berg 2013

2013

Annual Report

BERG | BioEngineering Research Group

Contents

04

About BERG

06 Executive Summary

07 The Research Group

08 Main Indicators

10

Research Activities

12 Bioprocess Engineering and

Biocatalysis Laboratory

14 Bioseparation Engineering Laboratory

16 Biosystems Engineering Laboratory

18 Molecular Bioengineering Laboratory

20 Stem Cell Bioengineering and

Regenerative Medicine Laboratory

24

Research Team

26 Full Professors

28 Associate Professors

30 Assistant Professors

37 Research Scientists

42

Scientific Output

44 Articles

45 Proceedings

46 Books

46 Book Chapters

46 Patents

46 Invited Oral Communications

47 Oral Communications

48 Poster Communications

51 Dissertations

About BERG

2013 BERG Annual Report

Executive Summary

The Research Group

Main Indicators

This report highlights the activities of the research

thrust areas and laboratories of BERG within the

Associated Laboratory Institute for Biotechnology

and Bioengineering.

The major activities in the Bioprocess Engineering

and Biocatalysis Laboratory (BEBL) included the

design of continuous flow systems for enzymatic

catalysis and the design of resilient PVA-based

matrices for entrapment of enzymes, with applica-

tions in the production of sweeteners and cellobi-

ose hydrolysis; and the adaptation of strains to

extreme conditions and their application in bio-

technological processes such as siderophore pro-

duction and bioremediation of hydrocarbons

The Bioseparation Engineering Laboratory

(BEL) in collaboration with Bayer Technology

Services demonstrated the feasibility of scaling-

up the continuous aqueous two-phase extrac-

tion of human antibodies from animal cell cul-

ture supernatants using a battery of mixer-

settlers. Stimuli-responsive cation-exchange

magnetic nanoparticles were also successfully

used to purify a monoclonal antibody from a

CHO cell culture supernatant, allowing a high

clearance of host cell proteins.

The main research topics at BioSystems Engi-

neering Laboratory (BSEL) were focused on

developing and demonstrating the industrial

feasibility of near-infrared spectroscopic for in-

situ multiparametric and reliable monitoring

within PAT, of small and large biomolecules’

manufacturing processes.

The Molecular Bioengineering Laboratory (MBL)

continued its efforts to develop integrated process-

es for the production and purification of plasmids

and minicircles by combining E. coli strain engi-

neering, tailored vector modifications and up-

stream and downstream processing strategies.

Microfluidic-based devices were also demonstrat-

ed for the detection of ochratoxin A and for the

trapping of E. coli cells by dielectrophoresis, and

biomimetic ligands were used to selectively bind

IgG molecules and stabilise proteins.

In the Stem Cell Bioengineering and Regenerative

Medicine Laboratory, (SCBL) a comparative study

of the proliferative and regenerative potential of

bone marrow mesenchymal stem/stromal cells

collected from healthy donors and acute myocardi-

al infarcted (AMI) patients was performed in col-

laboration with Department of Cardiology, Hospital

Santa Marta, Lisboa; and a novel bioprocess inte-

grating the serum-free and feeder-free expansion

and neural commitment of human iPSC and the

depletion of the remaining hiPSC through magnet-

ic-activated cell sorting (MACS) was successfully

developed.

Joaquim M.S. Cabral

BERG Head and Director of IBB

Executive Summary

20 7 13 Annual Report

The Research Group

BEBL BEL BSEL MBL SCBL

The BioEngineering Research Group (BERG) is a research unit in engineering and life

sciences at the Centre for Biological and Chemical Engineering (CEBQ). CEBQ is the

leading Centre of the Associated Laboratory Institute for Biotechnology and Bioengi-

neering (IBB), a network of research centres across Portugal. IBB has been identified

by the Portuguese Ministry of Science, Technology and Higher Education as a strate-

gic infrastructure for the development of the Portuguese R&D and innovation policies

in the areas of Biotechnology, Bioengineering, Life, Biomedical and Agricultural Sci-

ences. BERG activities within the Associated Laboratory IBB are focused on the The-

matic Areas of Industrial and Environmental Biotechnology/Bioenergy, Health Biotech-

nology and Nanobiotechnology.

BERG aims at excellence in research and advanced education in biotechnology and

bioengineering. The overall goal is to contribute for a better understanding of the

mechanisms that occur at the molecular and cellular levels, in order to translate them

into rational applications of biological systems relevant to the Industrial and Health

care sectors. BERG research priorities have special emphasis on Bioprocess and Bio-

systems Engineering, Molecular Bioengineering, Nanobiotechnology and Stem Cell

Engineering. BERG activities have been developed and coordinated within research

laboratories. This structure allows researchers in each laboratory to focus on particular

research topics of Bioengineering, while exploring and strengthening cross-cutting

competences. The current structure features five laboratories:

Bioprocess Engineering and Biocatalysis Laboratory (BEBL)

Bioseparation Engineering Laboratory (BEL)

BioSystems Engineering Laboratory (BSEL)

Molecular Bioengineering Laboratory (MBL)

Stem Cell Bioengineering and Regenerative Medicine Laboratory

(SCBL)

Main Indicators

BERG was established in 1991 as one of the initial three research groups of the Centre for Biological and

Chemical Engineering at IST, under the coordination of Prof. Joaquim Sampaio Cabral. The research carried

out throughout the years has been considered of excellent level by the international committees, which regu-

larly evaluate the research units funded by the Portuguese Ministry of Education and Science. The main

output of the activities performed by BERG members in 2012 is summarized in the following tables.

Human Resources

In 2013, BERG has 102 researchers integrated into the five laboratories, of these 25 have a PhD degree, 43

a master degree, 33 a bachelor degree and 1 undergraduate.

Publications

In 2013, the output of BERG’s activities includes the publication of 38 scientific articles in peer-reviewed

journals, 3 patents, 2 book and 7 book chapters, among other publications, including conference proceed-

ings, invited oral communications, oral communications and poster presentations in distinct international and

national conferences.

Human Resources Number

Faculty 11

Research Scientists 5

Post-doctoral Fellows 9

PhD Students 32

Research Assistants 11

MSc Students 33

Technicians 1

Male

Female

PhD

MSc

BSc

Undergraduate


Main Indicators

Type of Event Name of Event Committee

Course Scientific and Organising Committee of the International Advanced Course on Regenerative Medicine Manufacturing, Tavira, Algarve, Portugal, April

Joaquim Cabral, Margarida Diogo, Cláudia da Silva

Conference Scientific Committee of International Conference on BioPartitioning and Purification “BPP”, New Port, USA, October Raquel Aires Barros

Conference Coordinating Committee of the joint 9th European Congress of Chemical Engineering (ECCE9) / 2nd European Conference of Applied Biotechnolo-gy (ECAB2)

Joaquim Cabral,

Conference Scientific Committee of the 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, University of Algarve, Faro

Joaquim Cabral, Cláudia da Silva, Margarida Diogo

Conference Scientific Committee of the Portuguese Congress of Microbiology and Biotechnology | Microbiotec’2013, Aveiro, Portugal, December

Joaquim Cabral, Miguel Pra-zeres, Raquel Aires-Barros

Workshop Scientific and Organising Committee, “5º curso teórico-prático de Cartila-gem Articular”, Lisbon, Portugal, November Joaquim Cabral

Working Group Regenerative Medicine Manufacturing of the European Society of Bio-chemical Engineering Science “ESBES” Joaquim Cabral

Working Group Scientific Committee of European Section on Applied Biocatalysis “ESAB” Joaquim Cabral, Luís Fonse-ca

Working Group Downstream Processing of the European Society of Biochemical Engineer-ing Science “ESBES” Raquel Aires-Barros

Working Group Scientific Board of TERMIS Thematic Group on "Bioreactor Technologies" Joaquim Cabral

Scientific events

In 2013, the members of BERG have participate in organizing and scientific committees of national and in-

ternational conferences, research networks, working groups and sections of the European Federation of

Biotechnology and of the Tissue Engineering and Regenerative Medicine International Society (TERMIS).

Type of Publication Number

Articles in international peer-reviewed journals 38

Articles in conference proceedings 2

Books 2

Book chapters 7

Patents 3

Invited oral communications in international conferences 8

Invited oral communications in national conferences 8

Oral communications in international conferences 13

Oral communications in national conferences 10

Poster communications in international conferences 26

Poster communications in national conferences 17

PhD Thesis 7

MSc Thesis 69

Research Activities


Biosystems Engineering Laboratory BSEL

Molecular Bioengineering Laboratory MBL

Stem Cell Bioengineering and

Regenerative Medicine Laboratory SCBL

Bioprocess Engineering and Biocatalysis

Laboratory BEBL

Bioseparation Engineering Laboratory BELL

Bioprocess Engineering and Biocatalysis

BEB

L

Objectives

The Bioprocess Engineering and Biocatalysis La-

boratory aims at developing competitive and sus-

tainable technologic platforms and analytical meth-

odologies and tools with high potential and econom-

ic impact. In the field of biocatalysis the main goal is

to design and produce value-added bioproducts by

bioconversion using enzymes and microbial cells

from micro- to pilot-scale in the field of White Bio-

technology, namely in key areas such as of food

and feed, aroma, pharmaceutical and fine chemistry

industries, and biofuels, as well as to improve bio-

catalyst performance. A second area is the develop-

ment of new analytical methodologies and devices

specially biosensors and microfluidic systems de-

signed for monitoring and control of bioprocesses,

environment, food and water and healthcare. The

current projects are focused on the development of

technological platforms for biocatalysis and analyti-

cal tools to link process and product design orga-

nized in four major areas: Biocatalysis and Biotrans-

formation, ii) Bioreaction Engineering and iii) Bio-

sensors and Miniaturization.

Research Topics

1. Biocatalysis and Biotransformations - Design and

thorough characterization of reaction media and

operational strategies aiming at the implementation

of robust, high conversion bioconversion systems.

These are anchored in enzymatic platforms, namely

cutinase, penicillin acylase, inulinase and invertase,

targeted for the production of esters (flavors, bio-

diesel, chiral compounds and glycerol and oil inter-

mediates for bioplastic production), antibiotic inter-

mediates and semi-synthetic antibiotics and sweet-

eners. New methodologies on the use of lipases in

miniemulsion systems have been used on the enzy-

matic resolution of secondary alcohols with eco-

nomical interest. Bio-degradable zwitterionic com-

pounds are being synthesized in order to be used

as drug delivery vehicle. Moreover, the work devel-

oped contributed with valuable insight towards the

definition of major guidelines for rational bioprocess

design and development. Whole cells of mesophilic

bacteria have been improved, by favouring adaptive

mechanisms, to increase biocatalytic yields and

allow bioremediation processes under extreme con-

ditions of temperature and pH and in the presence

of high concentrations of salt and copper.

2. Bioreaction Engineering - Efficient and competi-

tive bioconversion systems aimed either at the pro-

duction of oligosaccharide syrups or at the hydroly-

sis of lignocellulosic waste, were developed. The

core of such systems relied on polyvinyl alcohol

based materials as enzyme carriers. Enzymatic (viz.

lipase, cutinase) and whole cell platforms (yeast

strains) are being used within the scope of an inno-

vative approach for the sustainable production of

biodiesel and jet biofuel. Further research efforts

are being made towards the production of jet-fuel

within the scope of microbial cell factories. Oxido-

reductases are used in combination with an innova-

tive material, Ion Jelly, for structuring enzymatic

biofuel cells. Zwitterionic compounds and fibers are

being synthesized as new electrolytes for the use

on the fabrication of thin film batteries based on Ion

Jelly technology. Rhodococcus cells are being as a

source of specialized fatty acids for biofuel produc-

tion and as a model bacterium to study biocatalyst

adaptation to reaction conditions. Pseudozyma spp

are being used for production of mannosylerythritol

lipids (MEL), a glycolipid/biosurfactant, for the first

time, from lignocellulosic materials.

3. Biosensors and Miniaturization - Nano/micro-

biocatalysts (biocomposites) are being developed

based on hydrogels, sol-gel, protein/cell assemblies

and magnetic nano-particles. New biomaterials

compatible with enzymes and other bio molecules

are being used as matrixes on the development of

biosensors. Miniaturized platforms, namely minia-

ture, meso- and microreactors, of either microstruc-

tured and non-microstructured nature are used for

bioprocess intensification. Reliable scaling strate-

gies, from those platforms to, at least bench-scale,

has been looked into. The design and assembly of

microreactors using low-cost, easily available mate-

rials and simple methodologies was performed and

the proof-of-concept was validated, using model

systems based on inulinase and invertase hydrolytic

activities. A multidisciplinary approach, from surface

characterization to hydrodynamics and catalytic

behavior, is being implemented for a thorough char-

acterization of enzymatic microreactors. High

throughput systems were also used to test the abil-

ity of essential oils from aromatic Mediterranean

plants to prevent biofilm formation and to study cel-

Luís Fonseca (PI), Carla Carvalho, Pedro Fernandes, Frederico Ferreira


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lular adaptation mechanisms to different toxic com-

pounds. A method involving bacterial cells was

used as a non-destructive technique to detect micro

defects in microfabrication components.

