Bioengineering Systems | PhD Alumni

IST | Bioengineering PhD | Entering year: 2007

Research topic/area: Acoustic Biosensors for Biomedical and Biotechnology Applications(Biomedical Devices & Technologies).

Communications/Conference presentations:

• Vistas, C.; Silva, A.C.; Thibaud, C.; Brayner, R. Biosynthesis of new hybrid materials based on Alginate-Au, and Carrageenan-Ag. SERS effect for bio-detection applications, Therapeutic Nano-objects Genoconference,12th June 2007, Evry/France.

Links:

www.cbme.ualg.pt

www.ibb.pt

FCTUNL | Bioengineering Systems PhD | Entering year: 2012 | Graduation year: 2017

FCUL | Bioengineering Systems PhD | Entering year: 2011| Graduation year: 2016

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Thesis Title: Analysis of the Gene Regulatory Network underlying pluripotenciality in mouse Embryonic Stem cells

Supervisors: Domingos Manuel Pinto Henrique and Cláudia Lobato da Silva

Summary: Pluripotentiality and self-renewal are the two main features that define the stemness state of Embryonic Stem (ES) cells. The gene network underlying pluripotentiality has been extensively studied and a consensual view is that the NOS (Nanog, Oct4 and Sox2) network of transcription factors plays a central role in regulating ES cell status. Still, how stemness emerges from the integrated activity of this network is far from understood. Recent work has revealed a critical interaction of between the NOS network and the FGF/ERK pathway, with the balance playing a crucial role in the maintenance of stemness. In this project, I propose to design novel reporter ES cell lines that can be used as tools to understand the dynamics of the NOS-FGF/ERK interactions, and how fluctuations in Nanog levels and variations in FGF/ERK signaling components underlie a state in which individual stem cells are able to simultaneously manifest their pluripotency features while being ready to respond to differentiation inducing signals.

FCTUNL | Bioengineering PhD | Entering year: 2007

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PhD supervisor: Margarida Archer (ITQB-UNL) ; Li-Huei Tsai (PILM-MIT)

Thesis Title (2013): Funcional and structural studies of two enzymes: membrane bound kinaseand Z-DNA/Z-RNA binding protein

Thesis Abstract: The neocortex is a unique structure designed for higher cognitive and associative functions. Herein, we will refer to the work performed to assess the role of TAOK2α, a specific membrane bound kinase, in the mammalian neocortical development. The results obtained, delineate a pathway whereby Semaphorin3A and Neuropilin1 transduce signals through TAOK2α and c-Jun N-terminal Kinase to regulate basal dendrite development and migration in cortical neurons. This work represents the first approach aimed at understanding the mechanisms responsible for the delineation of basal and apical dendrites during pyramidal neuron development in the embryo, and how such mechanism may evolve to neocortical disconnection disorders. Additional work performed on humanTAOK2α focused at the determination of its three-dimensional structure by X-ray crystallography to elucidate its regulatory mechanism. The 20th century exciting discovery of the DNA left-handed conformation, and the fact it binds to certain classes of proteins with high affinity and specificity, indicated a biological role to it. However, a full function is still to be elucidated. The human double-stranded RNA adenosine deaminase (ADAR1) is the best characterized of all Z-DNA binding proteins, where Zα domain binds and stabilizes Z-DNA/Z-RNA forms upon binding. The second part of this thesis describes the work on the ZαADAR1 domain that binds to Z-RNA/Z-DNA. When a section of a DNA or RNA molecule forms a left-handed Z-DNA/Z-RNA segment, two B-Z/A-Z junctions are formed. Herein, we describe the study carried out on the formation of Z-Z junctions from DNA and, also, the approach on trying to describe the Z-Z junction for RNA when interacting with ZαADAR1. The structure of the Z-Z-DNA junction consists of a single base pair that leads to partial or full disruption of the helical stacking. The junction region allows intercalating agents to insert themselves into the left-handed helix, which is otherwise resistant to intercalation.

Full thesis available for download at Universidade Nova de Lisboa’s Repository

Ana Rosário has successfully discussed her thesis onDecember, 2013, with the following members of the jury:

• Maria Armenia Abreu Fonseca de Carvalho Teixeira Carrondo, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa;
• Manuel Luis de Magalhaes Nunes da Ponte,Faculdade de Ciências e Tecnologia da Universidade Nava de Lisboa;
• Luis Miguel Gales Pereira Pinto, Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto;
• Domingos Manuel Pinto Henrique, Instituto de Histologia e Biologia do Desenvolvimento da Faculdade de Medicina da Universidade de Lisboa;
• Shabir Husein Najmudin, Faculdade de Medicina Veterinaria Universidade de Lisboa;
• Margarida Archer Baltazar Pereira da Silva Franco Frazão, Instituto de Tecnologia Química e Biológica da Universidade Nova de Lisboa;

Publications:

• Pikyee Ma, Filipa Varela, Malgorzata Magoch, Ana Rita Silva, Ana Lúcia Rosário, José Brito, Tânia Filipa Oliveira, Przemyslaw Nogly, Miguel Pessanha, Meike Stelter, Arnulf Kletzin, Peter J.F. Henserson, Margarida Archer. “An Efficient Strategy for Small-Scale Screening and Production of Archaeal Membrane Transport Proteins in Escherichia Coli.” Edited by Hendrik W. van Veen. PLoS ONE 8, no. 10 (October 7, 2013): e76913. doi:10.1371/journal.pone.0076913.
• Rosa, M. de, Sanctis, D. de, Rosario, A.L., Archer, M., Rich, A., Athanasiadis, A., Carrondo, M.A., 2010. Crystal structure of a junction between two Z-DNA helices. Proc. Natl. Acad. Sci. 107, 9088–9092. doi: 10.1073/pnas.1003182107.
• De Anda, F.C., Rosario, A.L., Durak, O., Tran, T., Gräff, J., Meletis, K., Rei, D., Soda, T., Madabhushi, R., Ginty, D.D., Kolodkin, A.L., Tsai, L.-H., 2012. Autism spectrum disorder susceptibility gene TAOK2 affects basal dendrite formation in the neocortex. Nat. Neurosci. 15, 1022–1031. doi: 10.1038/nn.3141

FCT-UNL | Bioengineering PhD | Entering year: 2011 | Graduation year: 2016

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Current position: Research Scientist at Isogenica

Thesis Title: Exploring new protein-based scaffolds for bioengineering applications

Supervisors: Cecilia Roque (FCT-UNL); Olga Iranzo (former at ITQB- UNL, Oeiras, Portugal at present in Institut des Sciences Moléculaires de Marseille, Aix Marseille Université CNRS, Marseille)

IST | Bioengineering PhD | Entering year: 2007

Research topic/area: Stem Cell BioEngineering

Publications:

• Fernandes, A.M., Fernandes, T.G., Diogo M.M., Lobato da Silva, C., Henrique D., Cabral, J.M.S. Mouse Embryonic Stem Cell Expansion in a Microcarrier-Based Stirred Culture System, Journal of Biotechnology, 132 (2007), 227-236 (doi:10.1016/j.jbiotec.2007.05.031)

Communications/Conference presentations:

• Ana M. Fernandes, Tiago G. Fernandes, Maria Margarida Diogo, Cláudia Lobato da Silva, Domingos Henrique, Jonathan S. Dordick and Joaquim M.S. Cabral, Micro-scale and Bioreactor Systems for the Expansion of mouse embryonic stem (mES) cells, CHEMPOR 2008: 10th International Chemical and Biological Engineering Conference, Braga, Portugal, 4-6 September 2008

• Fernandes, A.M., Diogo M.M., Lobato da Silva, C., Henrique D., Cabral, J.M.S., Mouse embryonic stem cell expansion in a microcarrier-based stirred culture system, Tissue Engineering and Regenerative Medicine International Society, 2008 Annual TERMIS – EU Meeting, Porto, Portugal, June 22-26, 2008

• Gemma Eibes, Ana M. Fernandes, Maria Margarida Diogo, Cláudia Lobato da Silva, Joaquim M. S. Cabral, Modeling of mouse embryonic stem cell expansion in a strirred culture system, III International Meeting of the Portuguese Society of Stem Cells and Celular Therapy, Portugal, April 23-24, 2008

• Maria Margarida Diogo, Ana M. Fernandes, Tiago G. Fernandes, Cláudia Lobato da Silva, Domingos Henrique, Jonathan S. Dordick and Joaquim M.S. Cabral, Large-scale and nano-scale approaches for the expansion of mouse embryonic stem (mES) cells, Third International Meeting of SPCE-TC, Faro, Portugal, 23-24 April 2008

• Diogo MM, Fernandes AM, Fernandes TG, Lobato da Silva C, Henrique D and Cabral JMS, Optimization of expansion and neural commitment of mouse embryonic stem cells, MicroBiotecXXXIII JPG 2007, Lisboa, Portugal, 30 Novembro-02 Dezembro 2007

• Fernandes, A.M., Diogo M.M., Lobato da Silva, C., Henrique D., Cabral, J.M.S., Scale-up of Mouse Embryonic Stem Cell Expansion in a stirred culture system, II International Meeting of the Portuguese Society of Stem Cells and Celular Therapy, Portugal, April 27-28, 2007

• Fernandes, A.M., Diogo M.M., Lobato da Silva, C., Henrique D., Cabral, J.M.S., Scale-up of Mouse Embryonic Stem Cell Expansion in a stirred culture system, International Courses on Toxicology 2007, Center for Neurosciences and Cell Biology, University of Coimbra, Portugal, March 21-23, 2007

• Cabral, J.M.S., Diogo, M.M., Lobato da Silva, C., Fernandes, A.M., Fernandes, T.G., Domingos, H., Optimization and Integration of the Expansion and Neural Commitment of Mouse Embryonic Stem Cells, 6th European Symposium on Biochemical Engineering Science, 2006

Research interests: Bioreactors for ex vivo expansion of mouse embryonic stem cells; Metabolic profiling of animal cell culture

Links:

http://www.ist.utl.pt/ (IST)

http://www.ibb.pt/ (Institute for Biotechnology and Bioengineering)

http://dequim.ist.utl.pt/cebq/berg/index.html (BioEngineering Research Group)

IST | Bioengineering PhD | Entering year: 2007 | Graduation year: 2011

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Current Position: Post-Doc Researcher in Stem Cell Bioengimeering and Regenerative Medicine at Instituto Superior Técnico

Thesis Title: Bioreactor culture systems for the expansion of mouse embryonic stem cells

Supervisors: Joaquim Sampaio Cabral (IST-UL), Cláudia Lobato da Silva (IST-UL), Margarida Diogo (IST-UL)

FCTUNL | Bioengineering PhD | Entering year: 2009

Supervisor: Jorge Manuel Mateus Martins; Co – Supervisor: Dava Jean Newman (MIT) and Miguel PedroTavares da Silva (IST)

Thesis (2014): On The Development Of An Active Soft Second-Skin Orthotic For Dropfoot Patients

FCT-UNL | Bioengineering PhD | Entering year: 2010 | Graduation year: 2015

Thesis Title: Green oil production from alternative sources

Supervisors: Susana Barreiros (FCTUNL), Alexandre Paiva (FCTUNL)

UMinho | Bioengineering Systems PhD | Entering year: 2013/2014

Research area: Bioengineering, Biotechnology and Biochemistry

Supervisor: Isabel Rocha (CEB-University of Minho)

Thesis topic: The growing global demand for new energy sources combined with environmental concerns had motivated the search for alternative fuels, produced from renewable raw materials. In this sense, butanol is considered the next generation of biofuels due to its superior fuel characteristics when compared with ethanol, including higher energy density, lower hygroscopicity and volatility. Besides its application as fuel, butanol has an important role in the manufacturing of pharmaceuticals, polymers, herbicide esters and butyl xanthate, and is also used as solvent for paints, coatings, natural resins, gums, synthetic resins, dyes, and alkaloids.

Butanol is naturally produced by solventogenic bacteria trough Acetone-Butanol-Ethanol (ABE) fermentation, usually with low productivities. Thus, most of butanol is currently chemical synthesised via petrochemical routes and its price is extremely sensitive to crude oil’s price, becoming imperative to seek for alternative ways to produce it. One possible approach is to express novel biosynthetic pathways in more user-friendly hosts as E. coli or Saccharomyces cerevisiae. In this sense, this work aims at evaluating and implementing in vivo novel pathways to produce butanol. These heterologous pathways, previously generated using a (hyper)graph-based algorithm, will be evaluated according to diverse criteria such as size of the solution, yield and novelty. Then, the pathways identified as the most promising ones will be implemented in vivo either in E. coli or S. cerevisiae. Finally, advanced techniques will be used to characterize and further improve the developed strains, including omics analyses and directed evolution.

