Ana Sofia Conceição Fernandes (A413-C6CD-2A77)

Curriculum Vitae

Ana Sofia Conceição Fernandes

I embarked on my journey in immunology research in 2008-2009, delving into the effects of antiretroviral therapies on HIV-2 infected patients. My passion lies in translating lab discoveries into impactful products, leading me to join Technophage during my master's studies (2009-2010). Here, I focused on producing and purifying recombinant viral proteins, aiming to revolutionize conventional antibiotics. These studies resulted in 3 original publications. My doctoral studies (2012-2016) expanded on these themes, unraveling the regulatory elements of these proteins and exploring their potential in enzibiotic therapy. The significant contributions to the field can be attested in 3 original publications and a PhD thesis. As a postdoc scientist at iNOVA4Health's Translational Medicine Program, I enriched my expertise in molecular biology and virology. My journey took an exciting turn towards gene therapy, particularly in optimizing adeno-associated virus (AAV) production platforms in both insect and mammalian cells (2017 – present). My contributions extend to implementing analytical methods and characterization protocols for assessing vector productivity, purity, and biological activity since 2017. My objective is to advance scientific knowledge in AAV-based gene therapies manufacturing and enhance accessibility for patients by lowering costs through process optimization. These results can be evaluated in 3 original publications. In 2021, my project secured funding from iBETXplore (50 k), wherein I implemented ddPCR technology to quantify AAV samples. This initiative led to the development of a fully characterized AAV reference material, validated through various analytics, facilitating analyses by other research teams. With ten scientific publications and involvement in grant applications and article reviews for prestigious journals like Scientific Reports, I've cultivated a diverse skill set. I've undergone a clinical trials course and honed my planning and organizational skills as a lab manager. My commitment to continuous improvement is evident in my pursuit of leadership and project management courses, enhancing my emotional intelligence and delegation abilities. Beyond research, my commitment extends to education. I actively contribute to teaching biopharmaceutical and BCA classes and have mentored junior investigators, guiding them through internships, master's dissertations, and professional challenges. Currently, I co-supervise a PhD student, contributing to their academic and professional growth.

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Identification

Personal identification

Full name: Ana Sofia Conceição Fernandes

Citation names

Fernandes, Sofia

Author identifiers

Ciência ID: A413-C6CD-2A77
ORCID iD: 0000-0002-9035-793X

Email addresses

as.fernandes@ibet.pt (Professional)

Telephones

Telephone

214469512 Ext.: 1512 (Professional)

Addresses

IBET - Instituto de Biologia Experimental e Tecnológica . Apartado 12 , 2780-901 , Oeiras, Oeiros, Portugal (Professional)

Websites

https://pt.linkedin.com/in/sofia-fernandes-6676051a (Social media)

Knowledge fields

Medical and Health Sciences - Medical Biotechnology - Technologies Involving the Manipulation of Cells, Tissues, Organs or the Whole Organism
Natural sciences - Biological Sciences - Microbiology

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
English	Advanced (C1)	Proficiency (C2)	Advanced (C1)	Advanced (C1)	Upper intermediate (B2)
Portuguese (Mother tongue)

Education

	Degree	Classification
2023 Concluded	Professional Development course (Outros) Hfp-Consulting, Germany
2021/10/04 - 2021/10/08 Concluded	Bioprocessing and Manufacturing of Gene and Cell Therapy Products Course 1st Ed (Outros) European Society for Animal Cell Technology, Germany
2021 - 2021 Concluded	Leading with Emotional Intelligence (Outros) Synergie, Portugal
2012/04/01 - 2016/11/22 Concluded	Pharmacy (Doutoramento) Major in Microbiology Universidade de Lisboa Faculdade de Farmácia, Portugal "Endolysins as Antibacterial Agents: from Engineering Approaches to the Uncovering of Holin as a Key Factor Influencing Lytic Activity " (THESIS/DISSERTATION)	Qualified with Distiction and Honours
2011/09 - 2011/11 Concluded	Clinical Trials Monitor 2nd Ed. (Diploma de especialização) Eurotrials Consultores Científicos SA, Portugal
2011 Concluded	Clinical Research Monitoring Course, (Outros) Eurotrials Consultores Científicos SA, Portugal	Aprovado
2009 Concluded	Microbiologia Aplicada (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal "Utilization of bacteriophage endolysins to control pathogenic Gram-positive bacteria" (THESIS/DISSERTATION)	18
2008 Concluded	Microbiologia (Licenciatura) Universidade de Lisboa Faculdade de Medicina, Portugal "Investigation of B lymphocyte abnormalities in Human Immunodeficiency Virus- 2 (HIV-2 ) infection" (THESIS/DISSERTATION)	16

Affiliation

Science

	Category Host institution	Employer
2017/01/02 - Current	Postdoc (Research)	iNOVA4Health, Portugal

2016 - 2016	Researcher (Research)	Instituto de Medicina Molecular, Portugal

2012 - 2016	Researcher (Research)	Universidade de Lisboa Instituto de Investigação do Medicamento, Portugal