Main Achievements

It was shown, for the first time that polyunsatu-

rated fatty acids (PUFA) are synthesized during

short-time responses of Rhodococcus to osmot-

ic stress. PUFA were thought to be only pro-

duced solely by marine bacteria.The under-

standing of bacterial adaptation mechanisms

was used to improve polyhydroxyalkanoate pro-

duction

Aresilient system for cellobiose hydrolysis an-

chored in β-glucosidase entrapped in polyvinyl

alcohol hydrogels was successfully implement-

ed.

Design and implementation of efficient, low-cost

flow enzyme microreactors, allowing for the con-

tinuous production of fructose syrup from inulin.

Microscopic analysis of the microreactors pro-

vided a better understanding of enzyme behav-

ior.

Development of a process for sustainable pro-

duction of mannosylerythritol lipids (MEL), a gly-

colipid/biosurfactant with potential industrial ap-

plication, from lignocellulosic materials was de-

veloped and patented exploiting the natural fea-

tures of Pseudozyma spp. (work performed in

collaboration with LNEG).

Economical and environmental assessment of

different processes for active pharmaceutical

ingredients degenotoxification combining experi-

mental and theoretical studies (work performed

in collaboration with Hovione FarmaCiencia SA).

Zwitterionic compounds and fibers are being

synthesized as new electrolytes for the use on

the fabrication of thin film batteries based on Ion

Jelly technology.

Enzymatic platforms in miniemulsion systems,

namely cutinase were targeted for the produc-

tion of esters as fruity flavors and hydrolysis of

oil used as intermediates for bioplastic produc-

tion and resolution of secondary alcohols with

economical interest.

New biomaterials compatible with enzymes and

other bio molecules are being used as matrixes

on the development of biosensors.

Selected Publications

Székely, G., Bandarra, J., Heggie, W., Ferreira,

F.C., Green Chem. 15 (2013) 210

Figueira, J.A., Sato, H.H., Fernandes, P., J. Agric.

Food Chem., 61 (2013) 626-634

Ribeiro, E.M., Fernandes, P., Current Biotechnol., 2

(2013) 47-52

de Carvalho, R.N.L., Lourenço, N.M.T., Gomes,

P.M.V., da Fonseca, L.J.P., J. Polym. Sci., Part B:

Polym. Phys., 51 (2013) 817-825

Lopes, J.M., Paninho, A.B., Molho, M.F., Nunes,

A.V.M., Rocha, A., Lourenco, N.M.T., Najdanovic-

Visak, V., J. Chem. Thermodyn., 67 (2013) 99-105.

Bioseparation Engineering BEL

Objectives

The Bioseparation Engineering Laboratory aims at

the design and development of novel purification

processes in order to intensify and optimize the

downstream processing of proteins and biopharma-

ceuticals, with special emphasis on monoclonal

antibodies (mAbs), virus and VLPs. Several alterna-

tives to the currently established downstream pro-

cessing platforms of recombinant proteins and bio-

nanoparticles are being explored, with main focus

on aqueous two-phase extraction, nano-magnetic

separation and monolithic chromatography, from a

nano-scale to industrial scale. Additionally, tailor-

made synthetic ligands are being used aiming to

improve protein purification.

Research Topics

1. Aqueous two-phase systems (ATPS) for biophar-

maceuticals purification – The overall goal of this

contribution is to design an innovative downstream

process based on ATPS, for the purification of high-

value biomolecules from complex media, compris-

ing cell separation and bioproduct selective extrac-

tion, envisaging process integration and intensifica-

tion. This extraction-based technology is applied to

mAbs, pDNA, VLPs, cellular bodies, and intracellu-

lar or secreted proteins. In the case of proteins lo-

cated in the intracellular space, ATPS are dove-

tailed with electroextraction to increase the selectivi-

ty of the whole processing scheme. Efficient models

are being developed in order to predict protein parti-

tion in ATPS, contributing for a better understanding

of the mechanisms responsible for partitioning of

biomolecules and the parameters governing parti-

tion.

2. Bio-inspired affinity nanoparticles for antibody

recognition – Novel biomimetic affinity nanoparti-

cles, based on the conjugation of a Protein L-mimic

affinity ligand with thermosensitive amino-

functionalised PNIPAM microgels, have been de-

signed and synthesised. Adsorption screening with

three different model-proteins (bovine serum albu-

min, a commercial monoclonal antibody (mouse

IgG1 isotype) and human IgG) demonstrated that

such bio-inspired nanoparticles are able to selec-

tively recognize and capture antibody molecules in

both pure and impure/complex media.

3. Nano-magnetic separation of biopharmaceuticals

– The main focus is on the development of magnet-

ic nanoparticles (MNPs) suitable for the purification

of mAbs envisaging process integration and imple-

mentation of high scale magnetic separators. Func-

tionalized magnetic particles, based on boronic ac-

id, with high capacities for the therapeutic targets

are being applied in high gradient magnetic separa-

tion (HGMS) units or combined with ATPS. Associa-

tion of ATPS with affinity MNPs can improve the

throughput of the process but also the selectivity of

the separation. Process integration is evaluated by

using unclarified extracts of mAbs directly in HGMS

or combined with ATPS.

4. Alternative chromatographic ligands for antibody

purification – Novel affinity and mixed-mode ligands

are being designed and developed for the purifica-

tion of mAbs. Particular focus is being given to phe-

nyl boronate derivatives, which have been shown to

interact in a specific way with antibodies. The immo-

bilization of these ligands on to the surface of su-

pramacroporous monoliths (cryogels) is also being

addressed as a tool to integrate both clarification

and capture in just one step, and thus to capture

mAbs directly from cell culture media without any

cell removal step upstream. Removal of residual

DNA, host cell proteins and aggregates is being

evaluated using membrane adsorbers functional-

ized with anion-exchanger and hydrophobic ligands.

5. High throughput bioseparation platforms – De-

sign of an automated high-throughput microfluidic

Lab-on-Chip (LOC) platform based on ATPS allow-

ing process integration, optimization, and analysis is

being performed. The ATPS microfluidic platform is

being applied to mAbs extraction as an effective

tool to accelerate bioprocess design and optimiza-

tion and to integrate cell separation with mAbs puri-

fication and detection. Using the same concept, a

prototype microfluidic Lab-on-Chip platform for the

detection of contaminants in food products integrat-

ing sample preparation and toxin detection is also

being developed.

M. Raquel Aires-Barros (PI), Ana Azevedo, M. Ângela Taipa


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Main achievements

It was demonstrated that aqueous two-phase

extraction (ATPE) process can be used as a

platform for the capture of antibodies, overcom-

ing some of the limitations encountered using

the typical chromatographic processes, besides

inherent advantages of scalability, process inte-

gration, capability of continuous operation, and

economic feasibility. A continuous ATPE pro-

cess based on a PEG/phosphate system was

developed for the capture of human immuno-

globulin G and successfully applied to a Chinese

hamster ovary and a PER.C6 cell supernatant.

Prediction of partition coefficient of eight ionized

compounds was achieved in different ATPS by

the multiple linear regression analysis using the

linear solvation energy relationship (LSER)

equation.

Affinity magnetic separation prooved to be a

versatile separation process for antibodies purifi-

cation and an alternative to Protein A chroma-

tography, considering the fast process, gentle

conditions, potentially high binding capacities

and lower cost of the ligands employed.

PNIPAM-based nanoparticles were conjugated

with a protein L mimetic ligand and used to bind

selectively to IgG molecules.

Stimuli-responsive magnetic nanoparticles were

successfully prepared by a miniemulsion

polymerization method and used to purify a

monoclonal antibody from a CHO cell culture

supernatant, allowing a removal of more than

98% of HCP.


Rosa, P.A.J., Azevedo, A.M., Sommerfeld, S., Mut-

ter, M., Baecker, W., Aires-Barros, M.R., Biotech-

nol. J., 8 (2013) 352-362

Madeira, P.P., Bessa, A., Alvares-Ribeiro, L., Aires-

Barros, M.R., Rodrigues, A.E., Zaslavsky, B.Y., J.

Chromatogr. A, 1274 (2013).82-86

Borlido, L., Azevedo, A.M., Roque, A.C.A., Aires-

Barros, M.R., Biotechnol. Adv., 31 (2013) 1374-

1385

Silva, C.S.O., Lansalot, M., Garcia, J.Q., Taipa,

M.A., Martinho, J.M.G., Colloids Surf. B, 112 (2013)

264-271

Borlido, L., Moura, L., Azevedo, A.M., Roque,

A.C.A., Aires-Barros, M.R., Farinha, J.P.S., Biotech-

nol. J.,8 (2013) 709-717.

BioSystems Engineering

BSEL

Objectives

To link process and product throughout design, de-

velopment and biomanufacturing, systems engi-

neering approaches must be used or developed

anew. Process analytical technology (PAT) repre-

sents the combined use of different tools applicable

through many of those stages. Though PAT is still

mostly process centred, it can be used within the

QbD (quality by design) context to link process to

product. The main research topics at BSEL

(BioSystems Engineering Lab) are focused on: i)

work with new or established PAT tools, ii) whole

process/product design and analysis (cell-process-

product), iii) systems engineering applied to modern

manufacturing, and iv) pharmaceutical engineering.

Research Topics

1. Process Analytical Technology Tools – PAT in-

volves the application of process analytical chemis-

try (i.e., in-process monitoring techniques and

chemometrics), multivariate data analysis (MVDA;

e.g., data-based modelling techniques), and pro-

cess control techniques (namely, use of process

data with multivariate supervision and diagnosis

strategies). All these activities are done with the aim

of characterizing the state of a system at any given

time real-time and to be used in process optimiza-

tion and control. The perspective taken in PAT is

that of the process (not the sample or that of a sin-

gle parameter over time). In this research topic the

use of spectroscopy techniques specially suited for

industrial applications is explored in diverse con-

texts (pharma/biopharma) and within the overall

PAT context and aims.

2. Whole Process/Product Design and Analysis –

Systems biology and ‘omic’ approaches have pro-

vided a general physiological and metabolic engi-

neering understanding of several important microor-

ganisms, while bioprocess systems engineering has

benefited from the integration of monitoring, model-

ling, control and optimization. In this topic the links

within and between USP (up-stream processing:

biotransformation) and DSP (down-stream pro-

cessing: bioseparation) are explored at the three

levels of cell-process-product. Concepts such as

process and product design spaces and all aspects

related to quality-by-design are examined for phar-

ma and biopharma processing.

3. Systems Engineering Applied to Manufacturing –

While product innovation has been the key issue in

pharma and biopharma in the past, manufacturing

has remained relatively static (e.g., locked-validated

processes). Continuous improvement and opera-

tional excellence practices are entering pharma/

biopharma manufacturing and transforming these

industries as happened elsewhere decades ago. In

this research track, science and technology driven

manufacturing paradigms are the main topics exam-

ined, as the way forward to achieve operational ex-

cellence and sustainability throughout process/

product life-cycle. Adapting tools and metrics from

the disciplines of operation excellence in other in-

dustries to biomanufacturing, is the main focus on

this topic.

4. Pharmaceutical Engineering – New paradigms in

design and manufacturing of small and large thera-

peutically active (API) molecules and drug products

(formulated APIs), include continuous microreaction

technologies (MRT). It is relatively straightforward

to scale-down and operate in continuous mode

some API chemical synthesis reactions in micro-

reactors. It is still very complex or yet unfeasible to

operate in continuous mode most unit operations

involving suspended solids (e.g., crystallization),

biotransformations and some bioseparations. In

this research topic work with off-the-shelf MRTs is

being initiated to examine both feasibility and opera-

bility issues of plant miniaturization and process

intensification of small API molecules manufactur-

ing. As experience and knowledge are established

more complex types of products and unit operations

will be examined.

José Menezes (PI)


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Main Achievements

New PhD students admitted to work on new

aspects of QbD on drug-substance (API) and

formulated drug-products (2013 – 2016):

Alexandra Hertrampf, Risk Mitigation for

Pharmaceutical Raw-Materials and Prod-

ucts, Using Quality by Design Techniques.

Supervised by Prof. J.C. Menezes and

Merck-Millipore (Germany) Dr J.Schewitz.