IST | Bioengineering PhD | Entering year: 2008

PhD Supervisor: João Sousa (IST), Stan Neil Finkelstein (MIT)

PhD Thesis (2012): Knowledge Discovery in Intensive Care Unit Shock Patients

Andre’s PhD work address a common clinical issue between patients in an intensive care unit (ICU) – Shock – by determining the extent to which variations in the processes of care influence outcome. By using a variety of advanced data mining/analytic techniques, the two main goals of his work includes the establishment of a robust quantitative basis for systems-based interventions to improve outcomes in the ICU shock patients; and the development of a reproducible framework for applying the data mining strategies to other healthcare venues.

IST | Bioengineering Systems PhD | Entering year: 2012/2013

Research area: Bioengineering

PhD Supervisor: Rogério Colaço (Instituto Superior Técnico – Universidade de Lisboa)

Thesis Topic: The main aim of the work plan is to develop and optimize surface modified/coated drug-releasing hydrogels to be used in therapeutic ophthalmic lenses. For that, different surface coating/modification strategies will be tested in order to create drug diffusion barriers, which lead to a continuous and gradual dispense of medication to the eye, at adjustable rates, and for extended periods. The drug release kinetics of antibiotics and an anti-glaucoma beta-blockers will be investigated through in vitro tests by using an equipment specially conceived to simulate the eye function, which allows a reliable extrapolation to the biological conditions. Appropriate physical-chemical and biological experimentation will be performed in view of future (pre)clinical validation.

IST | Bioengineering Systems PhD | Entering year: 2012 | Graduation year: 2017

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Thesis Title: “Scalable Manufacturing of Mesenchymal Stem/Stromal Cells for Cell Therapies and the Role of the Notch Signaling Pathway in the Human Hematopoietic Systems”.

Supervisors: Joaquim Sampaio Cabral (IST-UL) and Cláudia Lobato da Silva (IST-UL).

Thesis Abstract: My research focuses on the expansion/selection of regulatory T-cells, using a mesenchymal stem cell (MSC)-based co-culture system. Briefly, MSC are obtained from differente sources (bone marrow and adipose tissue) and cultured in vitro until confluent. Peripheral blood mononuclear cells (PBMC) or purified regulatory T-cells (Treg) are also added to examine the ability of MSC to induce and expand Treg in vitro. To determine if the mechanism by which MSC induce/expand Treg is due to cell-cell contact or the release of soluble factors, transwell experiments are performed and blocking antibodies against relevant soluble factors (e.g. IL-2, IL-10, TGF-β, IL-17) are used. Also, I have been studying the influence of a serum-free medium, containing human platelet lysate, in the expansion and immunomodulatory properties of adipose tissue and umbical-cord matrix-derived MSC.

FCTUNL | Bioengineering PhD | Entering year: 2008 | Graduation year: 2015

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Current position: Research Member at CENIMAT/CEMOP

Thesis Title: Development of nanomorphous silicon solar cells on ceramic substrates with biomedical application

Supervisors: Rodrigo Martins (FCT-UNL); Hugo Águas (FCT-UNL)

FCTUNL | Bioengineering Systems PhD | Entering year: 2012 | Graduation year: 2016

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Current Position: Senior Scientist: Cell & Gene Therapy Downstream Process Development at GlaxoSmithKline

Thesis Title: Development of integrated strategies for the downstream processing of human stem cells for clinical application

Supervisors: Margarida Serra (iBET/ITQB-UNL), Paula Alves (iBET/ITQB-UNL)

Research Summary: The aim of this PhD project was to establish scalable and integrated downstream processing (DSP) strategies, based on filtration technologies, for the clarification, concentration and washing unit operations for adult and pluripotent SC from human origin without compromising cells’ quality. Human mesenchymal stem cells (hMSC) and human induced pluripotent stem cells (hiPSC) will be used as challenging and complex cell-based products. A systematic approach will be developed by combining membrane technology and chromatographic tools in a robust, scalable, compatible with current good manufacturing practices (c-GMP), and affordable process, aiming at establishing a flexible platform, which can be transferred to clinical/industrial settings. This research as won an award for “best student poster prize” in the 2015 conference “Scale-up and Manufacturing of Cell-Based Therapies IV” in San Diego, California.

IST | Bioengineering Systems PhD | Entering year: 2010 | Graduation year: 2016

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Current Position: Researcher at 6he Centre for Rapid and Sustainable Product Development (CDRsp), Polytechnic Institute of Leiria

Thesis Title: Development of hydrogel-based constructs with encapsulated cells

Supervisors: Frederico Ferreira (IST-UL), Paulo Bartolo (IPL)

FCTUNL | Bioengineering PhD | Entering year: 2009 | Graduation year: 2015

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Current Position: Co-founder, Operations & Sales Officer at doDOC, Coimbra/Lisbon/Boston, Portugal/USA

Thesis Title: Leukemia Cell Differentiation by Light Activatable Nanoparticles

Supervisors: Lino Ferreira, Tariq Enver, Isidro Sanchez-Garcia

Thesis Abstract: The main goal of this project was to develop a light-activatable nanoparticle system to improve the intracellular delivery of RA in leukemic cells. The possibility of remotely activating the drug delivery system opens new therapeutic opportunities due to the possibility of activating the differentiation of the cells at the bone marrow niche and potentially interfering with the leukemic stem cell niche.

Publications:

• Carlos Boto, Emanuel Quartin, Yijun Cai, Alberto Martin-Lorenzo, Maria Begona Garcia Cenador, Sandra Pinto, Rajeev Gupta, Tariq Enver, Isidro Sanchez-Garcia, Deng Li, Ricardo Neves, Lino Ferreira. “Prolonged intracellular accumulation of light-inducible nanoparticles in leukemia cells allows their remote activation”. Nature Communications (Accepted) 2017
• Tiago Santos, Carlos Boto, Cláudia Saraiva, Liliana Bernardino, Lino Ferreira. “Nanomedicine approaches to modulate stem cells in brain repair”. Trends in Biotechnology 2016, 34(6), 437-439
• Tiago Santos, Raquel Ferreira, Emanuel Quartin, Carlos Boto, Cláudia Saraiva, José Bragança, João Peça, Cecília Rodrigues, Lino Ferreira, Liliana Bernardino. “Light potentiates retinoic acid-induced neuronal differentiation of neural stem cells”. (Submitted) 2016
• Patent: Cismondi, F., Boto, C., Melo, P., Jensen, S. “A Computer-implemented Method of Interacting with a Search Engine”. EP14195156, 2014
• Patent: Boto, C., Neves, R., Ferreira, L. “Light-activatable polymeric nanoparticles”. PAT20131000066281, 2013

UMinho | Bioengineering PhD | Entering year: 2007 | Graduation year: 2011

ThesisTitle: Novel modeling formalisms and simulation tools in Computational Biosystems

Supervisors: Eugénio Ferreira (UMinho), Isabel Rocha (UMinho), Bruce Tidor (MIT)

Thesis Abstract: The goal of Systems Biology is to understand the complex behavior that emerges from the interaction among the cellular components. Industrial biotechnology is one of the areas of application, where new approaches for metabolic engineering are developed, through the creation of new models and tools for simulation and optimization of the microbial metabolism. Although whole-cell modeling is one of the goals of Systems Biology, so far most models address only one kind of biological network independently. This work explores the integration of dierent kinds of biological networks with a focus on the improvement of simulation of cellular metabolism. The bacterium Escherichia coli is the most well characterized model organism and is used as our case-study.

An extensive review of modeling formalisms that have been used in Systems Biology is presented in this work. It includes several formalisms, including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, dierential equations, rule-based models, interacting state machines, cellular automata and agent-based models. We compare the features provided by these formalisms and classify the most suitable ones for the creation of a common framework for modeling, analysis and simulation of integrated biological networks. Currently, there is a separation between dynamic and constraint-based modeling of metabolism. Dynamic models are based on detailed kinetic reconstructions of central metabolic pathways, whereas constraint-based models are based on genome-scale stoichiometric reconstructions. Here, we explore the gap between both formulations and evaluate how dynamic models can be used to reduce the solution space of constraint-based models in order to eliminate kinetically infeasible solutions. The limitations of both kinds of models are leading to new approachesto build kinetic models at the genome-scale. The generation of kinetic models from stoichiometric reconstructions can be performed within the same framework as a transformation from discrete to continuous Petri nets. However, the size of these networks results in models with a large number of parameters. In this scope, we develop and implement structural reduction methods that adjust the level of detail of metabolic networks without loss of information, which can be applied prior to the kinetic inference to build dynamic models with a smaller number of parameters. In order to account for enzymatic regulation, which is not present in constraint-based models, we propose the utilization of Extended Petri nets. This results in a better scaold for the kinetic inference process. We evaluate the impact of accounting for enzymatic regulation in the simulation of the steady-state phenotype of mutant strains by performing knockouts and adjustment of enzyme expression levels. It can be observed that in some cases the impact is signicant and may reveal new targets for rational strain design. In summary, we have created a solid framework with a common formalism and methods for metabolic modeling. This will facilitate the integration with gene regulatory networks, as we have already addressed many issues also associated with these networks, such as the trade-o between size and detail, and the representation of regulatory interactions.

Publications:

• Daniel Machado, Nuno Preguiça, Carlos Baquero, J. Legatheaux Martins. VC^2 – Providing Awareness in Off-The-Shelf Version Control Systems. In IWCES9: Proceedings of the 9th International Workshop on Collaborative Editing Systems. November, 2007.

• Daniel Machado, Miguel Rocha. getALife – An Artificial Life Environment for the Evaluation of Agent-Based Systems and Evolutionary Algorithms for Reinforcement Learning. At the 21st International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems. June, 2008 (accepted).

Research interests: Computational Biology / Systems Biology; Formal Methods / Modeling, Specification and Software Development; Artificial Life / Machine Learning / Artificial Intelligence.

IST | Bioengineering PhD | Entering year: 2007

Research interests: Design and operation of bioreactor systems for the expansion and controlled neural differentiation of stem cells (Stem Cells Bioengineering).

Links:

http://www.ist.utl.pt/ (IST)

http://www.ibb.pt/ (Institute for Biotechnology and Bioengineering)

http://dequim.ist.utl.pt/cebq/berg/index.html (BioEngineering Research Group)

UCoimbra | Bioengineering Systems PhD | Entering year: 2013/2014

Research area: Cell and tissue engineering

PhD Supervisor: Lino Ferreira (CNC, UC)

Thesis Topic: During this PhD we will develop a cell-free therapy for myocardial infarction treatment that explores the endogenous modulation of CSCs. We aim at enhancing this intrinsic self-repair mechanism that exists in the mammalian heart. To accomplish this objective, we will use an innovative platform based on opto-nanomedicine for the remote delivery of biomolecules. The main objective of the project is to evaluate the regenerative potential of biomolecules released into the heart after light activation.

UMinho | Bioengineering Systems PhD | Entering year: 2012

Research topic/area: Nanotechnologies applied to the treatment of tuberculosis: Development of strategies for antimicrobial peptides delivery to infected macrophages

Research Summary: Drug delivery systems and Drug development; Protein engineering; Glycobiology; Molecular pharming.

Personal webpage

IST | Bioengineering PhD | Entering year: 2007

Research topic/area: Optical Nanosensors based on Semiconductor nanocrystals and metal nanoparticles for biomedical applications (Biomedical Devices & Technologies).

Communications/Conference presentations:

• Vistas, C.; Silva, A.C.; Thibaud, C.; Brayner, R. “Biosynthesis of new hybrid materials based on Alginate-Au, and Carrageenan-Ag. SERS effect for bio-detection applications”, Therapeutic Nano-objects Genoconference,12th June 2007, Evry/France

Links:

www.cbme.ualg.pt

www.ibb.pt

FCTUNL | Bioengineering Systems PhD | Entering year: 2011 | Graduation year: 2017

Thesis Title: Development of hydrogel-based constructs with encapsulated cells

Supervisors: Helena Santos (ITQB), Isabel Rocha (UM)

UCoimbra | Bioengineering PhD | Entering year: 2007

Research topic/area: Antimicrobial nanocoatings

Permanent antifungal materials and coatings: bioactivity and cytotoxicity characterization on November, 21st, 2012.

Publications:

• Paula V. Morais, Cristiana Paulo, Romeu Francisco, Rita Branco, Ana Paula Chung and Milton S. da Costa Leucobacter luti sp. nov., and Leucobacter alluvii sp. nov., two new species of the genus Leucobacter isolated under chromium stress. Syst Appl Microbiol. 2006 Volume 29 (5), 21 July 2006, pp. 414-421

Communications/Conference presentations:

• Cristiana Paulo, José Paulo Sousa and Paula Vasconcellos Morais, Bioaugmentation and enhanced Cr(VI) reduction in a lab-scale reactor, 9th International Symposium on Metal Ions in Biology and Medicine in Lisbon, 21-24 May 2006

• C. Paulo, J. Marques, C. Mourão, A. Meliço-Silvestre, A. Florinda, T. Gonçalves, A four-year epidemiological study of aetiological agents of yeast infections and antifungal susceptibility profiles in the centre of Portugal, 17th European Congress of Clinical Microbiology and Infectious Diseases and 25th International Congress of Chemotherapy Munich/Germany, 31 March – 3 April 2007

• A. Meliço Silvestre, C. Paulo, T. Gonçalves, J. Anjos, G. Rocha, The R77Q mutation and HIV Disease Progression in Children, Submitted to 25th Annual Meeting of the European Society for Paediatric Infectious Diseases, Porto, Portugal, May 2-4, 2007

Research interests: Biomaterials, Microbiology, Virology.