2010 - 2012	Researcher (Research)	Universidade de Lisboa Instituto de Investigação do Medicamento, Portugal
	Universidade de Lisboa Faculdade de Farmácia, Portugal
2008 - 2010	Research Trainee (Research)	Instituto de Medicina Molecular, Portugal
	Universidade de Lisboa Faculdade de Medicina, Portugal
2006/10/09 - 2007/02/28	Research Trainee (Research)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Others

	Category Host institution	Employer
2005/01/02 - 2011/10/31	Backoffice/Call center operator During my graduations , I have always worked, performing different activities of inbound and market research, being responsible for clients contact and sales registrat	Empresas Trabalho Temporário, Portugal

Projects

Grant

	Designation	Funders
2017/01/01 - 2017/06/30	iNOVA4Health - Programme in Translational Medicine (iBET, CEDOC/FCM, IPOLFG and ITQB) 001/BPD/2017 Post-doc Fellow Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2016/09 - 2016/12	AXIAL.EC - PRINCIPLES OF AXIAL POLARITY - DRIVEN VASCULAR PATTERNING IMM/BI/31-2016 Integration into Research Grant Fellow Instituto de Medicina Molecular, Portugal	European Research Council
2012/04 - 2016/04	Endolysins as Antibacterial Agents: from Engineering Approaches to the Uncovering of Holin as a Key Factor Influencing Lytic Activity SFRH/BD/81802/2011 PhD Student Fellow Universidade de Lisboa Faculdade de Farmácia, Portugal	Ministério da Ciência Tecnologia e Ensino Superior
2013/04 - 2014/09	PhageDuction: a new bacteriophage-based technology for efficient cell-targeted DNA delivery Provided by PTCRIS: 125218 125218 Integration into Research Grant Fellow Universidade de Lisboa Faculdade de Farmácia, Portugal	Fundação para a Ciência e a Tecnologia, I.P.
2009/01 - 2012/06	Bacteriophage genome delivery to Gram-positive bacteria: virus and host cell requirements for DNA traffic Provided by PTCRIS: 66412 66412 Integration into Research Grant Fellow Universidade de Lisboa Faculdade de Farmácia, Portugal	Fundação para a Ciência e a Tecnologia, I.P.

Contract

	Designation	Funders
2017/07/01 - Current	iNOVA4Health - Programme in Translational Medicine (iBET, CEDOC/FCM, IPOLFG and ITQB) info:eu-repo/grantAgreement/FCT/5876/147260/PT Post-doc Instituto de Biologia Experimental e Tecnológica, Portugal	Ongoing

Outputs

Publications

Journal article

Mariana Massapina Valentim Ferreira; Sofia Fernandes; Ana Isabel Almeida; Salomé Neto; João P. Mendes; R.J.S. Silva; Cristina Peixoto; Coroadinha, A.S.. "Extending AAV Packaging Cargo through Dual Co-Transduction: Efficient Protein Trans-Splicing at Low Vector Doses". International Journal of Molecular Sciences 24 13 (2023): 10524-10524. http://dx.doi.org/10.3390/ijms241310524.
10.3390/ijms241310524
Coroadinha, A.S.; Sofia Fernandes; Joana Diogo. "Mammalian Stable Cell Platforms for Recombinant Adeno-associated Virus (rAAV) Production: Development Strategies and their Impact on Viral Productivity". Current Gene Therapy 23 (2023): http://dx.doi.org/10.2174/1566523223666230331111336.
10.2174/1566523223666230331111336
Nikolaus Virgolini; Ryan Hagan; Ricardo Correia; Marco Silvano; Sofia Fernandes; Paula M. Alves; Colin Clarke; António Roldão; Inês A. Isidro. "Transcriptome analysis of Sf9 insect cells during production of recombinant Adeno-associated virus". Biotechnology Journal 18 2 (2023): 2200466-2200466. http://dx.doi.org/10.1002/biot.202200466.
10.1002/biot.202200466
Fernandes S; São-José C. "Enzymes and Mechanisms Employed by Tailed Bacteriophages to Breach the Bacterial Cell Barriers.". Viruses (2018): http://europepmc.org/abstract/med/30060520.
10.3390/v10080396
Fernandes S; São-José C. "Probing the function of the two holin-like proteins of bacteriophage SPP1.". (2017): http://europepmc.org/abstract/med/27825035.
10.1016/j.virol.2016.10.030
Fernandes S; Labarde A; Baptista C; Jakutytè L; Tavares P; São-José C. "A non-invasive method for studying viral DNA delivery to bacteria reveals key requirements for phage SPP1 DNA entry in Bacillus subtilis cells.". (2016): http://europepmc.org/abstract/med/27179995.
10.1016/j.virol.2016.05.004
Fernandes, S.; São-José, C.. "More than a hole: the holin lethal function may be required to fully sensitize bacteria to the lytic action of canonical endolysins". Molecular Microbiology 102 1 (2016): 92-106. http://www.scopus.com/inward/record.url?eid=2-s2.0-84988528084&partnerID=MN8TOARS.
10.1111/mmi.13448
Tendeiro R; Fernandes S; Foxall RB; Marcelino JM; Taveira N; Soares RS; Baptista AP; et al. "Memory B-cell depletion is a feature of HIV-2 infection even in the absence of detectable viremia.". (2012): http://europepmc.org/abstract/med/22695303.
10.1097/QAD.0b013e3283568849
Fernandes S; Proença D; Cantante C; Silva FA; Leandro C; Lourenço S; Milheiriço C; et al. "Novel chimerical endolysins with broad antimicrobial activity against methicillin-resistant Staphylococcus aureus.". (2012): http://europepmc.org/abstract/med/22432707.
10.1089/mdr.2012.0025
Proença D; Fernandes S; Leandro C; Silva FA; Santos S; Lopes F; Mato R; et al. "Phage endolysins with broad antimicrobial activity against Enterococcus faecalis clinical strains.". (2012): http://europepmc.org/abstract/med/22480295.
10.1089/mdr.2012.0024