Lúcia V. Sousa, Establishing QbD Principles

to Development and Lifecycle Managment

of Analytical Methods in Pharmaceutical

Quality Control. Supervised by Prof. J.C.

Menezes and Hovione (Portugal) Dr A. Ra-

mos.

Establishing an institutional cooperation with

Brazil’s top University (USP in Sao Paulo) to

establish a research and masters program in

Pharmaceutical Engineering at the Faculty of

Pharmacy, USP and to enable PhD and MSc

student exchange with IST (UL)

Presidential Award of Merit for Excellence in

Academia-Industry Collaborations – COTEC

2013


Hakemeyer, C., Strauss, U., Werz, S., Folque, F.,

Menezes, J.C., J. Biotechnol., 8 (2013) 835-846

Vicente J, Pinto J, Menezes JC, Gaspar F., Powder

Technol., 247 (2013) 1-7

Menezes JC, The PAT Toolbox & Skills-Set. 9th.

Kolloquium Prozessanalytik – 100 Years of PAT,

BASF-Ludwigshafen – Nov. 28-29, 2013. (Keynote

Invited Speaker)

Menezes JC. A Critical Discussion of EMA's NIR

Draft Guideline on the use of NIRS by the Pharma-

ceutical Industry. IFPAC-2013, Jan. 22-25, 2013,

Baltimore (MD), USA. (Invited Talk)

MB

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Molecular Bioengineering

Objectives

The Molecular Bioengineering Laboratory is dedi-

cated to the tailored modification of nucleic acids,

proteins and cells with the goal of creating useful

products and designing more efficient processes for

the industrial and health biotechnology areas. This

activity involves the convergence of research areas

such as molecular biology, microbiology, biochemis-

try and immunology. Three major research pro-

grams are pursued: i) plasmid vectors, ii) bio-

recognition and bio-interfacing and iii) microbial cell

factories. In the case of plasmid vectors, the goal is

to address the scientific/technological challenges

associated with the emergence of plasmid biophar-

maceuticals. In the bio-recognition and bio-

interfacing topic, the goal is to develop (bio)

molecular constructs to anchor biomolecules to sur-

faces, nano/microstructured biomimetic surfaces for

controlled cell adhesion, adsorption materials for

biomolecule purification and platforms for the ma-

nipulation/detection of DNA, proteins and cells at

the micro-scale. The goal of the microbial cell facto-

ries topic is to engineer microbial cells to improve

the production of specific biomolecules.

Research Topics

The following research topics are pursued within

each research line:

i) Plasmid vectors

1. Plasmid design for improved stability, delivery

and manufacturing. Vectors are designed to im-

prove the manufacturing of plasmids and minicircles

used for DNA vaccination, gene therapy and protein

production by transient transfection. Marine organ-

isms are screened for drugs that inhibit nucleases,

stabilise plasmids and increase transfection activity.

Delivery systems (electroporation, liposomes, car-

bon tubes, polymeric microparticles) are developed

to increase DNA uptake and transcription levels.

2. DNA vaccines and gene therapy. DNA vaccine

candidates are constructed by cloning antigenic

proteins associated with sleeping sickness/avian flu

and tested in animal models for their ability to gen-

erate cellular and humoral responses, and to pro-

vide immunisation. The possibility of using plasmids

to deliver the cytotoxic bacterial protein azurin to

cancer cell models is under evaluation

(collaboration with BSRG).

ii) Bio-recognition and bio-interfacing

1. Biomimetic ligands and surfaces. Synthetic pro-

tein-mimic affinity ligands are designed, synthe-

sized, screened and used to anchor, stabilise and

purify proteins, oligonucleotides and plasmid DNA.

Natural surface structures are transferred onto tech-

nical materials using replica moulding techniques

and characterized in terms of their nano/

microstructure, hydrophobicity, self-cleaning proper-

ties and ability to prevent/promote cell adhesion.

2. Adsorption materials. Chromatographic mem-

branes and supports are modified with specific lig-

ands to improve the purification of biomolecules

(plasmids, antibodies). Covalent immobilization of

biomolecules and assembling of molecular probes

on AFM cantilevers is pursued to characterize bind-

ing interactions with these adsorptive materials.

3. CBM-based fusions for bioactive paper applica-

tions. Carbohydrate Binding Modules (CBMs) are

screened, characterized, fused with specific pro-

teins (e.g. ZZ fragments, enzymes), produced and

used to functionalize cellulosic materials with the

goal of developing sensors for molecular diagnos-

tics, enzyme-based analytical test strips and spe-

cialised filters.

4. Platforms for the handling of DNA, proteins and

cells at the micron scale. Thin film technologies,

chemical modification, microfluidics, photodetectors

and photoreflectors are used to develop microchip

platforms for the colorimetric, chemiluminescent

and fluorescent detection of biorecognition events

like DNA hybridization, antigen-antibody interac-

tions, metabolic cell activity and receptor (GPCR)

binding.

iii) Microbial cell factories

1. Engineering of E. coli and Lactic Acid Bacteria

(LAB) strains. E. coli and LAB strains are engi-

neered to produce high amounts of biomolecules

Duarte Miguel Prazeres (PI), Gabriel Monteiro, Marília Mateus, José Santos, M. Ângela Taipa


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(plasmid DNA, curcumin (LAB strains) and pro-

teins) by mutating key genes on the glycolytic path-

way. The impact of the new strains on the down-

stream processing and overall quality and biological

activity of biomolecules is studied.

Main Achievements

A new pDNA production strain (GALG20) was

created by knocking out the pgi gene in E. coli,

which produces 25-fold more pDNA than the

parental strain.

The impact of quality attributes (impurity con-

tent, plasmid charge) of pDNA isolated with dif-

ferent purification methods on the characteris-

tics of lipoplexes prepared thereof (size, zeta

potential, stability) and on their ability to trans-

fect mammalian cells was demonstrated.

A hydrophobic interaction membrane chroma-

tography step which relies on phenyl membrane

adsorbers and a stepwise elution strategy was

integrated in a pDNA production process.

Protein stabilization was achieved by a novel

approach based on the adsorption and estab-

lishment of affinity-like interactions with a biomi-

metic triazine-scaffolded ligand.

An integrated analytical system that conjugates

an indirect competitive enzyme-linked immuno-

sorbent assay strategy developed in PDMS mi-

crofluidics with integrated microfabricated hy-

drogenated amorphous silicon was successfully

used for the determination of ochratoxin A.

Microfluidic channels with patterned electrodes

were developed to trap E. coli cells by dielectro-

phoresis in stagnant and in-flow fluidic situa-

tions.

A highthroughput methodology was developed

to characterize the binding of carbohydrate

binding module (CBM) to cellulose supports.


Gonçalves, G.A.L., Prazeres, D.M.F., Monteiro,

G.A., Prather, K.L.J., App. Microbiol. Biotechnol.,

97 (2013) 611-620

De la Vega, J., Braak, B., Monteiro, G.A., Azzoni,

A.R., Prazeres, D.M.F., J. Pharm. Sci. 102 (2013)

3932-3941

Raiado, L.P., Prazeres, D.M.F., Mateus, M., J.

Chromatogr. A, 1315 (2013) 145-151

Sousa, I.T., Lourenço, N.M.T., Afonso, C.A.M., Tai-

pa, M.A., J. Mol. Recognit., 26 (2013) 104-112

Novo, P., Moulas, G., Prazeres, D.M.F., Chu, V.,

Conde, J.P., Sensors Act. B: Chemical 176 (2013)

232-240

Donato, S.S., Chu, V., Prazeres, D.M.F., Conde,

J.P., Electrophoresis 34 (2013) 575-582.

SCB

L

Stem Cell Bioengineering and

Regenerative Medicine Laboratory

Objectives

The Stem Cell Bioengineering and Regenerative

Medicine Laboratory aims at developing controlled

bioreactor systems for the ex-vivo expansion of

stem cells and their controlled differentiation into

specific cell types, as well as their integration with

advanced bioseparation in order to purify Stem

Cells/progenitors and their derivatives targeting

their application in Regenerative Medicine settings

and toxicology/pharmacological testing. As stem

cells (SC) are rare, their isolation and expansion/

differentiation in vitro significantly increases the

cell population available for Cellular and Gene

Therapy, Tissue Engineering, high-throughput drug

screening and pharmacological toxicity testing and

stem cell research. Human hematopoietic stem/

progenitor cells (HSC), human mesenchymal stem/

stromal cells (MSC), as well as human and mouse

pluripotent stem cells (both embryonic (ESC) and

induced pluripotent stem cells (iPSC)) and neural

stem cells (NSC) are used as model systems. Four

main research topics are being pursued:

Research Topics

1. Clinical Manufacturing of SC-based Therapies

Our focus is the manufacturing of clinical-grade

Stem/Progenitor Cells (S/PC) to be used as

ATMPs for first-in-human studies in collaboration

with our clinical partners, specifically human Mes-

enchymal Stem Cells (MSC) for Acute Myocardial

Infarction treatment and Umbilical Cord Blood

Hematopoietic Stem/Progenitor Cells expanded in

co-culture with MSC to be infused in hemato-

oncological patients. The main goal is to optimize

our previously microcarrier-based platform for

MSC cultivation and its GMP implementation. A

systematic analysis of S/PC is being pursued

through culture parameters (shear, oxygen) control

and their impact on cell product potency

(immunomodulation, trophic activity, differentiation

ability). Specifically we aim to set-up a quality con-

trol platform by identifying reliable potency bi-

omarkers to assure safe and clinically effective

expanded cells. We propose to generate pre-

clinical data for the development of both ATMPs

and dosages to be tested will be determined based

on potency levels, according to EMA/INFARMED.

2. Multi-Scale Strategies for Human Pluripotent

Stem Cell Bioprocessing

The main objective is to develop Integrated Biopro-

cesses to overcome the main technological barri-

ers that presently limits the application of human

Pluripotent Stem Cells (PSC), embryonic (ESC)

and induced PSC (iPSC), and their derivatives.

Large-scale production of PSC-derived neural pre-

cursors and cardiomyocytes has been addressed

to leverage the emergence of alternative therapies

and screening tools for neurodegenerative and

cardiovascular diseases. Bioreactors will be used

to integrate PSC expansion and differentiation

based on tightly-controlled microenvironments us-

ing tailor-made niche-inspired microcarriers. Micro-

environments will be designed based on HTS stud-

ies on the effect of niche parameters. Modelling

will be used to uncover complex interactions be-

tween different niche components and systems

biology approaches will be applied for better un-

derstanding of pluripotency at the molecular level.

Affinity-based separation methods will be integrat-

ed with bioreactors for purification of PSC deriva-

tives, including the depletion of tumorigenic PSC.

In particular, monolithic matrices functionalized

with cost-effective and highly-selective ligands

(e.g. aptamers) will be used.

3. Ex-vivo Gene Therapy for Regenerative Medi-

cine Applications

Novel gene carriers (minicircles) will be tested into

SC/progenitors to prolong gene expression and

Joaquim Cabral (PI), Cláudia Lobato da Silva, Margarida Diogo, Frederico Ferreira, T. Catarina Madeira


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augment cell survival while guaranteeing extremely

low probability of genome integration. The main

focus is the development of Gene Activated Matri-

ces, composed by hydrogels embedding minicir-

cles, encoding genes involved in specific differenti-

ation fates. With this approach, these genes are

released in a sustained mode into SC/progenitors

and expressed at low levels assuring the formation

of native-like tissue and/or able to promote endog-

enous repair in vivo. By using human MSC our

main goal is to promote cartilage regeneration and

angiogenesis in ischemic heart for cardiac regen-

eration.

4. Tailoring biomaterials to support stem cell culti-

vation

The aim is to mimic the natural features of extra-

cellular matrix to promote cell-cell and cell-material

interactions and cellular adhesion, as well as to

add artificial functions facilitating cell processing.

The envisaged KET include i) Electrospun aligned

nanofiber scaffolds and scalable plate&frame bio-

reactors, to direct cell organization and function

targeting neural or cardiac regeneration ii) Encap-

sulation/hydrogel-based systems that will be tai-

lored for chondrogenesis, iii) Microcarriers for SC/

progenitors cultivation, and iv) stimulus-responsive

materials (e.g. glucose, temperature) facilitating

cell harvesting or controlled delivery of small mole-

cules and bio-macromolecules (genes and pro-

teins).