Links:

http://biomaterials.biocant.pt

FCTUNL | Bioengineering Systems PhD | Entering year: 2011 | Graduation year: 2016

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Current Position: Post-Doc Research Fellow at iBET – Instituto de Biologia Experimental e Tecnológica

Thesis Title: Development of Human Central Nervous System 3D in vitro Models for Preclinical Research

Supervisors: Paula M. Alves (IBET/ITQB-NOVA), Catarina Brito (IBET/ITQB-NOVA)

Thesis Summary: The current lack of predictable models in early stage development in the pharma industry strongly contributes for the high attrition rates registered. Thus, there is an increasing need for a paradigm shift towards more human relevant cell models, which can closely recapitulate the in vivo cell-cell and cell-ECM interactions. The main goal of this project was the development of human 3D in vitro neural models, making use of agitation-based culture systems and human stem cells as scalable supply of neural-subtype cells. The applicability of these models in a preclinical setting was explored by assessing the efficacy and safety assessment of novel viral vector candidates for gene therapy.

UMinho | Bioengineering PhD | Entering year: 2007

Research topic/area: Micro/Nano Processing Strategies as a tool to clarify surface mediated biological performance of degradable biomaterials (Nanobiotechnology & Biomaterials).

Publications:

• Daniela F. Coutinho, Pashkuleva I, Alves CM, Marques AP, Neves NM and Reis RL, 2008, The effect of chitosan on the in vitro biological performance of chitosan-poly(butylene succinate) blends, Biomacromolecules, 9 (4) : 1139-1145

Communications/Conference presentations:

• D. M. García Cruz, D. F. Coutinho, M. Salmerón Sanchez, J. F. Mano, J. L. Gómez Ribelles, Biodegradable Scaffolds made of poly(ε- caprolactone)/chitosan semi-interpenetrated polymer networks, 1-4 April, Materiais 2007, Porto, Portugal
• D.M. García Cruz, D. F. Coutinho, E. Costa Martínez, M. Salmerón Sánchez, J.F. Mano and J.L. Gómez Ribelles, Blends of chitosan and polycaprolactone. Structure, properties and biological response, 24-27 June, Frontiers in Biomedical Polymers 2007, Ghent, Belgium

Links:

www.uminho.pt (University of Minho)

www.3bs.uminho.pt (3B’s Research Group – Biomaterials, Biodegradables and Biomimetics)

www.ibb.pt/ (Institute for Biotechnology and Bioengineering)

FCTUNL | Bioengineering PhD | Entering year: 2007

Research topic/area: Determinants and Measurement of Innovation in Bioengineering: A Cross-National Study of Successful and Unsuccessful
Cases

Research interests: Technology Transfer; Innovation Dynamics; Technology Breakthrough; Market Pull

UMinho | Bioengineering Systems PhD | Entering year: 2012

Research topic/area: Osteoconductive and biomimetic composite materials containing new bioactive nanoparticles for orthopaedic applications

Research Summary: Electrospinning and nanofibers; antimicrobial materials and surfaces; nanoparticles for orthopaedic applications.

Publications: Botequim D., Maia J., Lino M., Simões P., Ilharco L., Ferreira L., “Nanoparticles and surfaces presenting antifungal, antibacterial and antiviral properties”, Langmuir, 28 (20), pp 7647-7656 (2012), DOI: 10.1021/la300948n.

Henriques C., Vidinha R., Botequim D., Borges J. P., Silva J. A. M. C., “A systematic study of solution and processing parameters on nanofibre morphology using a new electrospinning apparatus”, Journal of Nanoscience and Nanotechnology 9, 3535-3545 (2009), DOI: 10.1166/jnn.2009.NS27.

IST | Bioengineering PhD | Entering year: 2007

Research topic/area: Depicting the Bone Marrow Microenvironment Towards the Ex-vivo Expansion of Hematopoietic Stem/Progenitor Cells

Research interests:Ex-vivo Expansion of Hematopoietic Stem/Progenitor Cells Functional/Phenotypic assays for stem cell culture Cellular microarrays, microscale cell patterning, and microfluidic culture platforms for stem cells 3-D scaffold based bioreactor platform for stem cell culture

Links:

http://www.ist.utl.pt/ (IST)

http://www.ibb.pt/ (Institute for Biotechnology and Bioengineering)

http://dequim.ist.utl.pt/cebq/berg/index.html (BioEngineering Research Group)

http://lmrt.mit.edu/ (Laboratory for Multiscale Regenerative Technologies)

UMinho | Bioengineering PhD | Entering year: 2007

PhD supervisor: Graça Maria Henriques Minas; José Higino Gomes Correia

PhD Thesis (2011): Spectroscopy systems for the detection of gastrointestinal dysplasia

Thesis Abstract: The detection of gastrointestinal (GI) dysplasia is essential to improve the patient’s survival rate. The diagnosis of this condition can be performed using spectroscopy techniques, such as fluorescence and diffuse-reflectance, which have the potential to provide morphological and biochemical information regarding normal and dysplastic tissue. Research prototypes currently used for those clinical spectroscopy techniques have associated a few drawbacks: they are costly, bulky, too sophisticated and they use optical fibers, which are usually related with low-collection efficiency. Moreover, these catheterbased instruments are invasive and very uncomfortable for the patient. In this context, the present work had the purpose to develop a miniaturized spectroscopy system, based on those two techniques, that features low-complexity and costeffectiveness. Furthermore, the integration of optical components in a single chip allows a high level of reliability. Such a system can be integrated in less-invasive devices (e.g., the endoscopic capsules), for an effective and comfortable detection of GI dysplastic lesions. The developed spectroscopy system core is based on thin-film optical filters and lowcost silicon photodiodes, used for the selection and detection of a few light wavelengths significant for the diagnosis of dysplasia. Thin-film optical filters, centered at specific wavelengths, were designed, fabricated and characterized after the successful demonstration that the use of only 16 spectral bands (within the 350 to 750 nm spectral range) enabled an accurate extraction of tissue information. The feasibility of using the fabricated filters to establish a quantitative spectroscopy diagnosis was proved with measurements on tissue phantoms. Additionally, an even more compact device is proposed for qualitative diagnosis using only two different spectral bands, centered at 420 nm for fluorescence measurements and at 540 nm for diffuse-reflectance measurements. This approach enabled the construction of a diagnostic algorithm for the identification of dysplastic tissues, with a sensitivity and specificity of 77.8% and 97.6%, respectively. This thesis work was also directed towards the development of a fluorescence and diffuse-reflectance spectroscopy imaging system for excised tissue margins assessment, which results from mucosal resections in the GI tract. In the developed system, wide area imaging is achieved by mechanically scanning an optical probe along the tissue surface, with variable spatial resolution. This medical device can provide real-time feedback regarding the resected mucosal margins, which represents a huge impact in intra-operative diagnosis. The clinical utility of the spectroscopy imaging prototype was successfully demonstrated using biological samples, i.e., different images containing reliable quantitative tissue information were obtained using analytical models. These images can be subsequently used to establish a diagnosis. This system may enable the reduction of the patient anxiety, avoiding the follow-up surgery, once a fast and real-time data analysis can be performed inside the operating room.

Full thesis available upon request at Universidade do Minho’s Repositorium

Links:

http://www.uminho.pt (University of Minho)

http://www.dei.uminho.pt (Department of Industrial Electronics)

http://www.algoritmi.uminho.pt/ (R&D Centre ALGORITMI)

http://calg-mnt.dei.uminho.pt (Micro/Nanotechnologies and Biomedical Applications Group)

IST | Bioengineering Systems PhD | Entering year: 2013/2014

PhD Supervisor: Joaquim Sampaio Cabral – Instituto Superior Técnico

Thesis Topic: Development of a cell-based product with enhanced therapeutic features for myocardial regeneration through an integrative bioprocess approach

FCTUNL | Bioengineering PhD | Entering year: 2007

Research topic/area: Bioactive Beads for Local Modulation and Sensing of Cell Mechanical Environment in 3D Engineered Tissues

Research interests: Development of new biomaterials for mammalian cell culture

Links:

http://www.dq.fct.unl.pt/scf/

http://web.mit.edu/hammond/lab/

http://web.mit.edu/lgglab/

FCTUNL | Bioengineering PhD | Entering year: 2008 | Graduation year: 2013

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Current position: Cell Culture Development Scientist at Lonza

Thesis Title: Novel Cell Factories for the production of complex bioproducts: a synthetic biology approach for improved product stoichiometries

Supervisors: Paula Alves (FCTUNL), Kristala Prather (MIT)

IST | Bioengineering PhD | Entering year: 2008

PhD Supervisor: João Miguel da Costa Sousa (IST), Stan N. Finkelstein (MIT) and Shane Raymond Reti (Harvard).

PhD Thesis (2012): Preprocessing and Misclassifying Issues in Clinical Data Sets for Prediction and Intervention

During his PhD, Federico conducted research on modeling clinical data in order to optimize the use of resources in patients’ health care. Within the MIT Portugal Program, Federico has been able to work with a wide range of professionals with different scientific and operational backgrounds: medical doctors, nurses, epidemiologists, statisticians, information technologists, and people from business and management.

Collaborations with research groups in Portugal, the United States, and the Netherlands resulted in several publications in journals and international conferences, which could lead to needed changes in health care delivery. In addition to his own research, Federico is currently working on a private enterprise project with scientists from Portugal and other European countries.

UMinho | Bioengineering PhD | Entering year: 2008

PhD Thesis (2013): Process Intensification for the production of hydroxyapatite nanoparticles

Summary: Precipitation processes are widely used in chemical industry for the production of particulate solids. In these processes, the chemical and physical nature of synthesized particles is of key importance. The traditional stirred tank batch reactors are affected by non-uniform mixing of reactants, often resulting in broad particle size distribution. The main objective of this thesis was to apply meso and microreactors for the synthesis of hydroxyapatite (HAp) nanoparticles under near-physiological conditions of pH and temperature, in order to overcome the limitations associated with stirred tank batch reactors.

Meso and microreactors offer unique features in comparison with conventional chemical reactors. Their high surface-to-volume ratio enables enhanced heat and mass transfer, as well as rapid and efficient mixing. In addition to low consumption of reagents, meso and microreactors are usually operated in continuous flow, making them attractive tools for high throughput experimentation. Precipitation of HAp was first studied in a stirred tank batch reactor, mixing being assured by a novel metal stirrer. HAp was synthetized by mixing diluted aqueous solutions of calcium hydroxide and orthophosphoric acid at 37 °C. After process optimization, a suspension of HAp nanoparticles with pH close to 7 was obtained for a mixing molar ratio Ca/P=1.33. The precipitation process was characterized by three stages: precipitation of amorphous calcium phosphate, transformation of amorphous calcium phosphate into HAp and growth of HAp crystals. The reaction system was further characterized based on equilibrium equations. The resolution of the system, which was possible with the knowledge of three process variables (temperature, pH and calcium concentration), allowed identifying and quantifying all the chemical species present in solution. The proposed model was validated by comparing the experimental and theoretical conductivity. Precipitation of HAp was then investigated in a meso oscillatory flow reactor (meso-OFR). The mesoreactor was first operated batchwise in a vertical tube and experiments were performed under the same conditions of temperature, reactants concentration and power density applied in the stirred tank batch reactor. Despite hydrodynamic conditions being not directly comparable, it was possible to assess the effectiveness of both reactors in terms of mixing and quality of the precipitated particles. The experimental results show the advantages of the meso-OFR over the stirred tank due to the production, about four times faster, of smaller and more uniform HAp nanoparticles. Afterwards, continuous-flow precipitation of HAp was carried out in one meso-OFR and in a series of eight meso-OFRs. Experiments were carried out using fixed frequency (f) and amplitude (x0), varying only the residence time. HAp nanoparticles were successfully obtained in both systems, mean particle size and aggregation degree of the prepared HAp particles decreasing with decreasing residence time. In the present work continuous-flow precipitation of HAp was also investigated in two ultrasonic microreactors. Initially, the process was carried out in a tubular microreactor immersed in an ultrasonic bath, where single-phase (laminar) and gas-liquid flow experiments were both performed. Continuous-flow precipitation of HAp in single-phase flow was then done in a Teflon microreactor with integrated piezoelectric actuator. Rod-like shape HAp nanoparticles were yielded in both reactors under near-physiological conditions of pH and temperature. Further, particles showed improved characteristics, namely in terms of size, shape, particle aggregation and crystallinity. In summary, scale-down of the HAp precipitation process has resulted in the formation of HAp nanoparticles with improved characteristics when compared with HAp particles prepared in a stirred tank batch reactor. Therefore, we believe that the work developed can be a useful contribution to the development of a platform for the continuous production of high quality HAp nanoparticles.

