;47(5):1279-1289.

·     Viegas*1, S. C., Apura*, P., Martínez-García, E., de Lorenzo 1, V., Arraiano, C. M., “Modulating Heterologous Gene Expression with Portable mRNA-Stabilizing 5'-UTR Sequences",  ACS Synth Biol. 2018 Sep 21;7(9):2177-2188. *equal contribution


 

Year 1

Participation in the 1st Joint Workshop of the PhD Programs in Applied and Environmental Microbiology (DP_AEM) - Molecular And Environmental Biology (PDBMA), 26-30 September 2016, Anfiteatro ECUM, Campus de Gualtar, Universidade do Minho;

Oral presentation entitled "Noncoding RNAs as tools to modulate gene expression in synthetic biology” - Patrícia Apura (AEM PhD student – 15th February at 16h40) in the 2nd Joint Biotecnico and AEM PhD Programs Workshop, 15-16 February 2017 at Instituto Superior Te?cnico - South Tower, QA02.1;

Poster presentation entitled in the 2nd Joint Biotecnico and Aem PhD Programs Workshop, 15-16 February 2017 at Instituto Superior Te?cnico - South Tower, QA02.1;

Year 2

Oral presentation entitled “Post transcriptional control strategies in Synthetic Biology” – Patrícia Apura (AEM PhD student – 26th September at 15h30) in the 2nd Joint Workshop Of The Phd Programs In Applied And Environmental Microbiology (DP_AEM) Molecular And Environmental Biology (PDBMA), 25-29 September 2017, Anfiteatro ECUM, Campus de Gualtar, Universidade do Minho;

Oral presentation entitled “Post-transcriptional control strategies in Synthetic Biology” – Patrícia Apura (AEM PhD student – 12th June at 9h45) in the 3rd Joint Biotecnico and AEM PhD Programs Workshop, 11-12 June 2018, IST Congress Center, Instituto Superior Técnico, Campus Alameda;

Year 3

Participation in the 7th Workshop of the Doctoral Program in Applied and Environmental Microbiology, 24-27 September 2018, Auditório IB-S (edifico 18) Campus de Gualtar Universidade do Minho;

Year 4

Participation in the 8th Workshop of the Doctoral Program in Applied and Environmental Microbiology, 10-12 February 2020, Auditório IB-S (edifico 18) Campus de Gualtar Universidade do Minho;

Oral presentation entitled “Post-transcriptional control strategies in Synthetic Biology” – Patrícia Apura (AEM PhD student – 15th September at 14h30) in the PhD students’ seminars 20/21, videoconference; 

 

 

Oral communication: 

·     Apura, P., de Lorenzo, V., Gonc?alves, L. G., Marti?nez-Garci?a, E., Arraiano, C. M., and Viegas, S. C., “A short trip to the world of Pseudomonas putida’s ribonucleases” (14-16 Outubro 2021), XXI National Congress of Biochemistry “Tunning Biochemistry with Life and Society”, Évora, Portugal. Prémio de melhor apresentação flash.

·     Apura, P., Arraiano, C. M. and Viegas, S. C., “Post-transcriptional Control Strategies in Synthetic Biology”, DP_AEM PhD students’ seminar, 15 September 2020, videoconference.

·     Apura, P., Arraiano, C. M. and Viegas, S. C., “Post-transcriptional Control Strategies in Synthetic Biology”, 10th PhD students’ meeting, 22-24 January 2020, ITQB NOVA, Oeiras, Portugal.

·     Apura, P., Viegas, S. C., Martínez-García, E., de Lorenzo, V. and Arraiano, C. M., “How ribonucleases control different traits of P. putida metabolism”, EMBO Workshop – Creating is Understanding: Synthetic Biology Masters Complexity, 22-25 September 2019, Heidelberg, Germany.

·     Apura, P., Viegas, S. C., Martínez-García, E., de Lorenzo, V. and Arraiano, C. M., “Post-transcriptional control strategies in Synthetic Biology”, 3rd Joint Biotecnico and AEM PhD Programs Workshop, 11-12 June 2018, IST Congress Center, Instituto Superior Técnico, Campus Alameda.

·     Apura P., Saramago M., Viegas, S. C., Domingues S. M, Arraiano C. M., 5th General Assembly of EmPower Putida Project (EPP), 20-21 November 2017. Surgeons' Hall Prince Philip Building, Edinburgh, UK.

·     Apura, P., Arraiano, C. M., Viegas, S. C. ,“Post transcriptional control strategies in Synthetic Biology”, 2nd Joint Workshop Of The Phd Programs In Applied And Environmental Microbiology (DP_AEM) Molecular And Environmental Biology (PDBMA), 25-29 September 2017, Anfiteatro ECUM, Campus de Gualtar, Universidade do Minho, Braga, Portugal.

·     Apura, P., Arraiano, C. M., Viegas, S. C., "Noncoding RNAs as tools to modulate gene expression in synthetic biology”, 2nd Joint Biotecnico and AEM PhD Programs Workshop, 15-16 February 2017 at Instituto Superior Técnico - South Tower, QA02.1, Lisbon, Portugal.

·     Apura P., Saramago M., Viegas, S. C., Domingues S. M., Arraiano C. M., 3rd General Assembly of EmPower Putida Project (EPP), 21-23 November 2016. Spanish National Research Council (CSIC) - Belgium.