Main Achievements

Towards the definition of the pros and cons of

an allogeneic versus autologous MSC-based

therapy for acute myocardial infarction (AMI),

we performed a comparative study of the

proliferative, differentiative, immunomodulato-

ry and trophic potential of bone marrow (BM)-

derived MSC obtained from healthy donors

and AMI patients in collaboration with Depart-

ment of Cardiology, Hospital Santa Marta

(HSM), Lisboa. Also together with HSM, and

Faculdade de Medicina Veterinária, we suc-

cessfully implemented a pre-clinical in vivo

model for AMI – the swine. This model al-

lowed us to generate first pre-clinical data on

the safety of the intra-coronary (IC) admin-

istration of BM MSC, demonstrating definitive

evidence of microcirculatory disruption upon

IC MSC infusion in a large animal model

closely resembling human cardiac physiology,

function, and anatomy.

The scalable xeno-free microcarrier-based

reactor system previously established at

SCBL-RM for the production of MSC from

different human sources was successfully

optimized with the final aim of increasing

overall cell productivity. Initial cell adhesion to

the beads was maximized by establishing an

optimized protocol of cell seeding under inter-

mittent agitation and by using ready-to-use

xeno-free plastic microcarriers without the

need of a pre-coating step.

In collaboration with the Department of Urolo-

gy - Hospital Garcia de Orta and Wake Forest

Institute for Regenerative Medicine (WFIRM),

we successfully established a method for the

effective decellularization of animal urethra/

rhabdosphincter tissue towards the establish-

ment of a suitable scaffold as a basis of a

urological tissue engineering strategy specifi-

cally targeting the screening and development

of novel potential drugs and therapies for

Stress Urinary Incontinence.

A robust culture platform was established for

the expansion, neural commitment and neu-

ronal differentiation of hiPSC using serum-

free chemically-defined media and a xeno-

free culture substrate. Importantly, this culture

platform was successfully integrated with the

affinity-based purification of hiPSC-derived

neural precursors paving the way towards the

development of an integrated bioprocess for

the large-scale production and purification of

hiPSC-derived neurons that may be potential-

ly used for drug screening and disease mod-

elling and ultimately for Regenerative Medi-

cine applications. This culture platform is

presently being used for the robust production

of mature patient-specific neuronal cells from

hiPSC for disease modelling of Rett Syn-

drome, in collaboration with IMM.

In parallel, a robust culture platform has also

been established and optimized for differenti-

ation of model hiPSC lines into cardiomyo-

cytes under static conditions, using an adher-

ent monolayer culture system, and based on

the use of small molecules and a chemically-

defined culture medium.

The scalable microcarrier-based culture plat-

form previously developed for expansion of

hiPSC in spinner flasks has been adapted to

the new generation xeno-free E8 culture me-

dium and using xeno-free microcarriers.

A 3D microarray platform has been developed

in collaboration with Professor Jonathan

Dordick, at the Rensselaer Polytechnic Insti-

tute (RPI/USA), to perform high-throughput

studies of human Neural Stem Cell (hNSC)

Differentiation and Toxicology. By using this

platform it was possible to screen for the dif-

ferential toxicity of small molecules to hNSCs

which may help to predict, in vitro, which com-

pounds pose an increased threat to neural

development and should therefore be priori-

tized for further screening and evaluation.

Neural stem cells were successfully transfect-

ed with minicircles showing higher expression

of the gene of interest and higher cell viabili-

ties when compared with cells transfected

with the respective plasmid DNA.

Assessment of the effect of different layer-by-

layer extruded scaffolds configurations in cell

behaviour on human BM MSC expansion and

differentiation towards chondrocytes, showing

an higher impact in higher chondrocyte popu-

lation is obtained when expansion takes place

under hypoxia (5% O2) and that cell distribu-

tion and dimension of chondrocyte aggre-

gates depend strongly on fiber alignment

(work performed in collaboration with CDRsp,

Polytechnic Institute of Leiria, Portugal).


Fernandes, T.G., Diogo, M.M., and Cabral, J.M.S.,

"Stem Cell Bioprocessing: For Cellular Therapy,

Diagnostics and Drug Development", Woodhead

Publishing Series in Biomedicine No. 40, Wood-

head Publishing, Cambridge (ISBN: 978-1-907568-

88-6)


Madeira, C., Rodrigues, C.A.V., Reis, M.S.C., Fer-

reira, F.F.C.G., Correia, R.E. S. M., Diogo, M.M.,

Cabral, J.M.S., Biomacromolecules, 14 (2013)

1379-1387

Oliveira, P.H., Boura, J.S., Abecasis, M.M., Gim-

ble, J.M., da Silva, C.L., Cabral, J.M.S., Stem Cell

Res., 9 (2013) 225-236

dos Santos, F., Andrade, P.Z., da Silva, C.L., Ca-

bral, J.M.S., Biotechnol. J.,8 (2013) 644-654

Simões, I.N., Boura, J.S., dos Santos, F., Andrade,

P.Z., Cardoso, C.M.P., Gimble, J.M., da Silva,

C.L., Cabral, J.M.S., Biotechnol. J., 8 (2013) 448-

58.

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Research Team


Full Professors

Associate Professors

Assistant Professors

Research Scientists

Joaquim M.S. Cabral Ph.D. Instituto Superior Técnico, 1982 Full Professor Phone: +351-218419063 e-mail: [email protected]

Research Areas and Interests

Stem Cells Research for Tissue Engineering and Regenerative Medicine; Stem Cell Bioprocessing and

Manufacturing: development of novel stem cell bioreactors and advanced bioseparation and purification

processes.

Recent Selected Publications

T.G. Fernandes, M.M. Diogo and J.M.S. Cabral, “Stem Cell Bioprocessing: For cellular therapy, diagnos-

tics and drug development”, Woodhead Publishing Series in Biomedicine No. 40, UK, pp. 250 (2013)

C.A.V. Rodrigues, T.G. Fernandes, M.M., Diogo, C.L. da Silva, J.M.S. Cabral “Bioreactors for Stem Cell

Expansion and Differentiation”, in Stem Cell Engineering: Principles and Practices, Schaffer, D., Bronzino,

J.D., Peterson, D.R (eds), CRC Press, 10.1-10.28 (2013)

F.F. dos Santos, P.Z. Andrade, C.L. da Silva, J.M.S. Cabral, JMS “Bioreactor design for clinical-grade ex-

pansion of stem cells” Biotechnol. J. 8 (6) 644-654 (2013)

I.N. Simoes, J.S. Boura, F.F. dos Santos, C.L. da Silva, J.M.S. Cabral, “Human mesenchymal stem cells

from the umbilical cord matrix: Successful isolation and ex vivo expansion using serum-/xeno-free culture

media” Biotechnol. J. 8 (4) 448-458 (2013)

C. Madeira, C.A.V. Rodrigues, M.S.C. Reis, F.C.G. Ferreira, R.E.S.M. Correia, M.M. Diogo, J.M.S. Cabral

"Non-viral gene delivery to neural stem cells with minicircles by microporation", Biomacromolecules 14 (5)

1379-1387 (2013)

F. Gracio, J.M.S. Cabral, B. Tidor “Modeling Stem Cell Induction Processes” PLoS One 8 (5), DOI:

10.1371/journal.pone.0060240, ISSN: 1932-6203 (2013)



Responsible for the Bioprocess Engineering Laboratory (BEL) of the Bioengineering Research Group

(BERG) of Centre for Biological and Chemical Engineering, leader research unit of the Associate Labora-

tory Institute for Biotechnology and Bioengineering (IBB). Current research interests include bioseparation

of antibodies and cells through aqueous two-phase systems, magnetic nano-particles and chromatog-

raphy, and application of lab-on-a-chip microfluidic devices to biopharmaceuticals separation and process

integration, and biomolecules concentration.


Rosa, P.A.J., Azevedo, A.M., Sommerfeld, S., Mutter, M., Baecker, W., Aires-Barros, M.R., “Continuous

purification of antibodies from cell culture supernatant with aqueous two-phase systems: From concept to

process”, Biotechnol. J., 8(3), 352-362 (2013)

Borlido, L., Moura, L., Azevedo, A.M., Roque, A.C.A., Aires-Barros, M.R., Farinha, J.P.S., “Stimuli-

Responsive magnetic nanoparticles for monoclonal antibody purification”, Biotechnol. J., 8(6), 709-717

(2013)

Borlido, L., Azevedo, A.M., Roque, A.C.A., Aires-Barros, M.R., “Magnetic separations in biotechnology”,

Biotechnol. Adv., 31(8), 1374-1385 (2013)

Dsouza, R.N., Azevedo, A.M., Aires-Barros, M.R., Krajnc, N.L., Kramberger, P., Carbajal, M.L., Grasselli,

M., Meyer, R., Fernández-Lahore, M., “Emerging Technologies for the Integration and the Intensification of

Bioprocesses”, Pharm. Bioprocess., 1, 423-440 (2013)

Madeira, P.P., Bessa, A., Alvares-Ribeiro, L., Aires-Barros, M.R., Rodrigues, A.E., Zaslavsky, B.Y.,

“Analysis of amino acid-water interactions by partitioning in aqueous two-phase systems. I-Amino acids

with non-polar side-chains”, J. Chromatogr. A, 1274, 82-86 (2013)

Raquel Aires-Barros

Ph.D. Instituto Superior Técnico, 1990 Full Professor

Phone: +351-218419134 e-mail: [email protected]

Miguel Prazeres Ph.D. Instituto Superior Técnico, 1993 Associate Professor with Habilitation Phone: +351-218419133 e-mail: [email protected]


Responsible for the Molecular Bioengineering Lab of the Bioengineering Research Group at IBB-Institute

for Biotechnology and Bioengineering. Current research interests include nucleic acid engineering

(development of plasmid biopharmaceuticals and diagnostics), nanobiotechnology (lab-on-a-chip microflu-

idic devices with integrated biosensors using cells, proteins, and nucleic acids), bioactive paper applica-

tions and biomimetic surfaces, ligands and materials.


P. Novo, G. Moulas, D.M.F. Prazeres, V. Chu, J. P. Conde, “Detection of ochratoxin A in wine and beer

by chemiluminescence-based ELISA in microfluidics with integrated photodiodes”, Sens. Actuators B 176,

232-240 (2013)

S.S. Donato, V. Chu, D.M.F. Prazeres, J.P. Conde, “Metabolic viability of E.coli trapped by dielectrophore-

sis in microfluidics”, Electrophoresis 34, 575-582 (2013)

D.C. Martins, V. Chu, D.M.F. Prazeres, J.P. Conde, “Streaming currents in microfluidics with integrated

polarizable electrodes”, Microfluid. Nanofluid. 15, 361-376 (2013)

G.A.L. Gonçalves, D.M.F. Prazeres, G.A. Monteiro, K.L.J. Prather, “De novo creation of MG1655-derived

Escherichia coli strains specifically designed for plasmid DNA production”, App. Microbiol. Biotechnol. 97

611-620 (2013)

J. De la Vega, B. Braak, G.A. Monteiro, A.R. Azzoni, D.M.F. Prazeres, “Impact of plasmid quality on lipo-

plex-mediated transfection”, J. Pharm. Sci. 102, 3932-3941 (2013)

L.P. Raiado, D.M.F. Prazeres, M. Mateus, “Impact of plasmid size on the purification of model plasmid

DNA vaccines by phenyl membrane adsorbers”, J. Chromatog. A, 1315, 145-151 (2013)

S.A. Martins, G. Moulas, J.R. Trabuco, G.A. Monteiro, V. Chu, J.P. Conde, D.M.F. Prazeres, “Monitoring

intracellular calcium in response to GPCR activation using thin-film silicon photodiodes with integrated

fluorescence filters”, Biosens. Bioelectron. 52, 232-238 (2014)



Research Scientist at the BioEngineering Research Group (BERG), based in the Institute for Biotechnolo-

gy and Bioengineering (IBB), Centre for Biological and Chemical Engineering at I.S.T. His research areas

focus on the development of bioanalytical methods and biosensors integrated in FIA systems and lab-on-a

-chip devices for monitoring pathogens, toxic pollutants, and biological compounds. The development of

nano/micro-biocatalysts (biocomposites) mostly based on hydrogels containing protein/cell assemblies

and encapsulating nano-magnetic particles resulting as biocomposites used as nano/micro-biocatalysts is

another field of research.