IST | Bioengineering PhD | Entering year: 2008

PhD Supervisor: Bruce Tidor (MIT) and Arlindo Oliveira (IST).

PhD Thesis: Variability in Biological Systems: Modeling Consequences and Applications

UMinho | Bioengineering Systems PhD | Entering year: 2012 | Graduation year: 2017

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Research topic/area: Prokaryotic Arms Race – from exploration to exploitation

Research Summary: The gain of antibiotic resistance by pathogens urges scientists progressively to search for other ways to fight bacterial infections. A promising alternative to antibiotics is phage therapy, i.e. the use of bacterial viruses (bacteriophages) that have the capacity to specifically recognize and eliminate bacterial strains. However upon infection, also phages face various resistance mechanisms and their rate of success is determined by their ability to evade these antiviral systems. To date, the knowledge on the interaction between phages and their bacterial hosts is rather limited. Therefore, to be able to fully exploit the potential of phage therapy, it is imperative to better understand this relationship. Here we propose to explore this phage-host relationship for Salmonella sp. and E. coli, two Enterobacteriaceae members that include notorious pathogens. We will focus on the recently discovered CRISPR immune system of these strains, how resistance is gained and how it is avoided by phage.

Publications:

“Saturation-Transfer Difference (STD) NMR – A simple and fast method for ligand screening and characterization of protein binding” ; Aldino Viegas, João Manso, Franklin L. Nobrega and Eurico J. Cabrita; Journal of Chemical Education; Published May 2011; doi:10.1021/ed101169t

“Development of molecularly imprinted co-polymeric devices for controlled delivery of flufenamic acid using supercritical fluid technology”; Mara Silva, Franklin L. Nóbrega, Eurico J. Cabrita, Teresa Casimiro and Ana Aguiar-Ricardo; The Journal of Supercritical fluids; Published May 2011; doi:10.1016/j.supflu.2011.05.010

“Molecular aspects and comparative genomics of bacteriophage endolysins” ; Hugo Oliveira, Luís Melo, Sílvio Santos, Franklin Nóbrega, Eugénio Ferreira, Nuno Cerca, Joana Azeredo, and Leon Kluskens; Journal of Virology; Published February 2013, doi: 10.1128/JVI.03277-12

UMinho | Bioengineering Systems PhD | Entering year: 2010 | Graduation year: 2017

Research topic/area: Magnetotransfection – Exploring New Ways to Improve Clostridium pasteurianum for Better Butanol Yield

Research Summary: This project aims to develop products that simplify the laboratory methods used for the genetic improvement of microorganisms with commercial potential that can be applied in biotechnology, in areas such as food industry, environment or energy. These products will constitute a new methodological paradigm through its simplicity and will substitute classical procedures that are more time-consuming, more expensive and technically more demanding. Transformation of microorganisms is a cumbersome procedure normally needing three main steps. With our technology we envisage attaining transformation in a single step through spreading microorganisms and foreign DNA on novel transformation petri-dishes.

Thesis Title: Tribos transformation of Escherichia coli JM109

Supervisors: Manuel Mota, Senentxu Lanceros-Méndez, Leon Kluskens.

IST | Bioengineering PhD | Entering year: 2008

PhD Supervisor: Duarte Miguel Prazeres (IST) and Kristala Prather (MIT); Phd Co-supervisor: Gabriel António Amaro Monteiro.

PhD Thesis (2013): Rational engineering of E. coli strains and vectors for improved manufacturing of plasmid biopharmaceuticals

Thesis scope: The use of plasmid DNA (pDNA) as a biopharmaceutical has been gaining momentum over the last years with the approval of the first DNA vaccines. The goal of my project is to rationally engineer and test an Escherichia coli strain specifically adapted to thrive in high density cell cultures and synthesize the large amounts of supercoiled pDNA required to push the development of pDNA biopharmaceuticals.The results obtained thus far are encouraging and will hopefully represent an important contribution to the field of plasmid biopharmaceuticals.

FCTUC | Bioengineering System PhD | Entering year: 2011 | Graduation year: 2016

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Current Position: Postdoctoral fellow at Novartis Institutes for BioMedical Research (NIBR)

Thesis Title: Seeking general principles in the design of defense systems against hydrogen peroxide

Supervisor: Armindo J. Salvador (CNC-UC)

Thesis Summary: My work focus on the understanding of the phenotypic dichotomy that 2-Cys Peroxiredoxins, exhibit under high or sustained oxidative loads. They in fact may undergo substrate inactivation, by hyperoxidation of their peroxidatic cysteine, or accumulate into disulphide form. This not only between different organisms but also within different cell types of the same host. We have addressed this problem by combinatorially studying the components of a minimal model of the Peroxiredoxin, Thioredoxin and Thioredoxin Reductase system, in order to extract the core design requirements which would ensure one behaviour or the other. The obtained rule allows to correlate proteins abundance patterns with the modes of response, accordingly predicting the choice in several biological instances, and do shred an interesting light over the roles of this system in the defense/signal transduction integration.

UMinho | Bioengineering Systems PhD | Entering year: 2013/2014

Research area: Systems Biology, Metabolic Engineering.

PhD Supervisor: Isabel Rocha, CEB-Universidade do Minho

Thesis Topic: Accelerating metabolic engineering tasks by the in silico development of yeast cell factories Abstract: Saccharomyces cerevisiae is one of the most widely used cell factories in industrial biotechnology. However, the development of optimized yeast strains for the production of novel compounds is a time-consuming process and represents a significant cost and time burden. Key underlying reasons include the unavailability of suitable chassis cells and lack of proven modelling tools. This PhD proposal aims at contributing towards overcoming these limitations by using cutting-edge computational and experimental tools. These will be applied to improved production of polyketides and other industrially relevant compounds that originate from the same precursors.

In the first stage, we intend to complement the available metabolic models with phenotype information from Saccharomyces Genome Database (SGD), using a systematic analysis approach. Afterwards, the improved model will be used to identify targets for gene deletion or overexpression towards overproduction of compounds originating from the same building blocks, namely acetyl-CoA and malonyl-coA.

Experimental validation of the optimized predictions will be performed by constructing high-producer yeast strains for production of the model polyketide 6-methylsalicylic acid.

FCTUNL | Bioengineering Systems PhD | Entering year: 2012

Research topic/area: Developing Artificial Zinc Fingers with Peptidase Activity

Research Summary: The overall goal is to redesign the zinc domain of the zinc finger proteins to obtain stable peptidic scaffolds capable of coordinating transition metal ions and displaying peptidase activity. Development of recyclable catalysts will also be pursued by attaching the best candidates to solid supports and test their catalytic activity.

Biocant/CNC | Bioengineering Systems PhD | Entering year: 2011

Research topic/area: Cell and Tissue Engineering. Bioengineering. Nanobiotechnology and Biomaterials. Stem Cells and human pluripotent stem cells Cells.

FCT-UNL | Bioengineering PhD | Entering year: 2010 | Graduation year: 2015

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Current position: Postdoctoral Researcher at iBET

Thesis Title: Cell functional enviromics: Applications to Pichia pastoris

Supervisor: Rui Oliveira (FCTUNL)

IST | Bioengineering Systems PhD | Entering Year: 2015

Biomedical Engineer and PhD Candidate from the MIT Portugal Program working on medical image analysis for image-guided neurosurgery. Interests and expertise in machine learning for brain tumor resection.

Current Position: Researcher at the Surgical Planning Lab and the Department of Neurosurgery of the Brigham and Women’s Hospital (BWH) and Harvard Medical School (HMS), in Boston.

Research Area: Biomedical Engineering | Neurosurgery

Supervisors: Prof. Jorge Martins (IST), Professor Sarah Frisken (BWH, HMS), Professor Polina Golland (MIT)

Thesis Title: Non-linear registration of 3D intraoperative ultrasound for image-guided neurosurgery

Research Summary: The brain undergoes significant structural change over the course of neurosurgery, known as brain shift, which includes highly non-linear deformation and resection. To recover the spatial mapping between structures identified in pre-operative surgical planning and the intra-operative state of the brain, intraoperative imaging acquisition has been proposed to correct for brain shift. In our group, we investigate the use of intraoperative 3D-ultrasound to compensate for brain shift during neurosurgical procedures.

Other interests: Computer vision, medical image analysis, artificial intelligence, machine learning.

Links: http://golbylab.bwh.harvard.edu/

IST-UTL | Bioengineering Systems PhD | Entering year: 2011 | Graduation year: 2015

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Research topic/area: Cell and Tissue Engineering – Stem Cells

Research Summary: My main three areas of interest are Stem Cells Culture, Tissue Engineering and Immunemodulation. During the next 3 years of research I would like to have the opportunity to engage in a project that would allow me to work directly with tissues and animal models and that would ultimately open a door for me to apply some of the engineering concepts that I gained in these last years. Also, it would be important for me if my research would have an impact on clinical translation.

Thesis Title: Tissue Engineering Approaches to Stress Urinary Incontinence using Acellular Urethra Bioscaffolds

Supervisors: Claudia Lobato da Silva (IST-UL), Pedro Baptista (Centro de Investigacion Biomedica Aragon, Spain)

FCTUNL | Bioengineering PhD | Entering year: 2009 | Graduation year: 2014

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Current position: Associate Consultant at Cambridge Healthcare Research, UK

Thesis Title: Engineered Structures for the Profiling and Enrichment of the Phosphoproteome

Supervisors: Ana Roque (FCT-UNL), Christopher Robin (University of Cambridge), Olga Iranzo (ITQB-UNL)

UMinho | Bioengineering PhD | Entering year: 2007

Research topic/area: Regenerative Medicine / Tissue Engineering

Research interests: Stem cells differentiation, biomaterials for Tissue Engineering.

Other interests: Innovation, Clinical Economics.

Links:

http://www.3bs.uminho.pt/

http://www.ibb.pt/

IST | Bioengineering PhD | Entering year: 2007 | Graduation year: 2011

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Current position: Innovation and R&D product manager at Renova SA, Portugal

Research topic/area: Bioprocess engineering on microbial desulfurization: Cell immobilization and cell recycle for desulfurization of crude oil

Thesis Title: Biodesulfurization of Crude Oil by Whole Cells of Rhodoccocus Erythropolis

Supervisors: M.R. Aires Barros (IST) and D.I.C. Wang (MIT)

Publications:

• Ferreira, I.F.; Azevedo, A.M. Rosa, I.F., Aires-Barros, M,R; Optimization of temperature induced aqueous two-phase extraction of human antibodies; J. Chromat. A, xx, xxx-xxx doi:10.1016/j.chroma.2008.04.077 (2008)

• Azevedo, A. M., Gomes, A. G., Rosa, P. A. J, Ferreira, I. F., Pisco, A. M. M. O., Aires-Barros, M. R., Partitioning of human antibodies in polyethylene glycol – sodium citrate aqueous two-phase systems, Sep. Pur. Tecnhol., xx, xx-xx (2008)

• Azevedo, A.M. Rosa, P.A. J. Ferreira, I.F., Aires-Barros, M,R, Optimization of aqueous two-phase extraction of human antibodies, J. Biotechnolo., 132, 209-217 (2007)

• Rosa, P.A.J., Azevedo, A.M., Ferreira, I.F., de Vries, J; Korporaal, R; Verhoef, H.J.; Visser, T.J. Aires-Barros, M.R., Affinity partitioning of human antibodies in aqueous two-phase systems, J. Chromat. A, 1162, 103-113 (2007)

Communications/Conference presentations:

• Ferreira, IF; Azevedo, A.M.; Rosa, PAJ; Vries J.d.; Korporaal, R.; Verhoef, H.J.; Visser,T.J., Aires-Barros, MR; “Application of Aqueous-Two Phase Systems to Antibody Purification: Use of Thermosensitive Polymers”; XIV International Conference on Biopartitioning and Purification, 17th-20th June, Lisbon, 2007

• Ferreira, IF; Azevedo, A.M.; Rosa, PAJ, Vries J.D., Koorporaal R., Verhoef H.J., visser,T.J. Aires-Barros, M.R. “Application of aqueous two-phase on the extraction of monoclonal antibodies” European Technology Forum 2007, Sartorious College, May 2007,Goettingen, Germany. Research interests Bioprocess and process design aiming at the optimization of microbial desulfurization of crude oil

Other interests: Purification and extraction of proteins; Purification of human antibodies with aqueous two-phase systems; Monoclonal antibodies.