Thesis / Dissertation

Fernandes, Sofia. "Endolysins as antibacterial agents : from engineering approaches to the uncovering of holin as a key factor influencing lytic activity". PhD, Universidade de Lisboa Faculdade de Farmácia, 2016. http://hdl.handle.net/10451/26318.
Fernandes, Ana Sofia Conceição. "Utilização de lisinas de bacteriófagos no controlo de bactérias patogénicas gram-positivas". Master, 2009. http://catalogo.ul.pt/F/?func=item-global&doc_library=ULB01&type=03&doc_number=000574338.

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2021/11/16	Implementation of a High-Yield AAV Vector Production in 293T Cell Suspension Cultures	Addressing challenges in the Cell & Gene Therapy industry TFS
2021/10/21	Benefits of using a media panel to address the diversity of HEK293 cell lines	European Society of Gene and Cell Therapy (ESGCT) European Society of Gene and Cell Therapy

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2019 - 2021	Establishment of 293 based AAV packaging cell lines using shRNA-mediated rep silencing Co-supervisor of Joana Gaspar Diogo	Master of Science in Biotechnology (Master) Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Event participation

	Activity description Type of event	Event name Institution / Organization
2021/09/01 - 2021/09/04	Media development strategies to increase AAV titer at large scale Conference	6th European Congress of Immunology
2012/07/16 - 2012/07/20	Poster Presentation A novel universal method for studying molecular and biophysical requirements for bacteriophage infection: the case of phage SPP1 DNA entry into Bacillus subtilis Conference	Viruses of Microorganisms: From Exploration to Applications in the -omics Era
2011 - 2011	Poster presentation, Novel chimerical phage endolysins with antimicrobial activity against MRSA and other pathogenic Gram positive bacteria Conference	Microbial Viruses: Genomics, Evolution and Applications in Ecology, Biotechnology and Medicine Queen's University Belfast, United Kingdom
2010/06/21 - 2010/06/25	Poster Presentation: Recognition of segments of the B. subtilis YueB protein required for its phage SPP1 receptor activity Conference	Viruses of Microorganisms: From Bacteriophages to Viruses of Microorganisms Institut Pasteur Département de Virologie, France

Committee member

	Activity description Role	Institution / Organization
2014 - 2014	Member of iMed.ULisboa Postgraduate Students Commission, involved in organization of workshops, the 6th Postgraduate iMed.ULisboa Students Meeting and other social events that brings together all postgraduate students at iMed.ULisboa. Member	Universidade de Lisboa Faculdade de Farmácia, Portugal
2005 - 2007	Involved in the organization of meetings with Microbiology's Pedagogical committee. Member	Universidade de Lisboa Faculdade de Medicina, Portugal

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2018 - 2023	Biopharmaceuticals Teaching support in practical classes of Biopharmaceuticals and BCA, in 4 masters of Nova School of Science and Technology (Bioquímica, Bioquímica para a Saúde, Biotecnologia and Genética Molecular e Biomedicina).	(Mestrado)	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Mentoring / Tutoring

	Topic	Student name
2022/09 - Current	Deciphering Adeno-Associated Virus vectors replication and assembly: improving gene therapy vectors	Júlia Reis de Lidon Brandão Guerra
2015 - 2015	Pharmacy	Sandra Silva
2013 - 2013	Applied Microbiology	Nuno Santos
2011 - 2011		Nuno Santos

Other jury / evaluation

	Activity description	Institution / Organization
2022 - 2022	Chair in the 12th ITQB NOVA PhD Students' Meeting	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021 - 2021	Chair in the 11th ITQB NOVA PhD Students' Meeting	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020 - 2020	Chair in 10th ITQB NOVA PhD Student´s Meeting	Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Distinctions

Award

2021	iBETXplore Instituto de Biologia Experimental e Tecnológica, Portugal

Other distinction

2011	Winner of the second place in a Poster's Contest Queen's University Belfast, United Kingdom