F.R.R. Teles, L.P. Fonseca, “The contribution of smart materials and clinical diagnostic micro-devices on

the progress and improvement of human health care” in “Advanced Healthcare Nanomaterials” Editor

Ashutosh Tiwari, WILEY-Scrivener Publishing LLC, USA., 2014, chapter 6, in press

A.P.D. de Lima, E.M. Aschenbrenner, S.N. Oliveira, J.B. Doucet, C.K. Weiss, U. Ziener, L.P. Fonseca,

N.M.P.S. Ricardo, L.L. de Freitas, C.L. Petzhold, K. Landfester “Towards regioselective enzymatic hydrol-

ysis and glycerolysis of tricaprylin in miniemulsion and the direct preparation of polyurethane from the hy-

drolysis products”, J. Mol. Catal. B: Enzym, 98, 127–137 (2013)

F.R.R. Teles, M.L. Martins, M. R. Vieira, Nanotechnology for the diagnosis of parasitic infections” in Nano-

technology in Dermatology, Eds Adman nasir, Adam Firelman and Steven Wang, Springer 2013, chapter

20, pp 209-219

S.A.M. Martins, V.C. Martins, F.P. Cardoso, P.P. Freitas, L.P. Fonseca “Waterborne Pathogen Detection

Using a Magnetoresistive Immuno-Chip” Ed. S. M. Tiquia-Arashiro in Molecular Biological Technologies

for Ocean Sensing, Springer Protocols Handbooks 2012, chapter 13, pp 263-288

Luis P. Fonseca

Ph.D. Instituto Superior Técnico, 1995 Associate Professor with Habilitation



Dr. Menezes is Professor at IST (Technical University of Lisbon, Habilitation in 2005) and a Senior Re-

searcher at the Institute for Biotechnology and Bioengineering (IBB, TUL). His work deals with the devel-

opment and use of several systems engineering tools in diverse processing industries with a stronger fo-

cus in the bio/pharmaceutical areas, namely Process Analytical Technologies (PAT), Industrial Chemo-

metrics (IC), Multivariate Data Analysis (MVDA), Multivariate Statistics Process Control (MSPC) and Quali-

ty by Design (QbD). Main research areas are: Process Analytical Technology; Whole Process/Product

Design; Systems Engineering Applied to Manufacturing; and Pharmaceutical Engineering.


Patent WO 2012/059520 A1 “Spectroscopic finger-printing of raw-materials”, Hoffmann-La Roche AG

(Pub. May 10, 2012). Hakemeyer C, Strauss U, Werz S, Jose GE, Folque F, Menezes JC

Alcalà, M., Blanco, M., Menezes, J. C., Felizardo, P. M., Garrido, A., Pérez, D., Zamora, E., Pasquini, C.

and Romañach, R. J. (2012). Near-Infrared Spectroscopy in Laboratory and Process Analysis. Encyclope-

dia of Analytical Chemistry. (Review, 46 pgs), Wiley DOI:10.1002/9780470027318.a9361

Hakemeyer C, Strauss U, Werz S, Jose GE, Folque F, Menezes JC, “At-line NIR Spectroscopy as Effec-

tive PAT Monitoring Technique in Mab Cultivations During Process Development and Manufacturing”, Ta-

lanta 90, 12–21 (2012)

Lourenco V, Lochmann D, Reich G, Menezes JC, Herdling T, Schewitz J (2012), A Quality by Design

study applied to an industrial pharmaceutical fluid bed granulation. Eur. J. Pharm. Biopharm. 81(2), 438–

447.

Möltgen CV, Puchert T, Menezes JC, Lochmann D, Reich G (2012), A novel in-line NIR spectroscopy ap-

plication for the monitoring of tablet film coating in an industrial scale process. Talanta 92, 26-37.

Preisner OE, Menezes JC, Guiomar R, Machado J, Lopes JA (2012), Discrimination of Salmonella enter-

ica serotypes by Fourier transform infrared spectroscopy. Food Res. Int. 45(2),1058-1064.

José Menezes Ph.D. Instituto Superior Técnico, 1996 Assistant Professor with Habilitation Phone: +351-218417347 e-mail: [email protected]


Claudia Lobato da Silva

Ph.D. Instituto Superior Técnico, 2006 Assistant Professor



Current research interests are focused on the ex-vivo expansion of human stem cells, Cellular Therapies

with human adult stem cells, isolation and purification of stem cells, and bioreactors for stem cell culture.

In particular, I have been focused on establishing optimal conditions for the maximization of the expansion

of umbilical cord blood-derived hematopoietic stem/progenitor cells, as well as developing bioreactor strat-

egies for the clinical-scale production of mesenchymal stem/stromal cells from different human sources.


Ribeiro, A., Laranjeira, P., Mendes, S., Velada, I., Leite, C., Andrade, .P, Santos, F., Henriques, A., Grãos,

M., Cardoso, C.M., Martinho,A., Pais, M., da Silva, C., Cabral, J., Trindade, H., Paiva, A., “Mesenchymal

stem cells from umbilical cord matrix, adipose tissue and bone marrow exhibit different capability to sup-

press peripheral blood B, natural killer and T cells”, Stem Cell Res Ther 15;4(5):125 (2013)

dos Santos, F., Andrade, P.Z., da Silva, C.L., Cabral, J.M.S., “Bioreactor design for clinical-grade expan-

sion of stem cells”, Biotechnol. J., 8(6), 644-654 (2013)

Andrade, P.Z., de Soure, A.M., dos Santos, F., Paiva, A., Cabral J.M.S., da Silva, C.L., “Ex vivo expansion

of cord blood haematopoietic stem/progenitor cells under physiological oxygen tensions: clear-cut effects

on cell proliferation, differentiation and metabolism” J. Tissue Eng. Regen. Med. DOI: 10.1002/term.1731

(2013)

Andrade, P.Z., dos Santos, F., Cabral, J.M.S., da Silva, C.L., “Stem cell bioengineering strategies to widen

the therapeutic applications of haematopoietic stem/progenitor cells from umbilical cord blood”, J. Tissue

Eng. Regen. Med. DOI: 10.1002/term.1741 (2013)

Boura, J.S., dos Santos, F., Gimble, J.M., Cardoso, C.M., Madeira, C., Cabral, J.M., da Silva, C.L., “Direct

head-to-head comparison of cationic liposome-mediated gene delivery to mesenchymal stem/stromal cells

of different human sources: a comprehensive study”, Hum. Gene Ther. Methods, 24(1), 38-48 (2013)

Simões, I.N., Boura, J.S., dos Santos, F., Andrade, P.Z., Cardoso, C.M.P., Gimble, J.M., da Silva, C.L.,

Cabral, J.M.S., “Human mesenchymal stem cells from the umbilical cord matrix: Successful isolation and

ex vivo expansion using serum-/xeno-free culture media”, Biotechnol. J., 8(4):448-58 (2013)

Gabriel Monteiro Ph.D. Instituto Superior Técnico, 1998 Assistant Professor Phone: +351-218419195 e-mail: [email protected]


Manufacturing of plasmid- and minicircle-biopharmaceuticals by designing more efficiently expression vec-

tors for its in vivo administration and by engineering of bacterial host strains to improve vectors production.


J. de la Vega, B. ter Braak, A.R. Azzoni, G.A. Monteiro, D.M.F. Prazeres, “Impact of plasmid quality on

lipoplex-mediated transfection”, J. Pharm. Sci. 102, 3932-3941 (2013)

G.A.L. Gonçalves, D.M.F. Prazeres, G.A. Monteiro, K.L.J. Prather, “De novo creation of MG1655-derived

E. coli strains specifically designed for plasmid DNA production”, Appl. Microbiol. Biotechnol. 97, 611-620

(2013)

S.A.M. Martins, G. Moulas, J.R.C. Trabuco, G.A. Monteiro, V. Chu, J.P. Conde, D.M.F. Prazeres,

“Monitoring intracellular calcium in response to GPCR activation using thin-film silicon photodiodes with

integrated fluorescence filters”, Biosens. Bioelectron. 52, 232-238 (2013)

P.H. Oliveira, D.M.F. Prazeres, G.A. Monteiro, “DNA instability in bacterial genomes: causes and conse-

quences”, in Genome Analysis: Current Procedures and Applications, ISBN: 978-1-908230-29-4; M.S.

Poptsova (ed.) Caister Academic Press, UK, pp 263-285 (2014)


José L. Santos




My current research is focused on plasmid DNA (pDNA) manufacturing processes (production, separation, purification, quality control and monitoring) for application in gene therapy or DNA vaccination. The utiliza-tion of membrane processes (ultra and microfiltration) and the development of alternative methods (sonication and microfluidization) to alkaline lysis for plasmid release are under research. The develop-ment of alternative microbial GRAS (generally recognized as safe) platforms for pDNA production will be other goal of my research.


D.M.F. Prazeres, J.A.L. Santos, “Production and Purification of Adenovirus Vectors for Gene Therapy”, Handbook of Pharmaceutical Biotechnology, 1261-1295 (2010)

S. Freitas, S. Canário, J.A.L. Santos, D.M.F. Prazeres, “Alternatives for the intermediate recovery of plas-mid DNA: performance, economic viability and environmental impact”, Biotechnology journal 4 (2), 265-278 (2009)

M.L. Wu, S.S. Freitas, G.A. Monteiro, D.M.F. Prazeres, J.A.L. Santos, “Stabilization of naked and con-densed plasmid DNA against degradation induced by ultrasounds and high‐shear vortices”, Biotechnology and applied biochemistry 53 (4), 237-246 (2009)

S.S. Freitas, J.A.L. Santos, D.M.F. Prazeres, “Plasmid purification by hydrophobic interaction chromatog-raphy using sodium citrate in the mobile phase”, Separation and Purification Technology 65 (1), 95-104 (2009)

M. Ângela Taipa Ph.D. Instituto Superior Técnico, 1997 Assistant Professor Phone: +351-218419065 e-mail: [email protected]


Biomolecular Engineering: Biomimetics; combinatorial approaches; molecular recognition; synthetic mimic

affinity ligands for identification, separation and stabilization of biomolecules (antibodies, enzymes, plas-

mid DNA)

Nanobiotechnology: Bio-inspired affinity nanoparticles for immunorecognition


A.C.A. Roque, C.S.O. Silva, M.A. Taipa, “Affinity-based methodologies and ligands for antibody purifica-

tion: Advances and perspectives”, J. Chromatogr. A 1160, 44-55 (2007)

I.T. Sousa, L. Ruiu, C.R. Lowe, M.A. Taipa, “Synthetic affinity ligands as a novel tool to improve protein

stability“, J. Mol. Recognit. 22, 83-90 (2009)

I.T. Sousa, N.M.T Lourenço , C.A.M. Afonso, M.A. Taipa, “Protein Stabilization with a triazine- scaffolded

dipeptide-mimic synthetic affinity ligand”, J. Mol. Recognit. 26,104-112 (2013)

C.S.O. Silva, M. Lansalot, J.Q. Garcia, M.A. Taipa, J.G. Martinho, “Synthesis and characterization of bio-

mimetic nanogels for immunorecognition”, Coll. Surf. B: Biointerfaces 112, 264-271 (2013)

M.A. Taipa, “Immunological Assays: Biotools for High Throughput Screening and Characterisation of Com-

binatorial Libraries”, in: Advances in Combinatorial Chemistry & High Throughput Screening; Chaguturu,

R. (Ed.); Bentham Science Publishers e-book Series, Vol.1, pp. 130-158 (2013)

M.A. Taipa, “Affinity Separation | Rational Design, Synthesis, and Evaluation: Affinity Ligands”, in: Elsevier

Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, Reedijk, J. (Ed), Elsevier,

Waltham (MA): 26-Feb-2014 doi:10.1016/B978-0-12-409547-2.10738-3


M. Margarida Diogo




Current research interests include bioprocessing strategies for expansion and controlled differentiation of pluripotent and neural stem cells and purification of their derivatives envisaging applications in Regenera-tive Medicine and drug discovery and their integration with microscale culture systems to explore the effect of microenvironmental factors on stem cell fate.


T.G. Fernandes, M.M. Diogo, J.M.S. Cabral, "Stem Cell Bioprocessing: For Cellular Therapy, Diagnostics

and Drug Development", Woodhead Publishing Series in Biomedicine No. 40, UK, pp. 250 (2013)

M.M. Diogo, C. Lobato da Silva, J.M.S. Cabral, “Separation technologies for stem cell bioprocessing”, in Cell Engineering, Volume 8: Stem Cells and Cell Therapy (Mohamed Al-Rubeai and Mariam Naciri, Edi-tors), Springer, [publication date: October 2013]

C.A.V. Rodrigues, T.G. Fernandes, M.M. Diogo, C. Lobato da Silva, J.M.S. Cabral, Bioreactors for Stem Cell Expansion and Differentiation, in Stem Cell Engineering: Principles and Practices (Schaffer D, Bronzi-no JD and Peterson DR, Editors), CRC Press (2013), pp 10.1-10.28

C. Madeira, C.A. Rodrigues, M.S. Reis, F.F. Ferreira, R.E. Correia, M.M. Diogo, J.M.S. Cabral, “Nonviral gene delivery to neural stem cells with minicircles by microporation”, Biomacromolecules, 14(5):1379-87 (2013)

G.N.M. Rodrigues, A.F.S. Matos, T.G. Fernandes, C.A.V. Rodrigues, M. Peitz, S. Haupt, M.M. Diogo, O. Brüstle, J.M.S. Cabral, “Integrated Platform for Production and Purification of Human Pluripotent Stem Cell-derived Neural Precursors”, Stem Cell Rev. Rep., in press, D.O.I. 10.1007/s12015-013-9482-z.