Links:

http://dequim.ist.utl.pt/cebq/berg/f-members.html

IST | Bioengineering PhD | Entering year: 2009 | Graduation year: 2015

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Current position: Post-doctoral Fellow at 3B´s Research Group (Biomaterials, Biodegradables and Biomimetics) Department of Polymer Engineering, University of Minho, Portugal

Thesis Title: The Microenvironment Of Human Umbilical Cord Blood Hematopoietic Stem/Progenitor Cells Towards Efficient Megakaryocytic Lineage Differentiation And Platelet Production Ex‐vivo

Supervisors: Frederico Castelo Alves Ferreira (IST) and Cláudia Alexandra Martins Lobato da Silva (IST)

FCTUNL | Bioengineering PhD | Entering year: 2009

PhD supervisor: Ana Teresa Correia de Freitas

PhD Thesis (2014): Towards A Risk Assessment Model For Biocide Use

UMinho | Bioengineering PhD | Entering year: 2010 | Graduation year: 2014

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Current position: Post-Doc

Thesis Title: Design and construction of a new biosynthetic pathway for the production of curcuminoids in Escherichia coli

Supervisors: Ligia Rodrigues (UMinho), Leon Kluskens (UMinho), Kristala Prather (MIT)

Summary: Curcuminoids are produced by plants and due to their potential as novel cancer-fighting drugs have recently attracted increased attention. Nevertheless, they have a poor bioavailability. Cellular uptake is slow, and they are quickly metabolized once inside cells, requiring repetitive oral doses to achieve sufficient concentration inside the cells for therapeutic activity. The idea of this project is to engineer a model bacterium to trigger the release of a curcuminoid concurrent with ultrasound treatment. The proposed tasks involve several design and engineering steps to program Escherichia coli to execute a new synthetic pathway for curcuminoids production triggered by a temperature increase. The heat shock response (HSR) machinery of E. coli will be used as a sensor in the design of the model bacterium. Afterwards, the gene sequences of the enzymes that catalyze each reaction in curcuminoids pathway will be synthesized and introduced in the E. coli genome according to several cloning strategies.

Publications:
B. Fonseca, H. Figueiredo, J. Rodrigues, A. Queiroz, T. Tavares (2011) Mobility of Cr, Pb, Cd, Cu, and Zn in a loamy sand soil: A comparative study, Geoderma, 164, 232–237.

IST | Bioengineering PhD | Entering year: 2008

IST | Bioengineering PhD | Entering year: 2007

Research topic/area: High-Troughput Screening of Chemical and Physical Cues for the Ex-vivo Expansion of Human Embryonic Stem Cells

PhD Supervisor: Cláudia Lobato da Silva (Técnico Lisboa, ULisboa)

PhD co-supervisor: Joaquim Sampaio Cabral (Técnico Lisboa, ULisboa) ; Robert Samuel Langer (MIT); and Daniel Griffith Anderson (MIT).

João Guerreiro has successfully discussed his thesis on January, 21st, 2014 with Merit.

PhD Thesis (2014): Strategies For Myogenic Differentiation of Adult Stem Cells Towards Therapeutic Applications

Thesis abstract: Adult stem cells have shown enormous promise in the field of cell and tissue engineering due to their therapeutic potential while being from a more accessible and less controversial source than their embryonic counterparts. One field in particular that can benefit from stem cell therapies would be in the repair of muscle damage and disorders.

Mesenchymal Stem / Stromal Cells (MSC) are adult stem cells that have been reported to differentiate into skeletal muscle cells, have a fast proliferation in vitro, low immunogenic potential and are considered safe for use in human therapies making them good targets to treat damaged skeletal tissues. This potential is limited by current differentiation strategies that are still not well established. The main goal of this thesis was to identify defined conditions by which the differentiation of MSC into the skeletal myogenic lineage can be achieved while maintaining therapeutic applications as an endpoint. With that in mind, different approaches were employed. Transfection by non-viral methods, poly-β-aminoesters nanoparticles and microporation, was optimized to deliver myogenic regulatory factors (MRF) to induce myogenic differentiation on MSC. As MRF over expression showed insufficient to induce differentiation, the MSC myogenic potential was investigated by employing the different myogenic differentiation protocols available in the literature. No myogenic induction was ever observed raising questions over MSC true myogenic potential. Finally, electrospun nanofibers were developed as scaffolds for stem cells growth and differentiation evaluating their ability of providing physical cues capable of directing cell fate and serving as an in situ drug delivery system.

Keywords – Mesenchymal Stem / Stromal Cells; Transfection; Microporation; Nanofibers; Electrospinning; Myogenic Differentiation; Adult Stem Cells; Biomaterials; pDNA

Publications:

• F.B. De Sousa; J. D.T. Guerreiro; M. Ma; D.G.Anderson; C.L.Drum; R.Sinisterra; R. Langer; 2010 “Photo-response behavior of electrospun nanofibers based on spiropyran-cyclodextrin modified polymer”. Journal of Materials Chemistry. 20(44):9910; DOI: 10.1039/C0JM01903H
• M. Ma, L. Minglin; W.F. Liu, P.S. Hill Paulina, K.M. Bratlie,D.J.Siegwart, J. Chin, M. Park, J.D.T. Guerreiro, D.G. Anderson; 2011; ” Development of cationic polymer coatings to regulate foreign-body responses”. Advanced Materials. 23(24):H189.DOI: 10.1002/adma.201100513
• N. M. Nathaniel, H. Cheng,P.S.Hill, J.D.T.Guerreiro, T.T. Dang, M.Ma, S. Watson, H.Shanée, S. Nathaniel R. Langer, D.G. Anderson; 2012 ; “Localized delivery of dexamethasone from electrospun fibers reduces the foreign body response”. Biomactomolecules. 13(10):30131.
• C.Rendeiro, J.D.T. Guerreiro, C.M. Williams,J.P.E. Spencer ; 2012; “Flavonoids as modulators of memory and learning: molecular interactions resulting in behavioural effects”. The Proceedings of the Nutrition Society. 71(2):246. doi: 10.1017/S0029665112000146

IST | Bioengineering PhD | Entering year: 2008

PhD Supervisor: Guilherme Matos Ferreira

PhD Co-supervisor: Joaquim Sampaio Cabral.

PhD Thesis (2024): Impedance Spectroscopy Analysis of Protein-Surface Interaction Using Acoustic and Interdigital Label-Free Sensors

EEUM | Bioengineering PhD | Entering year: 2010 | Graduation year: 2015

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Current position: Computational Biologist at The University of Chicago, USA

Thesis Title: Modeling Microbes: New Methods for Integrated Metabolic and Regulatory Network Reconstruction

Supervisor: Isabel Rocha (UMinho), Miguel Rocha (UMinho), Christopher Henry (Argonne National Laboratory)

EEUM | Bioengineering PhD | Entering year: 2010 | Graduation year: 2015

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Current position: Postdoctoral Researcher at Argonne National Laboratory

Thesis Title: Modeling Microbes: New Methods for Integrated Metabolic and Regulatory Network Reconstruction

Supervisors: Isabel Rocha (UMinho), Miguel Rocha (UMinho), Christopher Henry (Argonne National Laboratory)

FCTUNL | Bioengineering PhD | Entering year: 2008 | Graduation year: 2013

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Current position: Science and Technology Management Fellowship at Universidade de Coimbra, Portugal

Supervisor: Manuel Ponte, João Malva, Armen Saghayelyan, Liliana Bernardino

Thesis Title: Migration and differentiation of neuronal precursors in the postnatal brain: insights from the subventricular zone and cerebellum

Supervisors: Manuel Ponte, João Malva, Armen Saghayelyan, Liliana Bernardino

Thesis Abstract: In the adult mammalian brain, neurogenesis occurs constitutively in the subventricular zone (SVZ), subgranular zone (SGZ) of the hippocampal dentate gyrus (DG) and at some extent at the cerebellum. These neurogenic niches are sources of new neurons that functionally integrate existing circuits. The proper development of the brain depends thus on continuous balance between new cells’ neurogenesis and their proper final placement. In spite of the enormous advances of neural stem cell research, there is still a lack of knowledge about the niches, and factors that modulate their dynamics. Among the several factors that affect neural cell fate, histamine and brain-derived neurotrophic factor (BDNF) emerge. Histamine, an inflammatory mediator and neurotransmitter, seems to foster neuronal differentiation. In embryonic neural stem cells, histamine induces both proliferation and neuronal differentiation. However, its role in adult SVZ neurogenesis has never been properly addressed. Concerning BDNF, abnormal cerebellum development has been observed upon this neurotrophin removal, and it has been described as a key molecule promoting cell migration. Yet, no data is available on the BDNF dependent cellular source effect controlling cerebellum precursor migration. The present thesis dissects the proneurogenic effect of histamine in the SVZ, and unravels the role of endothelial derived-BDNF on neuronal cell precursor migration in the postnatal cerebellum. To achieve so, different biological approaches were used, such as primary cell cultures and transgenic animal models. State of the art methodologies were employed including single cell calcium imaging, in vivo stereotaxic surgery, time-lapse imaging and quantitative real-time PCR. This doctoral thesis reveals a novel role for histamine, as an important modulator of neuronal differentiation in the SVZ; and BDNF, as a key player of endothelial-neuronal cell crosstalk that drives cerebellar precursor cell migration. Altogether, the disclosed cellular processes contribute to a better understanding of the SVZ and cerebellum dynamics.

Full thesis available upon request at Universidade Nova de Lisboa’s Repositorium.

Francisca Eiriz has successfully discussed her thesis on December, 2013, with the following members of the Jury:

• Manuel Luís Magalhães Nunes da Ponte,Faculty of Science and Technology, NOVa
• Joana de Almeida Santos Pacheco Palha, School of Sciences, UMinho
• Ana Maria Ferreira de Sousa Sebastião, IMM, ULisboa
• João José Oliveira Malva, Institute for Biomedical Imaging and Life Sciences, UCoimbra
• Liliana Inácio Bernardino,UBI
• Inês Maria Pombinho de Araújo, UAlg
• Lino da Silva Ferreira, BIOCANT, Biotechnology Innovation Center

Publications:

• Eiriz MF, Malva JO, Agasse F*, Bernardino L* (2014) Histamine in the neural and cancer stem cell niches. Stem Cells and Cancer Stem Cells 12, 3-17 Edited by Hayat MA; Springer.L.
• Bernardino*, M.F. Eiriz *, T. Santos, S. Xapelli, S. Grade , A.L. Rosa, L. Corte, R. Ferreira , J. Bragança,F. Agasse, L. Ferreira, J.O. Malva (2012) Histamine Stimulates Neurogenesis in the RodentSubventricular Zone. Stem Cells, 30: 773-784.
• J. Goméz-Lobo, M.F. Eiriz, T. Santos, I. Neiva, R. Ferreira and J. O. Malva (2012) Microglia: the bodyguard and the hunter of the adult neurogenic niche. Advances in Stem Cell Research, 245-79, Edited by Baharvand H; Springer
• M. F. Eiriz, S. Grade, A. Rosa, S. Xapelli, L. Bernardino, F. Agasse, J. O. Malva (2011) Functional evaluation of neural stem cell differentiation by single cell calcium imaging. Current Stem Cell Research & Therapy, 6 (3): 288-96

IST | Bioengineering Systems PhD | Entering year: 2013/2014

Research topic/area: Towards novels stem cell-based therapies for myocardium regeneration

IST | Bioengineering PhD | Entering year: 2008

PhD Supervisor: Lino Ferreira (CNC) ; PhD co-supervisor: Joaquim Manuel Sampaio Cabral (IST) and Jeffrey Michael Karp (HMS).

PhD Thesis (2013): Platforms for tissue reconstruction: compliant biomaterials for local drug delivery and tissue adhesion

Publications:

• Nora Lang, Maria J. Pereira, Yuhan Lee, Ingeborg Friehs, Nikolay V. Vasilyev, Eric N. Feins, Klemens Ablasser,Eoin D. O’Cearbhaill, Chenjie Xu, Assunta Fabozzo, Robert Padera, Steve Wasserman, Franz Freudenthal, Lino S. Ferreira,Robert Langer, Jeffrey M. Karp, and Pedro J. del Nido; A Blood-Resistant Surgical Glue for Minimally Invasive Repair of Vessels and Heart Defects Sci Transl Med 8 January 2014: Vol. 6, Issue 218, p. 218ra6 Sci. Transl. Med. DOI: 10.1126/scitranslmed.3006557

You can find more on Maria José research here:

Bio-inspired glue keeps hearts securely sealed

MPP Student selected to attend the Novartis International Biotechnology Leadership Camp: only 60 students were chosen worldwide.

IST | Bioengineering PhD | Entering year: 2007 | Graduation year: 2012

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Current position: Design leader, teacher of Maths, Science and Computer Technology at Oeiras International School

Research topic/area: Hybrid Human-Machine Systems: Powered Ankle-Foot Prosthesis, Exoskeleton Suit Development and Wearable Sensing

Thesis Title: Multibody dynamics and control of hybrid active orthoses

Supervisors: Miguel Pedro Tavares da Silva (IST-UL), Dava Newman (MIT), Jorge Martins (IST-UL)

UMinho | Bioengineering PhD | Entering year: 2007

Research topic/area: Wireless Wearable Braincap for Hybrid Human-Machine Application.