 

Poster communication:

 

·     Apura, P., de Lorenzo, V., Gonc?alves, L. G., Marti?nez-Garci?a, E., Arraiano, C. M., and Viegas, S. C., “A short trip to the world of Pseudomonas putida’s ribonucleases” (14-16 Outubro 2021), XXI National Congress of Biochemistry “Tunning Biochemistry with Life and Society”, Évora, Portugal.

·     Apura, P., Saramago, M., Peregrina, A., Viegas, S.C., Carvalho, S. M., Saraiva, L. M., Domingues, S. M., and Arraiano, C. M., “Small noncoding RNAs as a tool to modulate gene expression” (Julho 2021), 45th FEBS congress, online conference.

·     Apura, P., Saramago, M., Peregrina, A., Viegas, S.C., Carvalho, S. M., Saraiva, L. M., Domingues, S. M., and Arraiano, C. M., “Small noncoding RNAs as a tool to modulate gene expression” (Junho 2021), 20th FEBS Young Scientist Forum meeting, online conference.

·     Apura, P., de Lorenzo, V., Arraiano, C. M, Martínez-García, E., and Viegas, S. C., “Looking into the effects of ribonucleases’ absence in Pseudomonas putida’s traits” (May 2021), RNA 2021, Online Conference.

·     Apura, P., Peregrina, A., Viegas, S.C., Saramago, M., Sandra M. Carvalho, Lígia M. Saraiva, Domingues, SM., and Arraiano, C.M., "small noncoding RNAs as a tool to modulate gene expression" (March 2020), 6th Joint Conference of the DGHM & VAAM, Leipzig, Germany.

·     Apura, P., Viegas, S. C., Martínez-García, E., de Lorenzo, V. and Arraiano, C. M., “How ribonucleases control different traits of P. putida metabolism” (September and October 2019), FEBS Advanced Lecture Course – Biosystem Design: Computational and Experimental Approaches, Spetses, Greece.

·     Apura, P., Viegas, S. C., Martínez-García, E., de Lorenzo, V. and Arraiano, C. M., “How ribonucleases control different traits of P. putida metabolism” (September 2019), EMBO Workshop – Creating is Understanding: Synthetic Biology Masters Complexity, Heidelberg, Germany.

·     Apura, P., Viegas, S. C., Martínez-García, E., de Lorenzo, V. and Arraiano, C. M., “How ribonucleases control different traits of P. putida metabolism” (July 2019), Encontro Ciência 19, Lisboa, Portugal.

·     Apura, P., Viegas, S. C., Martínez-García, E., de Lorenzo, V. and Arraiano, C. M., “Modulating heterologous gene expression with portable mRNA-stabilizing 5’-UTR sequences” (July 2018), Encontro Ciência 18, Lisboa, Portugal.

·     Apura, P., Viegas, S.C., Saramago, M., Domingues, SM., Casinhas, J. and Arraiano, C.M., “Using small noncoding RNAs to modulate gene expression in Synthetic Biology” (July 2017), Encontro Ciência 17.

·     Apura, P., Viegas, S.C., Saramago, M., Domingues, SM., Casinhas, J. and Arraiano, C.M., “Small noncoding RNAs as tools to modulate gene expression in Synthetic Biology” (June 2017), XLI Jornadas Portuguesas de Genética. Best Poster Presentation Prize at XLI JPG.

·     Apura, P., Viegas, S.C., Saramago, M., Domingues, SM. and Arraiano, C.M “Studies of small non-coding RNAs and ribonucleases in Pseudomonas putida: a stress-resistant microorganism with industrial interest” (December 2016), Jornadas Portuguesas de Bioquímica. Best Poster Presentation Prize at SPB2016.

-Member of the organizer committee of the 8th ITQB NOVA PhD Student’s Meeting, 14-16 November 2018, ITQB NOVA, Portugal.

-Exhibiton and Dissemination of Science in the context of the “ITQB Week Science” in EB/JI Fernando Teixeira Lopes School, February 2020, Oeiras.

 

 

 

Training

-FEBS Advanced Lecture Course – Biosystem Design: Computational and Experiemntal Approaches, 29th September - 7th October 2019, Spetses, Greece.

Awards

- Awarded as the best flash poster communication at the Symposium 6 Functional Genomics and Systems Biology /8 Proteins in Health and Environment /9 Chemical Biology, Drug Discovery and Development, at the XXI National Congress of Biochemistry “Tunning Biochemistry with Life and Society”, 14-16 October 2021, Évora, Portugal.

-EMBO Travel Grant for the EMBO Workshop: Creating is Understanding: Synthetic Biology Masters Complexity, 22-25 September 2019, EMBL Heidelberg.

-Awarded with best Poster Presentation Prize at XLI JPG, with the work entitled “Small noncoding RNAs as tools to modulate gene expression in Synthetic Biology”, XLI Jornadas Portuguesas de Genetica, June 2017, Aveiro, Portugal.

-Awarded best Poster Presentation Prize at SPB2016 with the work entitled “Studies of small non-coding RNAs and ribonucleases in Pseudomonas putida: a stress-resistant microorganism with industrial interest”, Jornadas Portuguesas de Bioquimica, December 2016, Guimarães, Portugal.

 

Current position:

-Research fellow at the Control of Gene Expression Laboratory, ITQB-NOVA.