T.G. Fernandes, C.A.V. Rodrigues, M.M. Diogo, J.M.S. Cabral, “Stem cell bioprocessing for Regenerative Medicine”, J. Chem. Technol. Biotechnol., in press, DOI: 10.1002/jctb.4189

A. Fernandes-Platzgummer, M.M. Diogo, C. Lobato da Silva, J.M.S. Cabral, “Maximizing mouse embryon-ic stem cell production in a stirred tank reactor by controlling dissolved oxygen concentration and continu-ous perfusion operation”, Biochem. Eng. J. 82, 81-90 (2014)

Marilia Mateus Ph.D. Instituto Superior Técnico, 1994 Assistant Professor Phone: +351-218419136 e-mail: [email protected]


Focus on the application of synthetic membranes to bioengineering fields, entailing membrane processing

(membrane crossflow filtration and membrane chromatography), modification of the surface of membranes

(for biocompatibility and selective adsorption capacity), and membrane bioreactors. Recent research pro-

jects address the development of membrane adsorbers and membrane chromatography for the purifica-

tion of protein and plasmid biopharmaceuticals and the characterization of nanoparticles designed for de-

livery of plasmids.


L. Raiado-Pereira, D.M.F. Prazeres, M. Mateus, “Impact of plasmid size on the purification of model plas-

mid DNA vaccines by phenyl membrane adsorbers”, J. Chromatogr. A 1315, 145-15 (2013).

M.E. Monteiro, L. Raiado-Pereira, D.M.F. Prazeres, M. Mateus, “FRAP biophysical tool to probe nucleic

acids membrane ligand interactions in pDNA purification”, 9th European Biophysics Congress |

EBSA2013, Lisbon, Portugal, 13-17 July (2013).

L. Raiado-Pereira, J. de la Vega, D.M.F. Prazeres, M. Mateus, “Impact of plasmid size on the purification

of model pDNA vaccines by HIC on phenyl membrane adsorbers”, oral communication to the International

Symposium on the Separation of Proteins, Peptides and Polynucleotides | ISPPP 2013, Boston, USA, 17-

19 July (2013).

L. Raiado-Pereira, J. de la Vega, D.M.F. Prazeres, M. Mateus, “Purification of pharmaceutical grade plas-

mid DNA by HIC membrane chromatography – Impact of plasmid size and process throughput”, oral com-

munication to the Portuguese Congress of Microbiology and Biotechnology| Microbiotec’2013, Aveiro, Por-

tugal, 6-8 December (2013).


Carla C.C.R. Carvalho

Ph.D. Instituto Superior Técnico, 2003 Principal Research Scientist



Formation of persister cells. Effect of toxic compounds and stressful conditions on cellular membranes and

cell surface properties of bacteria and mechanisms of bacterial adaptation. Prevention and eradication of

biofilms. Fluorescence microscopy and image analysis to assess cell physiology and morphology. Produc-

tion of compounds with marine bacteria. Biotransformation and design of bioreactors for the production of

high-value compounds from low-value substrates in organic:aqueous systems using whole cells.


C.C.C.R de Carvalho, M.J. Caramujo, “Bacterial diversity assessed by cultivation-based techniques show

predominance of Staphylococccus species on coins collected in Lisbon and Casablanca”, FEMS Microbi-

ology Ecology. doi: 10.1111/1574-6941.12266 (in press). (DOI: 10.1111/1574-6941.12266)

M.J. Caramujo, C. Cunha, C.C.C.R de Carvalho, C. Luís, “Trapped in the pond”, Museus da Universidade

de Lisboa, Lisboa, pp.32. ISBN 978-989-98300-2-8 (2013).

J.M.B.T. Cavalheiro, M.C.M.D. de Almeida, M.M.R. da Fonseca, C.C.C.R de Carvalho, “Adaptation of Cu-

priavidus necator to conditions favoring polyhydroxyalkanoate production”, Journal of Biotechnology 164,

309-317 (2012). (DOI:10.1016/j.jbiotec.2013.01.009)

C.C.C.R. de Carvalho,” Adaptation of Rhodococcus erythropolis cells for growth and bioremediation under

extreme conditions”, Research in Microbiology 163, 125-136 (2012). (DOI: 10.1016/j.resmic.2011.11.003)

C.C.C.R. de Carvalho, M.J. Caramujo, “Lipids of prokaryotic origin at the base of marine food webs”, Ma-

rine Drugs 10, 2698-2714 (2012) (DOI:10.3390/md10122698).

Patent: C.C.C.R. de Carvalho, M.P.C. Marques, “Dispositivo para diluições sucessivas em microplacas”,

PT105887 (2013) (priority date: 14 September 2011).

Frederico Ferreira

Ph.D. Imperial College London, 2004 Principal Research Scientist Phone: +351-218419598 e-mail: [email protected]


Member of the BioEngineering Research Group at Institute for Biotechnology and Bioengineering. My cur-

rent research interests, balance between fundamental and applied research, with potential translation into

the market of sustainable products and processes. The three current research lines aim at the develop-

ment of new processes, reactors and materials, with an emphasis on membrane based systems, for (i)

tailored materials to mimicking stem cell microenvironments, (ii) advanced separations in pharmaceutical

industry and (iii) biorefineries for sustainable aviation biofuels and added value products.


G. Székely, J. Bandarra, W. Heggie*, F.C. Ferreira, “Environmental and economic analysis for selection

and engineering sustainable API degenotoxification processes”, Green Chem. 15, 210-225 (2013)

Patent: C.S, Fonseca, N.F. Faria, F.C. Ferreira "Processos para a produção de glicolípidos microbianos

do tipo manosileritritolípidos, a partir de materiais lenhocelulósicos e suas aplicações", Instituto Superior

Técnico, Universidade Técnica de Lisboa, Laboratório Nacional de Energia e Geologia, PT 106959 (2013)

(priority date: 17 May 2013)

C.S Moura., S. Biscaia, T. Viana,, P. J. Bartolo, C. L. Silva, J. S. Cabral, F. C. Ferreira, “Adhesion, prolifer-

ation and distribution of human mesenchymal stem/stromal cells (MSCs) in poly(caprolactone) (PCL) scaf-

folds with different pore sizes”, in High Value Manufacturing – Advanced Research in Virtual and Rapid

Prototyping, Edited by P.J. Bártolo et al, CRC Press, 2014 (ISBN: 978 1 138 00137 4)

G. Székely, J. Bandarra, W. Heggie, B. Sellergren, F.C. Ferreira “Organic solvent nanofiltration: A platform

for removal of genotoxins from active pharmaceutical ingredients”, J. Membrane Sci, 381 (1-2), 21-33

(2011)

L.C. Branco, F.C. Ferreira, J.L. Santos, J.G. Crespo, C.A.M. Afonso, "Sharpless asymmetric dihydroxyla-

tion of olefins in water-surfactant media with recycling of the catalytic system by membrane nanofiltration”,

Adv Synth Catal, 350, 2086 – 2098 (2008)

R.Valadez-Blanco, F.C. Ferreira, R.F. Jorge, A.G. Livingston “A membrane bioreactor for biotransfor-

mations of hydrophobic molecules using organic solvent nanofiltration (OSN) membranes” J Membrane

Sci, 317, 50–64 (2008)


Ana M. Azevedo

Ph.D. Instituto Superior Técnico, 2004 Research Scientist



Research Scientist of the Bioseparation Engineering Laboratory (BEL) of the Bioengineering Research

Group (member of the Associated Laboratory IBB – Institute for Biotechnology and Bioengineering). Cur-

rent research interests include the development alternative downstream processes for the purification of

biopharmaceutical biomolecules, including monoclonal antibodies, recombinant proteins, plasmid DNA

and bionanoparticles such as virus and VLPs. A key feature of these novel processes is that they should

allow for scalable and integrated purification platforms. Another focus of my research is the development

of animal cell factories for the production of monoclonal antibodies based on Chinese hamster ovary cells

(or alternatively hybridoma cells).


P.A.J. Rosa, A.M. Azevedo, S. Sommerfeld, W. Bäcker, M.R. Aires-Barros, "Continuous purification of

antibodies from cell culture supernatant: from concept to process", Biotechnol. J., 8, 352-362 (2013)

L. Borlido, L. Moura, A.M. Azevedo, A.C.A. Roque, M.R. Aires-Barros, J.P.S. Farinha, "Stimuli-Responsive

Magnetic Nanoparticles for Monoclonal Antibody Purification", Biotechnol. J., 8, 709-717 (2013)

L. Borlido, A.M. Azevedo, A.C.A. Roque, M.R. Aires-Barros, "Magnetic separations in biotechnology", Bio-

technol. Adv., 31, 1374–1385 (2013)

R.N. D‘Souza, A.M. Azevedo, M.R. Aires-Barros, N.L. Krajnc, P. Kramberger, M.L. Carbajal, M. Grasselli,

R. Meyer, M. Fernández-Lahore, “Emerging technologies for the integration and intensification of down-

stream bioprocesses”, Pharm. Bioprocess., 1, 423-440 (2013)

A.G. Gomes, A.M. Azevedo, M.R. Aires-Barros, D.M.F. Prazeres, “Validation and scale-up of plasmid DNA

purification by phenyl-boronic acid chromatography”, J. Sep. Sci., 35, 3190–3196 (2012)

D.F.C. da Silva, A.M. Azevedo, P. Fernandes, V. Chu, J.P. Conde, M.R. Aires-Barros, “Design of a micro-

fluidic platform for monoclonal antibody extraction using an aqueous two-phase system”, J. Chromatogr.

A, 1249, 1-7 (2012)

Pedro Fernandes Ph.D. Instituto Superior Técnico, 1999 Research Scientist Phone: +351-218419594 e-mail: [email protected]


Current research interests focus on bioprocess intensification through miniaturization. Emphasis is given

to the development of enzymatic and whole cell based processes within the pharmaceutical and food and

feed areas, and in the production of chemicals from renewable resources. Pedro also has a distinct inter-

est in the immobilization of enzymes and whole microbial cells.


M.A.P. Nunes, P.C.B. Fernandes, M.H.L. Ribeiro, “Microtiter plates versus stirred mini-bioreactors in bio-

catalysis: A scalable approach”, Bioresource Technol. 136, 30-40 (2013).

J.A. Figueira, H.H. Sato, P. Fernandes, “Establishing the feasibility of using β-glucosidase entrapped in

Lentikats® and in sol-gel supports for cellobiose hydrolysis”, J. Agric. Food Chem. 61, 626-634 (2013).

E. Aguiar-Oliveira, P. Fernandes, J.M.S. Cabral, F. Maugeri, “Characterisation of biocatalysts immobilised

in niobium—a new inorganic solid support”, Canadian J. Chem. Eng. 91, 432–440(2013).

F.J. Contesini, J.A. Figueira, H.Y. Kawaguti, P.C.B. Fernandes, P.O. Carvalho, M.G. Nascimento, H.H.

Sato, “Potential Applications of Carbohydrases Immobilization in the Food Industry”, Int. J. Mol. Sci. 14,

1335-1369 (2013).

E.M. Ribeiro, P. Fernandes, “Coated-wall mini reactor for inulin hydrolysis”, Current Biotechnol. 2, 47-52

(2013).

F. Carvalho, P. Paradiso, P. Fernandes, A microscopic perspective of a microreactor. Microsc. Microanal.

19, Suppl. 4, 33-34 (2013).


T. Catarina Madeira

Ph.D. Instituto Superior Técnico, 2005 Research Scientist



Research Scientist at Stem Cell Bioengineering and Regenerative Medicine Laboratory. Current research

interest is focused on setting-up gene delivery strategies for stem cells expansion, differentiation or for

being used as drug delivery vehicles, specially using non-viral vectors such as plasmids or minicircles as-

sociated with cationic liposomes or physical methods.