Research interests: Medical Informatics & Electronics

Links:

http://www.algoritmi.uminho.pt/ (Algoritmi Center – CAlg)

FCTUNL | Bioengineering Systems PhD | Entering year: 2010 | Graduation year: 2015

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Current position: Intellectual Property & Technology Transfer Officer at RIA, FCT NOVA

Research topic/area: Identifying TAU Interactors: new drug targets for neurodegenerative diseases

Research Summary: The main research fields that I am interest at the moment are molecular and cell biology, directed to the study of CNS disorders. I am interested in the biology and pathology of beta-amyloid and tau protein in Alzheimer’s disease (AD). The goal of my PhD project is to study the interaction between these proteins in yeast, a powerful and useful cell model organism for neurodegenerative disorders. Taking advantage of the power of yeast genetics, it will be possible to identify modulators of beta-amyloid and tau biologic and pathologic functions, using genome wide studies strategies, that can later be validated as potential targets for new therapeutic strategies in AD.

Supervisors: Ana Rego (Faculdade de Medicina, Universidade de Coimbra) and Helena Vieira, Faculdade de Ciências , Universidade de Lisboa.

Publications:

Cerejo M., Andrade G., Roca C., Sousa J., Rodrigues C., Pinheiro R., Chatterjee S., Vieira H. & Calado P. (2012) A powerful yeast-based screening assay for the identification of inhibitors of Indoleamine 2,3 Dioxygenase. Journal of Biomolecular Screening. In pub.

Escalera L., Reguera B., Moita T., Pazos Y., Moroño A., Cerejo M.,Cabanas J. M. & Ruiz-Villarreal M. (2009). Bloom dynamics of Dinophysis acuta in an upwelling system: in situ growth versus transport. Harmful Algae 9 (3): 312-322.

Cerejo M., Dias J. (2005) Transport and dispersal of marine toxic plankton algae in a shallow, temperate coastal lagoon. Marine Environmental Research 63: 313-340.

IST | Bioengineering Systems PhD | Entering year: 2012 | Graduation year: 2017

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Thesis Title: Effect of a spatiotemporal controlled delivery of growth factors on the maintenance of MSC pluripotency

Supervisors: Frederico Ferreira (IST-UL), Claudia Lobato da Silva (IST-UL)

FCTUNL | Bioengineering PhD | Entering year: 2009

Thesis Title (2013): Development of a process for the production and purification of minicircles for biopharmaceutical applications

Michaela Simcikova has successfully discussed her thesis on December (2013), under the Gabriel António Amaro Monteiro’s supervision.

Read more on Michaela Simcikova PhD experience at the MIT100K and at Revista Exame.

IST | Bioengineering Systems PhD | Entering year: 2012

Research topic/ area: Research on risk governance with a direct application to science, technology and public policy: development of new regulatory frameworks on Regenerative Medicine.

Research summary: The purpose of my work is to support a deep study of the transitional process from scientific research to clinical research regarding cell therapies technology. Studying ongoing research and clinical trials, the objective is to understand how regulation shape practices, and establish barriers in the move to the clinical usage. Understanding the impacts of public policies through legal and regulatory frameworks in the development of such breakthrough treatments, that challenges our scientific knowledge, and common medicinal practices, is a requirement to adapt it, in the ultimate goal of fostering public health.

FCTUNL | Bioengineering PhD | Entering year: 2009 | Graduation year: 2015

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Current position: Senior Research Scientist at Thomson Reuters, UK

Thesis: Immunomodulatory Activity of Mesenchymal Stromal Cells

Supervisors: Joaquim Sampaio Cabral (IST, University of Lisbon) and Francesco Dazzi, Faculty of Life Sciences & Medicine King´s College, London

UMinho | Bioengineering PhD | Entering year: 2009

PhD supervisor: Nuno Neves (3 B’s research group)

PhD Thesis (2013) : Development of advanced release systems for stem cell based therapies

Thesis abstract: The increasing incidence of bone, cartilage, tendon and ligament injuries is stimulating the development of less invasive surgical procedures and of treatment modalities that overcome the limitations of conventional therapies, while enhancing the functional recovery. Tissue Engineering and Regenerative Medicine (TERM) strategies are promising alternatives to stimulate the formation of functional tissues after trauma or disease.

The purpose of Tissue Engineering is to develop strategies promoting the development of new tissue similar to that previously lost. It relies on the use of a biomaterial scaffold, which can be combined with cells and bioactive factors. The scaffolds have a significant role in these strategies because they are designed to help and guide the cells to contribute for the tissue regeneration process. A scaffold should mimic the main properties and structure of the extracellular matrix (ECM) of the tissue of interest. The fibrous nature of the natural ECM has led many researchers to focus on the development of fiber-based scaffolds. Electrospinning is a very promising technology that enables for the production of synthetic or natural polymeric ultrafine fibers. These fibers organized in a mesh-like structure have diameters in the submicron range which results in a high surface area-to-volume ratio and high micro-porosity. The meshes have frequently a random orientation distribution or, in some special cases preferential directions of alignment. The electrospun nanofibers can also be used as a bioactive factors delivery system and this has been the subject of intensive research in recent years. However, the control of the bioactive factors release loaded into the electrospun nanofibers has been a challenge due to fabrication processes and fast release of those factors from the electrospun nanofibers. The main goal of this thesis was to develop a multi-functionalized system combining electrospun nanofibers and nanoparticles, namely liposomes, for the release of bioactive factors. Liposomes are well-established nano delivery devices presenting significant advantages, namely a high load carrying capacity, a relative safety and an easy production, as well as a versatile nature in terms of possible formulations and surface functionalization. The objective of the first study was to evaluate the efficacy of the liposomes as carriers of functional bioactive factors. Our results showed that the optimized dexamethasone-loaded liposomes do not have any cytotoxic effect over primary human bone marrow-viii derived mesenchymal stem cells (hBMSCs). More importantly, they were able to promote an earlier induction of hBMSCs differentiation into the osteogenic lineage. In the following studies, bioactive agent loaded-liposomes were combined with electrospun nanofibers meshes in order to develop multi-functionalized systems, able to promote a local and sustained delivery of bioactive agents. To achieve this goal, the electrospun nanofiber meshes were functionalized using different techniques, such as UV-Ozone and wet chemicals, to create functional groups (e.g. amino and thiol groups) that allow further immobilization of bioactive agents-loaded liposomes. We immobilized liposomes loading different bioactive agents (i.e. osteogenic differentiation factor, antibiotic and a plasmid encoding a gene of interest) at the surface of electrospun nanofiber meshes made of two different polymers (i.e. polycaprolactone and chitosan) for different applications. The results showed that the dexamethasone released from the liposomes immobilized at the surface of electrospun polycaprolactone NFM can promote the osteogenic differentiation of hBMSCs. The in vitro susceptibility tests confirmed that the antibiotic gentamicin released from the liposomes immobilized at the surface of electrospun chitosan nanofiber meshes do successfully inhibit the growth of Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. Therefore, the developed system could be successfully used as wound dressing, preventing possible infections caused by common pathogens. We also demonstrated that liposomes encapsulating a plasmid encoding the transcription factor gene RUNX2 and immobilized at the surface of electrospun polycaprolactone nanofiber meshes can lead to long-term gene expression in vitro, which may be employed to enhance the osteoinductive properties of scaffolds used for bone tissue engineering strategies. The last work of the thesis focused on the simultaneous encapsulation of two bioactive factors (i.e. dexamethasone and ascorbic acid) into the different compartments of a liposome. The dual bioactive agent release study showed that dexamethasone was released more rapidly from the liposomes than ascorbic acid. Dexamethasone and ascorbic acid loaded liposomes promoted the hBMSCs differentiation into the osteogenic lineage both in basal medium and incomplete osteogenic medium (without dexamethasone and ascorbic acid). We propose herein a versatile platform using liposomes and electrospun nanofibers for Tissue Engineering and Regenerative Medicine related applications, namely bone tissue regeneration. This strategy can be used in vitro to induce the osteogenic differentiation of stem cells or, in another perspective, can be applied into a patient wound or tissue defect in order to act as an instructive scaffold either for antibacterial protection or to stimulate the regenerative process.

Publications:

N. Monteiro, A. Martins, D. Ribeiro, S. Faria, N. A. Fonseca, J. N. Moreira, R. L. Reis, N. M. Neves. “On the Use of Dexamethasone Loaded Liposomes to Induce the Osteogenic Differentiation of Human Mesenchymal Stem Cells”. Journal of Tissue Engineering and Regenerative Medicine, 2013, doi -10.1002/term.1817.

FCTUNL | Bioengineering PhD | Entering year: 2009 | Graduation: 2014

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Current Position: Postdoctoral Research Scientist at Instituto Superior Técnico

Thesis Title: Yeast mannosylerythritol lipids from lignocellulose: a novel strategy for the production of jet biofuel

Supervisors: Frederico Ferreira (IST-UL), César Fonseca (LNEG), Bruce Tidor (MIT)

FCTUNL | Bioengineering PhD | Entering year: 2011| Graduation: 2016

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Current Position: Postdoctoral Researcher at CEDOC NOVA Medical School

Thesis Title: Development of hydrogel-based dressings for skin wound regeneration using supercritical fluids technology

Supervisors: Ilídio Correia (Faculdade de Ciências da Saúde, Universidade da Beira Interior), Ana Aguiar-Ricardo (FCT-UNL)

Thesis Summary: Asymmetrical structures have arisen over the last two decades as suitable wound dressings. However, the production methods used so far, present some limitations: are time-consuming, need the use of toxic organic solvents and few polymers could be used. In addition, taking into account the worldwide economic status, sustainable procedures should be adopted for wound-management. This project presents a sustainable alternative to the previous methods: supercritical carbon dioxide (scCO2)-phase inversion technique demonstrated to be a suitable method to produce asymmetric membranes, being certainly the method of the future in tissue engineering and regenerative medicine.

UMinho | Bioengineering Systems PhD | Entering year: 2010 | Graduation year: 2016

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Research topic/area: Development of a tissue engineered intestine

Research Summary:
A number of gut disorders, including Crohn’s disease, can lead to Short Bowel Syndrome (SBS). SBS compromises (i) the nutrient transport function of the mucosa layer and (ii) the peristalsis function of the muscularis propria layer. A potential treatment for SBS would be the development of a living, tissue engineered small intestinal graft to replace the lost tissue. Several attempts have been made to tissue engineer small intestine; however, they fail to reproduce the complexity and functionality of living tissue. The general aim of this work is to develop a tissue engineered intestine.

UMinho | Bioengineering PhD | Entering year: 2009 | Graduation year: 2015

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Current Position: Head of Development at SilicoLife

Thesis Title: Algorithms and tools for in silico design of cell factories

Supervisors: Isabel Rocha (UMinho); Miguel Rocha (UMinho)

IST | Bioengineering PhD | Entering year: 2008

IST | Bioengineering Systems PhD | Entering year: 2013/2014

Research area: Biomechanics, Intelligent Systems

PhD Supervisor: Jorge Martins (IST) ; Dava Newman (MIT)

Thesis Topic: Impedance Shaping and Inertial Sensing for the design and control of hybrid Human-Machine system.The broad aim of this research project is to explore new designs of robotic devices for physical rehabilitation and augmentation of humans. Under the hypotheses that impedance shaping, achieved through a control network of muscle actuation and proprioceptive sensing, regulates human motion, the proposed research targets the following key points: To devise and implement human performance experiments in order to uncover and model the biological impedance variation methods adopted during different tasks in locomotion and manipulation.

1. To devise bio-inspired sensing estimation and control algorithms for impedance shaping.
2. To explore the embodiment of the developed algorithms in compliant exoskeletons, as well as in functional electrical stimulation.

This research follows and builds on previous work developed at IST, in the development of hybrid active orthotics for the ankle joint, and on the research performed at MIT leading to the development of the BioSuit – a second skin compliant counter pressure suit for space exploration.

IST | Bioengineering PhD | Entering year: 2007

Research topic/area: Stem Cell BioEngineering

Communications/Conference presentations:

• Andrade, P.Z., dos Santos, F., Lobato da Silva, C.,Almeida-Porada, G.,Cabral, J.M.S., Expansion of human bone marrow mesenchymal stem cells using macroporous microcarriers under stirred conditions, 2nd annual meeting of Portuguese Society for Stem Cells and Cell Therapies, Coimbra, Portugal, April 27-28, 2007 (Oral Presentation)

• Lobato da Silva, C., Gonçalves, R., dos Santos, F., Andrade, P.Z., Almeida-Porada, G.,Cabral, J.M.S., Defining culture conditions to maximize the ex-vivo expansion of human umbilical cord blood (CB) hematopoietic stem/progenitor cells: how to start?, International Stem Cell Meeting: Stem Cells and their Regulatory Microenvironment, Tel-Aviv, Israel, June 5-7, 2007

• Lobato da Silva, C., Gonçalves, R., Andrade, P.Z., dos Santos, F., Almeida-Porada, G.,Cabral, J.M.S., Expansion of human adult bone marrow mesenchymal stem cells using microcarriers under dynamic culture conditions, 36th International Annual Scientific Meeting, ISEH Society for Hematology and Stem Cells, Hamburg, Germany, September 28-30, 2007

• Lobato da Silva, C., Gonçalves, R., dos Santos, F., Andrade, P.Z., Almeida-Porada, G.,Cabral, J.M.S., Maximization of the ex-vivo expansion of umbilical cord blood hematopoietic stem/progenitor cells by direct contact culture with human mesenchymal stem cells,36th International Annual Scientific Meeting, ISEH Society for Hematology and Stem Cells, Hamburg, Germany, September 28-30, 2007

• Andrade, P.Z., Temtem, M., dos Santos, F., Lobato da Silva, C., Aguiar-Ricardo, A., Cabral, JMS., “”Green” Chitosan Membranes for the ex-vivo expansion of Human Mesenchymal Stem Cells, 3rd annual meeting of Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal, April 23-24, 2008 (Oral Presentation)

Research interests: Human hematopoietic stem cells expansion and differentiation; Functional/Phenotypic assays for stem cell culture; Bioreactors for stem cell expansion and/or differentiation

Links:

http://www.ist.utl.pt/ (IST)

http://www.ibb.pt/ (Institute for Biotechnology and Bioengineering)

http://dequim.ist.utl.pt/cebq/berg/index.html (BioEngineering Research Group)

UMinho | Bioengineering PhD | Entering year: 2009 | Graduation year: 2015

Thesis Title: Novel approaches for dynamic modelling of E. coli and their applications in metabolic engineering

Supervisors: Isabel Rocha (UMinho); Miguel Rocha (UMinho); Bruce Tidor (MIT) Monitoring

FCTUNL | Bioengineering PhD | Entering year: 2009

UMinho | Bioengineering Systems PhD | Entering year: 2013/2014

Research area: Bioengineering

PhD Supervisor: Bruno Fernandes (Centre of Biological Engineering, University of Minho); António Vicente (Centre of Biological Engineering, University of Minho); Vítor Vasconcelos (Interdisciplinary Centre of Marine and Environmental Research, University of Porto)

Thesis Topic: Development and optimization of cultivation systems and techniques in order to improve cyanotoxin productivity and cost effectivenes. Worldwide occurrence of hepatotoxic cyanobacteria and their toxins pose serious threats to public health. However, cyanotoxins can be used as laboratory standards in human and environmental risk assessment or even as tools for molecular and cell biology studies. Presently, their availability is low due to difficulties found in production and purification processes, which influence the final price. On the other hand, the variation of cyanobacterial blooms toxicity is probably due to environmental factors. Thus, the study of the influence of environmental factors on cyanobacteria growth and toxicity might help to control them just by monitoring environmental factors. The aim of this project is to evaluate the influence of environmental conditions (temperature, etc.) in cyanobacteria growth and toxin production. Cyanotoxin extraction and purification methods will also be developed.

UMinho | Bioengineering Systems PhD | Entering year: 2013

Research Area: Stem Cell, Tissue Engineering and Regenerative Medicine

Supervisor: Manuela E. Gomes (3B’s Research Group, Universidade do Minho)

Thesis Title: Biomimetic microengineered hydrogels for tendon tissue engineering

Research Summary: Musculoskeletal diseases are one of the leading causes of disability worldwide. Among them, tendon injuries are responsible for substantial morbidity, pain and disability, affecting athletes, active working people, and elder population whose joint movements rely on the biomechanical interplay of intrinsic and extrinsic musculotendinous forces.

IST | Bioengineering Systems PhD | Entering year: 2013/2014

Research area: Stem cell research

Thesis topic: Development of clinical grade stem cell-based products with enhanced therapeutic potential for cardiac regeneration

PhD Supervisors: Cláudia Lobato da Silva, Instituto Superior Técnico and MD. António Fiarresga, Centro Hospitalar de Lisboa Central, Hospital de Santa Marta

FCTUNL | Bioengineering PhD | Entering year: 2009

PhD Supervisor: Steven Cramer (Rensselaer Polytechnic Institute-EUA); PhD Co-supervisor: Ana Margarida Nunes da Mata Pires de Azevedo (IST).

PhD Thesis (2013): Phenylboronic Acid as Ligand for Multimodal Chromatography

UMinho | Bioengineering PhD | Entering year: 2008

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PhD Supervisor : Lígia Rodrigues and Madalena Alves (CEB – Centre of Biological Engineering).

PhD Thesis (2013): New strategies for the production of butanol and 1,3-propanediol from glycerol

Thesis Abstract: The increasing demand for use of renewable resources as feedstock for the production of chemicals combined with advances in biotechnology is generating a renewed interest in the fermentative production of n-butanol and 1,3-propanediol(1,3-PDO). In this context, glycerol, a by-product of biodiesel and ethanol production, arises as a potential substrate for this purpose. In this work, Clostridium pasteurianum DMS 525 was studied for butanol production using biodiesel-derived crude glycerol and pure glycerol as the carbon source.

The main products obtained were butanol and 1,3-PDO. Moreover, the competitive nature of butanol and 1,3-PDO pathways was evident, and a shift to the former for higher glycerol concentrations was clearly observed. In preliminary experiments conducted in serum bottles using crude glycerol, the maximum glycerol consumption achieved was 31.83 ± 0.98 g l-1, which resulted in 6.71 ± 0.42 g l-1 of butanol and 6.86 ± 0.51 g l-1 of 1,3- PDO. To improve the butanol tolerance of C. pasteurianum DSM 525, random chemical mutagenesis (N-ethyl-N-nitrosourea) in solid medium was performed. Experiments resulted in the isolation of colonies growing in culture medium containing 12 g l-1 butanol (except in the controls). Mutant cells showed 20 % higher butanol production than the parent strain when grown in liquid medium. Optimization of the culture medium composition and the inoculum age resulted in a glycerol consumption and a butanol titer of 45.62 ± 3.81 g l-1and 12.4 ± 0.26 g l-1, respectively. The concentration of 1,3-PDO reached 7.45 ± 0.86 g l-1. In particular, iron was found to play a key role in this process. Supplementation of 3 mg l-1 FeCl2.7H2O in the culture medium led to 140% increase in butanol titer. In pH-controlled experiments, it was possible to increase glycerol consumption to a maximum of 75 g l-1. Nevertheless, butanol production was around 9 g l-1and higher concentrations of 1,3-PDO were obtained (20 g l-1). Finally, the production of 1,3-PDO was studied in continuous culture (EGSB reactors). Two pre-treatments (heat and disruption) were applied to the granular sludge in order to minimize the methane production. 1,3-PDO was always found to be the main product and only small amounts of acids were detected. Molecular biology tools (DGGE, cloning and sequencing) were used to evaluate the microbial community. A maximum 1,3-PDO yield and productivity of 0.43 g g-1 and 57 g l-1d-1, respectively, were achieved in the reactor operated with nontreated granular sludge (control). The results obtained provide a deeper understanding of a complex process such as the anaerobic fermentation of glycerol using Clostridium spp. C. pasteurianum shows a great potential for butanol and 1,3-PDO production from crude glycerol. However, butanol toxicity seriously limits its titer, thus it is important to find ways to overcome this problem. On the other hand, this study proves the feasibility of 1,3-PDO production in EGSB reactors, which have the advantage of being operated under non-sterile conditions and represent a novel strategy to valorise glycerol generated as by-product in the biodiesel industry. Keywords: Clostridium pasteurianum 1,3-propanediol glycerol butanol

Publications

• Gallardo R, Faria C, Pereira MA, Rodrigues LR, Alves MM. Production of 1,3-propanediol in EGSB reactors by open mixed cultures using glycerol as the carbon source. In 13th World Congress on Anaerobic Digestion. Santiago de Compostela, 2013, p. 1-4
• Gallardo R, Faria C, Rodrigues LR, Pereira MA, Alves MM. Anaerobic granular sludge as a biocatalyst for 1,3-propanediol production from glycerol in continuous bioreactors. Bioresource Technology 155() 28-33, 2014.

FCTUNL | Bioengineering PhD | Entering year: 2009

PhD supervisor: João Miguel da Costa Sousa; PhD co-supervisor: Stan Neil Finkelstein

PhD Thesis (2014): Data-Based Modeling And Classification to Improve Outcomes In the Intensive Care Unit

Thesis Abstract: “Patients in intensive care units (ICU) are usually the weakest in the hospital and are constantly monitored, resulting in high amounts of data available. However, its use can only be met economically through the use of computers. The work developed aims to apply current and novel soft computing techniques to ICU data in order to build predictive mathematical models that can impact the management of two major concerning medical disorders: septic shock and heart disease. Preprocessing clinical data and feature selection are crucial in the use of the data. This thesis suggests the use of missing data imputation approaches that maintain the temporal trend of the incomplete signal to improve predicting performance. Moreover, a modified version of the sequential selection method that spans the search space and maintains the advantages of the regular algorithm is presented. A classifier of the outcome of septic shock patients at the end of the ICU stay, which is highly correlated with the medical risk scores calculated daily, is presented. Contrasting to these, the model assesses the risk of death hourly and is based on only 4 physiological variables frequently acquired in the ICU. Left ventricular ejection fraction (LVEF) is a well-established diagnostic parameter of coronary artery disease and heart failure and this is the first study addressing its assessment through soft computing techniques. The model developed can predict the risk class 1 hour after admission, achieving best performance after 6 hours. Using this model can reduce the standard imaging diagnostic time in up to 80%. Further work would include validation of the results in other databases and prospective studies to determine impact in clinician decision-making cost-efficiency.”

Keywords: Septic Shock; Left Ventricular Ejection Fraction; Intensive Care Unit; Data Mining; Takagi-Sugeno Fuzzy-Modeling; Feature Selection

Publications

R.D. Pereira

R.J. Almeida; U. Kaymak ; S.M. Vieira ; J.M.C. Sousa ; S.R. Reti ; M.D. Howell ; S.N.Finkelstein , Predicting Septic Shock Outcomes in a Database with Missing Data using Fuzzy Modelling in Proceedings of the 2011 IEEE International Conference on Fuzzy Systems, 27-30 June 2011, Taipei, Taiwan, pp. 2507-2512. (doi: 10.1109/FUZZY.2011.6007606)

R.D. Pereira, J. Sousa, S. Vieira, S. Reti, S.Finkelstein ,Modified Sequential Forward Selection Applied to Predicting Septic Shock Outcome in the Intensive Care Unit , in Synergies of Soft Computing and Statistics for Intelligent Data Analysis: Advances in Intelligent Systems and Computing, R. Kruse, M. R. Berthold, C. Moewes, M. A. Gil, P. Grzegorzewski, O. Hryniewicz, Springer-Verlag Berlin Heidelberg, 2013, pp. 469-477.

R.D. Pereira, New Insights on Septic Shock Goal-Directed Therapies, in American Medical Informatics Association (AMIA) Annual Symposium, Informatics: Transforming Health and Healthcare, 3-7 November 2012, Chicago, USA.

R.D. Pereira, etal. Data Mining to Predict Severely Depressed Left Ventricular Ejection Fraction Following Admission to the Intensive Care Unit Using Clinical Physiology, (submitted to journal Circulation)

R.D. Pereira, etal. Risk Monitoring System for Septic Shock Patients using Fuzzy Classification, (to be submittedto Journal of Critical Care)

EEUM | Bioengineering PhD | Graduation year: 2014

Current position: Head of development at SilicoLife, Portugal

Thesis Title: Improvement of in silico strain engineering methods in Saccharomyces cerevisiae

Supervisors: Isabel Rocha (UMinho), Jens Nielsen (Chalmers University of Technology)

FCTUNL | Bioengineering PhD | Entering year: 2007 | Graduation year: 2012

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Current Position: Senior Process Engineer at FloDesign Sonics

Thesis Title: Bioprocess engineering of Liver cells for drug testing applications

Research topic/area: High Trough-Put Screening Using Micro-Bioreactors

Supervisors: Paula Alves (IBET), Manuel Carrondo (IBET), Daniel Wang (MIT)

FCTUNL | Bioengineering PhD | Entering year: 2008 | Graduation year: 2015

Thesis Title: Monitoring serotonergic neuronal activity in behaving rodents

Supervisors: Zachary F. Mainen (Champalimaud Centre for the Unknown); Manuel Nunes da Ponte (REQUIMTE, Departamento de Química, FCT-UNL)

EEUM | Bioengineering PhD | Entering year: 2010 | Graduation year: 2014

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Current position: Postdoctoral Research Fellow at INL – International Iberian Nanotechnology Laboratory

Thesis Title: Novel 3D scaffolds modified with nanostructured polymeric coatings or micro/nanofibers for tissue engineering applications

Supervisor: João F. Mano (UMinho); Rui L. Reis (UMinho)

IST | Bioengineering PhD | Entering year: 2008

Thesis Title (2013): Platforms to modulate the activity of hematopoietic stem cells and their progenies

Sezin Aday has successfully discussed her thesis on December 2013.