A. Santhagunam, F. dos Santos, C. Madeira, J. Salgueiro, J.M.S. Cabral, “Isolation and ex-vivo expansion

of Synovial Mesenchymal Stromal Cells for Cartilage Repair” Cytotherapy in press (2014)

C. Madeira, C.A.V. Rodrigues, M.S.C. Reis, F.C.G. Ferreira, R.E.S.M. Correia, M.M. Diogo, J.M.S. Cabral,

“Non-viral gene delivery to neural stem cells with minicircles by microporation,” Biomacromolecules 14

1251-1710 (2013)

J. Boura, F. dos Santos, J.M. Gimble, C.M.P. Cardoso, C. Madeira, J.M.S. Cabral, C.L. da Silva, "Direct

head-to-head comparison of cationic liposome-mediated gene delivery to mesenchymal stem/stromal cells

of different human sources: a comprehensive study," Human Gene Therapy Methods 24, 38-48 (2013)

S. Ribeiro, J. Mairhofer, C. Madeira, M. Diogo, C.L. da Silva, G. Monteiro, R. Grabherr, J.M. Cabral,

“Plasmid DNA size does affect non-viral gene delivery efficiency in stem cells”, Cellular Reprogramming

14, 130-137 (2012)

C. Madeira, F. dos Santos, P.Z. Andrade, C.L. da Silva, J.M.S. Cabral, “Mesenchymal stem cells for cellu-

lar therapies”, Stem cells and cancer stem cells, Springer Edition 3, 179-187 (2012)

Scientific Output


Articles

Proceedings

Book Chapters

Invited Oral Communications

Oral Communications

Poster Communications

Dissertations

Books

Patents

Articles in Peer-reviewed Journals

Aguiar-Oliveira, E., Fernandes, P., Cabral, J.M.S.,

Maugeri, F., “Characterisation of biocatalysts immo-

bilised in niobium—a new inorganic solid support”,

Canadian J. Chem. Eng., 91, 432–440

Almeida-Porada, G, Soland, M, Boura, J, Porada,

CD., “Regenerative medicine: prospects for the

treatment of inflammatory bowel disease”. Regen.

Med., 8, 631-44

Borlido, L., Moura, L., Azevedo, A.M., Roque,

A.C.A., Aires-Barros, M.R., Farinha, J.P.S., “Stimuli-

Responsive magnetic nanoparticles for monoclonal

antibody purification”, Biotechnol. J., 8, 709-717

Borlido, L., Azevedo, A.M., Roque, A.C.A., Aires-

Barros, M.R., “Magnetic separations in biotechnolo-

gy”, Biotechnol. Adv., 31, 1374-1385

Boura, J.S., dos Santos, F., Gimble, J.M., Cardoso,

C.M., Madeira, C., Cabral, J.M., da Silva, C.L.,

“Direct head-to-head comparison of cationic lipo-

some-mediated gene delivery to mesenchymal

stem/stromal cells of different human sources: a

comprehensive study”, Hum. Gene Ther. Methods,

24, 38-48

Campenni, L., Nobre, B.P., Santos, C.A., Oliveira,

A.C., Aires-Barros, M.R., Palavra, A.M.F., Gouveia,

L., “Carotenoid and lipid production by the auto-

trophic microalga Chlorella protothecoides under

nutritional, salinity, and luminosity stress condi-

tions”, Appl. Microbiol. Biotechnol., 97, 1383-1393

Carvalho, F., Paradiso, P., Fernandes, P., “A mi-

croscopic perspective of a microreactor”, Microsc.

Microanal., 19, 33-34

Contesini, F.J., Figueira, J.A., Kawaguti, H.Y., Fer-

nandes, P.C.B., Carvalho, P.O., Nascimento, M.G.,

Sato, H.H., “Potential applications of carbohydrases

immobilization in the food industry”, Int. J. Mol. Sci.,

14, 1335-1369

de Carvalho, R.N.L., Lourenço, N.M.T., Gomes,

P.M.V., da Fonseca, L.J.P., “Swelling behavior of

gelatin-ionic liquid functional polymers”, J. Polym.

Sci., Part B: Polym. Phys., 51, 817-825

Cavalheiro, J.M.B.T.,de Almeida, M.C.M.D., da Fon-

seca, M.M.R., de Carvalho, C.C.C.R. “Adaptation of

Cupriavidus necator to conditions favoring polyhy-

droxyalkanoate production”. J. Biotechnol. 164, 309

–317.

Donato, S.S., Chu, V., Prazeres, D.M.F., Conde,

J.P., “Metabolic viability of Escherichia coli trapped

by dielectrophoresis in microfluidics”, Electrophore-

sis, 34, 575-582

D`Souza, R.N., Azevedo, A.M., Aires-Barros, M.R.,

Krajnc, N.L., Kramberger, P., Carbajal, M.L.,

Grasselli, M., Meyer, R., Fernández-Lahore, M.,

“Emerging technologies for the integration and the

intensification of bioprocesses”, Pharm. Biopro-

cess., 1, 423-440

Figueira, J.A., Sato, H.H., Fernandes, P.,

“Establishing the feasibility of using β-glucosidase

entrapped in Lentikats® and in sol-gel supports for

cellobiose hydrolysis”, J. Agric. Food Chem., 61,

626-634

Gonçalves, G.A.L., Prazeres, D.M.F., Monteiro,

G.A., Prather, K. L. J., “De novo creation of MG1655

-derived E. coli strains specifically designed for plas-

mid DNA production”, Appl. Microbiol. Biotechnol.,

97, 611-620

Hakemeyer, C., Strauss, U., Werz, S., Folque, F.,

Menezes, J.C., “Near-infrared and two-dimensional

fluorescence spectroscopy monitoring of monoclo-

nal antibody fermentation media quality: Aged me-

dia decreases cell growth”, Biotechnol. J., 8, 835-

846

de Lima, A.P.D., Aschenbrenner, E.M., Oliveira,

S.N., Doucet, J-B., Weiss, C.K., Ziener, U., Fonse-

ca, L.P., Ricardo, N.M.P.S., Freitas, L.L., Petzhold,

C.L., Landfester, K., “Towards regioselective enzy-

matic hydrolysis and glycerolysis of tricaprylin in

miniemulsion and the direct preparation of polyure-

thane from the hydrolysis products”, J. Mol. Catal.

B: Enzym., 98, 127-137

Madeira, C., Rodrigues, C.A.V., Reis, M.S.C., Fer-

reira, F.F.C.G., Correia, R.E. S. M., Diogo, M.M.,

Cabral, J.M.S., "Nonviral gene delivery to neural

stem cells with minicircles by microporation”, Biom-

acromolecules, 14, 1379-1387

Madeira, P.P., Bessa, A., Alvares-Ribeiro, L., Aires-

Barros, M.R., Rodrigues, A.E., Zaslavsky, B.Y.,

“Analysis of amino acid-water interactions by parti-

tioning in aqueous two-phase systems. I-Amino ac-

ids with non-polar side-chains”, J. Chromatogr. A,

1274, 82-86

Madeira, P.P., Bessa, A., de Barros, D.P.C., Teixei-

ra, M.A., Alvares-Ribeiro, L., Aires-Barros, M.R.,

Rodrigues, A.E., Chait, A., Zaslavsky, B.Y.,

“Solvatochromic relationship: Prediction of distribu-

tion of ionic solutes in aqueous two-phase systems”,

J. Chromatogr. A, 1271, 10-16

Madeira, P.P., Bessa, A., Teixeira, M.A., Alvares-

Ribeiro, L., Aires-Barros, M.R., Rodrigues, A.E.,

Zaslavsky, B.Y., “Study of organic compounds-

water interactions by partition in aqueous two-phase

systems”, J. Chromatogr. A, 1332, 97-104

Publications


Martins, D.C., Chu, V., Prazeres, D.M.F., Conde,

J.P., “Streaming currents in microfluidics with inte-

grated polarizable electrodes”, Microfluid. Nanoflu-

id., 15, 361-376

Moreira, F., Badenes, S.M., Cabral, J.M.S.,

“Biocatalytic transesterification of triglycerides and

alcohols for the production of biodiesel using cu-

tinase in organic media”, Biocatal. Biotransform., 31,

246-254

Novo, P., Moulas, G., Prazeres, D.M.F., Chu, V.,

Conde, J.P., “Detection of ochratoxin A in wine and

beer by chemiluminescence-based ELISA in micro-

fluidics with integrated photodiodes”, Sens. Actua-

tors B, 176, 232-240

Nunes, M.A.P., Fernandes, P.C.B., Ribeiro, M.H.L.,

“Microtiter plates versus stirred mini-bioreactors in

biocatalysis: A scalable approach”, Bioresource

Technol., 136, 30-40

Oliveira, P.H., Boura, J.S., Abecasis, M.M., Gimble,

J.M., da Silva, C.L., Cabral, J.M.S., “Impact of hy-

poxia and long-term cultivation on the genomic sta-

bility and mitochondrial performance of ex-vivo ex-

panded human stem/stromal cells”, Stem Cell Res.,

9, 225-236

Oliveira, P.H., da Silva, C.L., Cabral, J.M.S., “An

appraisal of human mitochondrial DNA instability:

new insights into the role of non-canonical DNA

structures and sequence motifs”, PLoS One, 8,

e59907

Raiado-Pereira, L., Prazeres, D.M.F., Mateus, M.,

“Impact of plasmid size on the purification of model

plasmid DNA vaccines by phenyl membrane ad-

sorbers”, J. Chromatogr. A, 1315, 145-151

Ribeiro, A., Laranjeira, P., Mendes, S., Velada, I.,

Leite, C., Andrade, P., Santos, F., Henriques, A.,

Grãos, M., Cardoso, C.M., Martinho, A., Pais, M., da

Silva, C.L., Cabral, J.M.S., Trindade, H., Paiva, A.,

“Mesenchymal stem cells from umbilical cord matrix,

adipose tissue and bone marrow exhibit different

capability to suppress peripheral blood B, natural

killer and T cells”, Stem Cell Res. Ther., 4:125

Ribeiro, E.M., Fernandes, P., “Coated-wall mini re-

actor for inulin hydrolysis”, Curr. Biotechnol., 2, 47-

52

Rosa, P.A.J., Azevedo, A.M., Sommerfeld, S., Mut-

ter, M., Baecker, W., Aires-Barros, M.R.,

“Continuous purification of antibodies from cell cul-

ture supernatant with aqueous two-phase systems:

From concept to process”, Biotechnol. J., 8, 352-362


bral, J.M.S., “Bioreactor design for clinical-grade

expansion of stem cells”, Biotechnol. J., 8, 644-654

Santos, R., Rocha, A., Matias, A., Duarte, C., Sá-

Nogueira, I., Lourenço, N., Borges, J.P., Vidinha, P.,

“Development of Antimicrobial Ion Jelly Fibers”,

RSC Advances, 3, 24400-24405

Silva, C.S.O., Lansalot, M., Garcia, J.Q., Taipa,

M.A., Martinho, J.G., “Synthesis and characteriza-

tion of biomimetic nanogels for immunorecognition”,

Colloids Surf. B, 112, 264-271

Simões, I.N., Boura, J.S., dos Santos, F., Andrade,

P.Z., Cardoso, C.M.P., Gimble, J.M., da Silva, C.L.,

Cabral, J.M.S., “Human mesenchymal stem cells

from the umbilical cord matrix: Successful isolation

and ex vivo expansion using serum-/xeno-free cul-

ture media”, Biotechnol. J., 8, 448-458

Sousa, I.T., Lourenço, N.M.T., Afonso, C.A.M., Tai-

pa, M.A., “Protein stabilization with a dipeptide-

mimic triazine-scaffolded synthetic affinity ligand”, J.

Mol. Recognit., 26, 104-112

Szekely, G., Gil, M., Sellergren, B., Heggie, W., Fer-

reira, F.C., “Environmental and economic analysis

for selection and engineering sustainable API de-

genotoxification processes”, Green Chem., 15, 210-

225

De La Vega, J., Ter Braak, B., Azzoni, A.R., Mon-

teiro, G.A., Prazeres, D.M. F., “Impact of Plasmid

Quality on Lipoplex-Mediated Transfection”, J.

Pharm. Sci., 102, 3932-3941

Vicente, J., Pinto, J., Menezes, J.C., Gaspar, F.,

“Fundamental analysis of particle formation in spray

drying”, Powder Technol., 247, 1-7

Articles in National Journals

Prazeres, D.M.F., "Histórias de Inovação Aberta",

Ingenium, Jul/Ago, 68-71

Simcikova, M., Prazeres, D.M.F., Monteiro, G.A.,

“Design, construção e produção de minicírculos

como vectores de entrega de genes”, Boletim de

Biotecnologia, 4, 28-30

Articles in Conference Proceedings

Monteiro, B.J.C., Guerreiro, J.D.T., dos Santos, F.,

Cabral, J.S.M., da Silva, C.L., Ferreira, F.C., “Study

of the Effects of Electrospun Poly(epsloncapro-

lactone)/Gelatin Matrices on Human Mesenchymal

Stem Cell Culture”, IEEE 3rd Portuguese Bioengi-

neering Meeting | ENBENG 2013, Univ. Minho, Bra-

ga, February

Carvalho, F., Marques, M.P.C., Fernandes, P.