Sezin Aday’s research work was supervised by Lino da Silva Ferreira and co-supervised by Cláudia Alexandra Martins Lobato da Silva

UMinho | Bioengineering PhD | Entering year: 2009

PhD Supervisor : Luís A. Rocha ; Manuel L. Nunes ; Paula Varanda Ferreira

PhD Thesis (2013): An Approach to Develop Sustainable Medical Devices.

Thesis Abstract: The development and commercialization of contemporary Medical Devices is inherently of a multidisciplinary nature. Consequently, they have to undergo a stringent regulatory compliance procedure in conformity with an ever increasingly fierce and competitive business environment. Throughout the product life cycle, medical devices would significantly consume renewable as well as non-renewable resources and as a result exert a substantial social, economic and environmental impact(s). Accordingly, it is imperative to consider the criteria of the aforementioned domains of sustainability in the initial phases of product development. The proposed conceptual multifaceted framework comprehensively explores a broader scope of sustainable product development, mainly from the pragmatic standpoint of systems engineering in comparison to the contemporary evaluation and development approaches. The underpinnings of the proposed framework encompasses the critical role of a decision model titled ‘Multi Criteria Hierarchical Model (MCHM)’ which is in fact an extensive revision of the Analytical Hierarchy Process decision modelling approach. The MCHM contains three tiers of pertinent criteria to attain overall sustainability. The structure of MCHM illustrates the tolerable level of sustainability in Tier 1, which is non-negotiable and compulsory, and the additional degrees of sustainability that increases from Tier 2 to Tier 3. Furthermore, the proposed framework elucidates the active participation of the MCHM in product design and development by conjoining with a wide spectrum of technical and conceptual tools. The research methodologies in the thesis are comprised of interviews, questionnaires and case studies that mainly involved active participatory observation. The objective of incorporating case studies in the thesis is to evaluate the effectiveness of the MCHM in an Industrial environment. In this doctoral research the contemporary medical devices explored during the case studies included a wide spectrum of materials and technologies that range from metal and non-metal prosthesis (external and sometimes internal), instruments, advanced implantable devices and biodegradable scaffolds used in regenerative medicine. The research activities commenced with a thorough literature review that directed the researcher to the need for an exploratory study, accomplished by interviews with experts from academia and industry. These experts provided their feedback on the Sustainability related criteria outlined in the MCHM based on their expertise and knowledge of product development in diverse economic circumstances. The feedback was obtained in the form of assigning numerical scores during pair-wise comparison between two criteria at a time. The scores and recommendations were documented for being incorporated within the case studies. In the case studies, the MCHM was incorporated in the early stage of product development to prioritize bare minimum environmental sustainability and profitability in accordance with regulatory compliance. During the decision making process, the product design was investigated in order to simultaneously accomplish the aforementioned facets by way of incorporating the expert recommendations. Furthermore, these expert recommendations obtained in conjunction with business strategies and technical problem solving techniques, such as Case based Reasoning (CBR), Design by Analogy (DA) and Theory of Inventive Problem Solving (TRIZ) were considered for resolving conflicts between the criteria of Tier 1 and other Tiers. The thesis provides decision makers and the product development teams with a framework to gain a more holistic perspective on sustainable product development with respect to policies, technical/non-technical tools and business strategies. The goal is to enable these product development teams to implement pragmatic solutions for ensuring long-term competitiveness and the welfare of the Stakeholders.

Full thesis available upon request at Universidade do Minho Repositorium.

IST | Bioengineering Systems PhD | Entering year: 2013/2014

PhD Supervisor: Frederico Ferreira (IST)

Thesis Topic: Bioengineering skin-mechanoreceptor sensing to enhance function in hybrid human machine interface systems.Throughout human existence, limb loss has been considered an irreversible detriment and permanent loss of sensory function. Prosthetics have attempted to act as replacements for lost limbs and digits for thousands of years. Until the 19th century, they were mainly passive, cosmetic devices, giving the user minimal sensory feedback and acting as little more than hooks. Today, there are various ongoing clinical trials related to surgical attachment of prosthetics utilizing osseointegration and incorporation of implantable electrodes. This, alongside the simultaneous design of lightweight, integrated prosthetics, has led to revolutionary breakthroughs with sensory feedback, control, and range of motion for amputees. Despite these breakthroughs, however, prosthetics remain years away from successfully mimicking a complete motor and somatosensory function. Lack of innervated skin, which allows for a myriad of tactile stimuli to be detected and interpreted, is perhaps the greatest hindrance in giving amputees complete sensory feedback. This too has been combated through design of artificial skin substitutes, enabling users with increased –but not standard– sensory feedback. Finally, novel advances in composite tissue surgeries have enabled complete limb transplantation. However, as with other transplantations, psychological assessment and lifelong immunosuppressants are mandatory, making this technique unsuitable for everyone. This project focuses on analysis of skin-mechanoreceptor sensing in order to understand aspects of somatosensory function that are difficult to replicate in artificial limb replacement, as well as fully regain through transplantation. Successful bioengineering of the somatosensory system can be integrated into the novel, bi-directional human-machine interface, leading to enhanced sensory function.

UMinho | Bioengineering PhD | Entering year: 2008 | Graduation year: 2014

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Current position: Postdoctoral fellow at Radboud University Medical Center, The Netherlands

Thesis Title: Routes to Advanced Vascularized Tissue Engineering Constructs

Supervisors: Manuela Estima Gomes (3B’s Research Group/UMinho), Alexandra Marques (3Bs Research Group/UMinho)

FCT-UNL | Bioengineering PhD | Entering year: 2011 | Graduation year: 2015

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Current position: Post-Doctoral Researcher at Fellow at iBet – Instituto de Biologia Experimental e Tecnológica

Thesis Title: Development of 3D in vitro models for prediction of hepatic metabolism and toxicity

Supervisors: Paula M. Alves (iBET/IQTB-UNL); Catarina Brito (iBET/IQTB-UNL) T-UNL| Bioengineering PhD | Entering year: 2011 | Graduation year: 2015

FCT-UNL | Bioengineering PhD | Entering year: 2010 | Graduation year: 2015

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Current position: Post-Doctoral Research Fellow at FCT-UNL, Portugal

Thesis Title: Engineered MRI nanoprobes based on superparamagnetic iron oxide nanoparticles

Supervisor: Ana Cecília Roque (FCTUNL)

IST | Bioengineering PhD | Entering year: 2008

PhD Supervisor: Ramiro Almeida(CNC) & Martha Constantine-Paton (MIT)

PhD Thesis (2012): Flailer – a myosin Va neurological mutant displays autistic-like behavior and synaptic defects.

Thesis abstract: Myosin Va is a processive F-actin motor protein present in synaptic fractions and known to transport inositol triphosphate receptors and associated smooth endoplasmic reticulum into Purkinje cell spines. Its role in other synaptic functions is controversial. In Flailer, a spontaneous mouse mutant expressing a dominant negative Myosin Va protein, trafficking of synaptic proteins is severely disrupted; AMPA current frequency is abnormally high and it also lacks mGluR5-LTD. Here we examine the effects of this “flailer protein” in the hippocampus and visual cortex. In synaptosomes all major glutamate receptor scaffolds and TLS/FUS, an mRNA binding protein, are significantly reduced. Flailer CA1 pyramids show increased dendritic protrusions. Flailer mice also exhibit highly repetitive grooming behavior, low sociability, elevated anxiety and they lack spatial and contextual memory. These data suggest that Flailer may provide new approaches to identifying brain regions involved in these autism-like behaviors because their dominant negative protein can be manipulated independent of normal Myosin Va.

FCTUNL | Bioengineering Systems PhD | Entering year: 2012

Research topic/area: Biotechnology

UMinho | Bioengineering PhD | Entering year: 2007

PhD Supervisor: Lucília Domingues and Merja Penttilä

PhD Thesis (2013): Understanding the biotechnological potential of Ashbya gossypii.

Thesis Abstract: Ashbya gossypii (syn. Eremothecium gossypii) is a filamentous Saccharomycete which has long been known in the scientific and industrial communities, first as a cotton pathogen and subsequently as a riboflavin overproducer. This fungus has the smallest free living eukaryotic genome known, which shares a high degree of gene homology and gene order conservation with that of Saccharomyces cerevisiae. It has haploid nuclei and is prone to genetic manipulation, allowing the use of simple PCR-based gene targeting strategies and free propagation of plasmids containing replicons from S. cerevisiae. Moreover, it grows well in a variety of defined, complex and waste-based media, and has a long history of safe use in the industrial production of riboflavin (vitamin B2). These unique features led to expanded interest in A. gossypii as a “minimal” host for the production of, yet unexploited, valuable compounds other than riboflavin, namely heterologous proteins. However, although two heterologous proteins have already been successfully secreted by A. gossypii, little is still known about the protein secretion ability of this fungus. To further understand the biotechnological potential of A. gossypii as a cell factory organism, this thesis primarily focused on the characterization of theA. gossypii protein secretory pathway at the genomic, transcriptomic and proteomic levels. Based on experimental observations and on the data from the genomic and transcriptomic analyses, a hydrolytic enzyme, invertase, was deduced to be natively secreted by A. gossypii and molecularly characterized. To further address A. gossypii as a heterologous protein producer, the β-galactosidase from Aspergillus niger was expressed in this fungus under the regulation of different native and heterologous promoters. In addition, a new molecular tool for use inA. gossypii was developed to generate mutant strains free of exogenous selection markers, allowing the creation of improved A. gossypii strains suitable for industrial applications. The results presented in this thesis demonstrate that the amount and variety of proteins natively secreted byA. gossypii to the culture medium is rather low, being more similar to that of yeast than to that of other filamentous fungi. Similarly, the N-glycosylation patterns produced by A. gossypii are generally more similar to those produced by yeast than to those produced by other filamentous fungi. However, extensive hyperglycosylation only occurs in certain culture conditions. Like other filamentous fungi, A. gossypii also seems to be able to trim its N-glycans. A conventional unfolded protein response (UPR) was not activate in A. gossypii in response to heterologous protein secretion nor to dithiothreitol (DTT)-induced secretion stress, as generally observed in other fungi. However, the transcriptional responses of A. gossypii to DTT-induced stress indicate that alternative mechanisms exist in this fungus to cope with protein secretion stress. The A. gossypii invertase was demonstrated to be encoded by the AFR529W (AgSUC2) gene, which is functionally complemented by the S. cerevisiae SUC2 (ScSUC2) gene. The signal sequences of both AgSuc2p and ScSuc2p were able to direct the secretion of invertase into the culture medium in A. gossypii. Similarly to the invertases of other fungi, the expression of the A. gossypii invertase is regulated by the sugars present in the medium. These results expanded our knowledge about the A. gossypii native secretion capacities, being invertase the second hydrolytic enzyme natively secreted by this fungus to be experimental characterized. The β-galactosidase from A. niger was successfully expressed in A. gossypii under the regulation of different promoters. The native TEF promoter revealed to be the best promoter for overexpressing heterologous β-galactosidase in A. gossypii, inducing 2-fold higher secreted activity than the A. gossypii GPD promoter and 7-fold higher than the S. cerevisiae PGK1 and ADH1 promoters. The levels of active β-galactosidase secreted by a S. cerevisiae laboratorial strain transformed with the same plasmids were up to 37 times lower than those obtained in A. gossypii. The secretion of active β-galactosidase by AA. gossypii was approximately 1.5-fold higher in glycerol- than in glucose-containing medium. These results highlight the potential of A. gossypii as a heterologous protein producer and open new opportunities to further optimize its secretion capacities using this enzyme as a model. As its activity is easy to detect, the screening for improved secretion will be facilitated. The Cre-loxP recombination system, which has been widely used in other organisms, was successfully adapted for use in A. gossypii, allowing the removal and reuse of selection marker genes in targeted engineering of this fungus. The set of disruption cassettes and plasmids constructed greatly expand the possibilities for genetically engineer A. gossypii being these suitable for use in both laboratorial and industrial strains, as they do not required any predetermined genetic background. In the future, targeted improvement of A. gossypii strains for industrial applications will benefit from this molecular tool.

Full thesis available upon request at Universidade do Minho’s Repositorium

Links: http://www.deb.uminho.pt/ | http://www.vtt.fi/

FCTUNL | Bioengineering PhD | Entering year: 2011 | Graduation year: 2016

Thesis Title: High Gradient Magnetic Separation of Therapeutics

Supervisors: Cecilia Roque (FCT-UNL), Raquel Aires-Barros (IST-UL)

Thesis Summary: Research work is mainly focused on development of functionalised magnetic nanoparticles based process technology for monoclonal antibody purification. Amino-phenyl boronic acid modified magnetic nanoparticle were used as basic building blocks for process development for selective capture and purification of antibodies.