“Continuous sucrose hydrolysis in microchannel

reactors”, 2nd International Conference on Imple-

mentation of microreactor technology into biotech-

nology | IMTB 2013, Cavtat, Croatia, May

Books

Caramujo M.J., Cunha C., de Carvalho, C.C.C.R.,

Luís, C. “Trapped in the pond”. Publisher: Museus

da Universidade de Lisboa, Lisboa, pp.32. ISBN

978-989-98300-2-8

Fernandes, T.G., Diogo, M.M., Cabral, J.M.S.,

“Stem Cell Bioprocessing: For Cellular Therapy,

Diagnostics and Drug Development”, Biohealthcare

Publishing, Cambridge, pp.236. ISBN: 978-1-

907568-88-6

Book Chapters

BadenesBadenes, S.M., Ferreira, F.C., Cabral,

J.M.S., “Membrane bioreactors for biofuel produc-

tion”, in: “Separation and Purification Technologies

in Biorefineries”, S. Ramaswamy, H.-J. Huang and

B.V. Ramarao (Eds.), Wiley, Chichester, 377-407

Diogo, M.M., da Silva, C.L., Cabral, J.M.S.,

“Separation technologies for stem cell biopro-

cessing”, in: Cell Engineering, Volume 8: Stem Cells

and Cell Therapy, M. Al-Rubeai and M. Naciri (Eds),

Springer, Dordrecht, 157-181

Fernandes, P., Cabral, J.M.S., “Production of

Sweeteners”, in: Biotechnology in Agriculture and

Food Processing: Opportunities and Challenges,

P.S. Panesar, and S.S. Marwaha. (Eds.), CRC

Press, Boca Raton, Florida, 387-415

Fernando S.R.R., Teles, M.L.M., Vieira, M.R., Fon-

seca, L.P., “Nanotechnology for the diagnosis of

parasitic infections” in: Nanotechnology in Dermatol-

ogy, A. Nasir, A. Firelman and S. Wang (Eds),

Springer, Dordrecht, 209-219

Rodrigues, C.A.V., Fernandes, T.G., Diogo, M.M.,

da Silva, C.L., Cabral, J.M.S., “Bioreactors for Stem

Cell Expansion and Differentiation”, in: Stem Cell

Engineering: Principles and Practices, D. Schaffer,

J.D. Bronzino and D.R. Peterson (Eds), CRC Press,

Boca Raton, Florida, 10.1-10.28


bral, J.M.S., “Scalling-up ex-vivo expansion of mes-

enchymal stem cells for cellular therapies”, in: Mes-

enchymal Stem Cell Therapy , L. Chase and M.

Vemuri (Eds.), Humana Press, New York, 1-14

Taipa, M.A., “Immunological Assays: Biotools for

High Throughput Screening and Characterisation of

Combinatorial Libraries”, in: Advances in Combina-

torial Chemistry & High Throughput Screening, R.

Chaguturu (Ed); Bentham Science Publishers, 130-

158

Patents

Fonseca, C.S, Faria, N.F, Ferreira, F.C., “Processos

para a produção de glicolípidos microbianos do tipo

manosileritritolípidos, a partir de materiais lenhoce-

lulósicos e suas aplicações”, IST/UL, LNEG, Paten-

te de Invenção Nacional n.º 106959; Priority date:

17 Maio 2013

de Carvalho, C.C.C.R., Marques, M.P.C..

“Dispositivo para diluições sucessivas em micropla-

cas”, PT105887, 8 August 2013 (Priority date: 14

September de 2011)

da Silva, C.L., Cabral, J.M.S., Andrade, P.Z., dos

Santos, F., Almeida-Porada, G. "Processo De Ex-

pansão Ex Vivo De Células Estaminais Em Biorre-

actor", IST/UL, Provisional patent no. 106225; Prio-

rity date: 23 March 2013

Invited Oral Communication

International Conferences

Aires-Barros, M.R., “Aqueous two-phase systems: a

new platform for biopharmaceuticals purification”,

40th International Conference of Slovak Society of

Chemical Engineering, Vysoké Tatry, Slovak Re-

public, May

Azevedo, A.M., Aires-Barros, M.R., “Aqueous Two-

Phase Systems for Bioprocessing Integration”, 20th

Biennial meeting of the International Society for Mo-

lecular Recognition | Affinity 2013, Vienna, Austria,

June

Cabral J.M.S., Bioengineering strategies for ex-vivo

cultivation and purification of human stem cells,

New Directions for Tissue Engineering and Regen-

erative Medicine, Sonoma, California, US, July

Cabral J.M.S., Bioengineering strategies for ex-vivo

cultivation and purification of human stem cells, Ox-

ford Global Stem Cell Congress, London, UK, No-

vember

Fonseca, L.P., “Emulsions and nanoparticles on

innovative biocatalysis, design of drug delivery and

cell-free protein expression systems“, XXI Interna-

tional Conference on Bioencapsulation, Berlin, Ger-

many, August

Menezes JC, The PAT toolbox & skills set, 9th. Kol-


loquium Prozessanalytik – 100 Years of PAT, BASF

-Ludwigshafen, Germany, November

Menezes JC. A Critical Discussion of EMA's NIR

Draft Guideline on the use of NIRS by the Pharma-

ceutical Industry. IFPAC-2013, Baltimore (MD),

USA, January

da Silva, C.L., “Scalable production of human stem/

progenitor cells in microcarrier-based culture sys-

tems”, Cell Therapy Manufacturing, Brussels, Bel-

gium, December

National Conferences

Azevedo, A.M., Aires-Barros, M.R., “Aqueous Two-

Phase Systems for Antibodies Purification: from

macro to micro-scale”, 8º Encontro Nacional de Cro-

matografia, Universidade da Beira Interior, Covilhã,

Portugal, December

Badenes, S.M., Fernandes, T.G., Pusch, A., Haupt,

S., Rodrigues, C.A.V., Bear, M., Hervy, M., Diogo,

M.M., Brüstle, O. and Cabral, J.M.S., “Evaluation of

microcarrier-based suspension cultures for human

induced pluripotent stem cells”, 8th International

Meeting of the Portuguese Society for Stem Cells

and Cell Therapies, University of Algarve, Faro, Por-

tugal, May

Diogo, M.M., “Integrated Platform for Production

and Purification of Human Pluripotent Stem Cell-

Derived Neural Precursors”, MicroBiotec’13, Univer-

sidade de Aveiro, Aveiro, Portugal, December

Ferreira, F.C., “Tailoring biomaterials to support

stem cell cultivation”, International Advanced

Course on Regenerative Medicine Manufacturing,

Tavira, Algarve, Portugal, Apr-May

Ferreira, F.C., “Electrospinning: Potential for Appli-

cation in Regenerative Medicine”, 3rd Advanced

Course on Regenerative Medicine, Marinha Grande,

Portugal, March

Madeira, C., “Investigação e cartilagem”, 5º Curso

teórico-prático de Cartilagem Articular, Teatro Aber-

to, Lisbon, Portugal, November

Madeira, C., “Nanovectors for widening stem cell-

based therapies”, UL Summer course Lecture Se-

ries, Universidade de Lisboa, Lisbon, Portugal, July

Santhagunam, S., dos Santos, F., Madeira, C., Sal-

gueiro, J., Cabral, J.M.S., “Isolation and ex-vivo ex-

pansion of Synovial Mesenchymal Stromal Cells for

Cartilage Repair”, 5º Curso teórico-prático de Carti-

lagem Articular, Teatro Aberto, Lisbon, Portugal,

November

Oral Communications


Azevedo, A.M., Aires-Barros, M.R., “Integration and

Intensification of Downstream Bioprocessing based

in Aqueous Two-Phase Systems “, 33th Internation-

al Symposium on the Separation of Proteins, Pep-

tides and Polynucleotides | ISPPP, Boston, MA/

USA, July

Azevedo, A.M., Silva, M.F.F., Aires-Barros, M.R., “A

novel approach for mAbs bioprocessing: Clarifica-

tion and capture by aqueous two-phase extraction”,

17th International Conference on Biopartitioning and

Purification | BPP2013, Newport, RH/USA, October

Boura, J.S., Soland, M., Yin, W., Kuo, C., Madeira,

C., da Silva, C.L., Porada, C., Almeida-Porada, G.,

“Gene Delivery Strategies to Efficiently Over-

express HLA-G in Bone Marrow-Derived Mesenchy-

mal Stromal Cells”, MSC 2013, Cleveland, USA,

August (selected from abstracts)

Canadas, R.F., Cavalheiro, J.M.B.T., Guerreiro,

J.D.T., de Almeida, M.C.M.D., Pollet, E., Lobato da

Silva, C., da Fonseca, M.M.R., Ferreira, F.C.,

“Fabrication and application of electrospun fibrous

scaffolds, using polyhydroxyalkanoates bioproduced

from crude glycerol, to support human mesenchy-

mal stem cell cultivation”, European Symposium on

Biopolymers - ESBP2013, Lisbon, Portugal, October

Hatami, J., Andrade, P.Z., Cabral, J.M.S., Lobato da

Silva C., Ferreira, F.C. “A multi-phase protocol for

the expansion and megakaryocytic differentiation of

umbilical cord blood hematopoietic stem/progenitor

cells”, 9th European Congress of Chemical Engi-

neering & 2nd European Congress of Applied Bio-

technology, Hague, The Netherlands, April

Matos, J.C., Domingues, I., Monteiro, G.A., Gon-

çalves, M.C., “Design and production of silica and

ORMOSIL nanoparticles for gene delivery”, Interna-

tional Conference on Chemical and Bioprocess En-

gineering-INDIA, Warangal, Andhra Pradesh, India,

November

Monteiro, M.E., Raiado-Pereira L., Prazeres,

D.M.F., Mateus, M., “FRAP biophysical tool to probe

nucleic acids membrane ligand interactions in pDNA

purification”, 9th European Biophysics Congress |

EBSA2013, Lisbon, Portugal, July

Moura, C.S., Biscaia, S., Viana, T., Bártolo, P.J., da

Silva, C.L., Cabral, J.M.S., Ferreira, F.C.,

“Adhesion, proliferation and distribution of human

mesenchymal stem/stromal cells (MSCs) in Poly(ɛ-

caprolactone) (PCL) scaffolds with different pore

sizes”, International Conference on Advanced Re-

search in Virtual and Rapid Prototyping (VRAP

2013), Leiria, Portugal, October

Pereira, P.M., Moita, A.S., Moreira, A.L.N., Mon-

teiro, G.A., Prazeres, D.M.F., “Characterization of

the Topography and Wettability of Biomimetic Repli-

cas of the Surfaces of Rose Petals and Clover

Leaves”, 4th International Conference in Bionic En-

gineering, Nanjing, China, August

Raiado-Pereira, L., de la Vega, J., Prazeres, D.M.F.,

Mateus, M., “Impact of plasmid size on the purifica-

tion of model pDNA vaccines by HIC on phenyl

membrane adsorbers”, International Symposium on

the Separation of Proteins, Peptides and Polynucle-

otides | ISPPP 2013, Boston, USA, July

Rodrigues, G.M.C., Matos, A.S., Fernandes, T.G.,

Diogo, M.M., Cabral, J.M.S., “Purification of Human

Induced Pluripotent Stem Cell-Derived Neural Pro-

genitors for Regenerative Medicine Applications”,

9th European Congress of Chemical Engineer-

ing/2nd European Congress of Applied Biotechnolo-

gy, The Hague, Netherlands, April (selected from

abstracts)

Rosa, A.M., Louro, A.F., Azevedo, A.M., Martins,

S.A.M., Prazeres, D.M.F. “Molecular Detection of

Nucleic Acids Based on Antibodies Immobilized in

Paper-based Microfluidic Devices via Carbohydrate-

binding Modules”, 20th Biennial meeting of the Inter-

national Society for Molecular Recognition | Affinity

2013, Viena, Austria, June

Šimčíková, M., Prazeres, D.M.F., Prather, K.L.J.,

Monteiro, G.A. “Design of resolvase expression sys-

tems for minicircle production”, 5th PEGS – Proteins

& Antibody Engineering Summit - Europe 2013, Lis-

bon, Portugal, November


Altas, M.C., Fonseca, L.P., Lourenço, N.M.T.,

“Enzymatic Resolution of Secondary Alcohols in

Miniemulsion Media”, 10th Portuguese National

Meeting of Organic Chemistry, Lisbon, September

de Barros, D.P.C., “Prediction of Biomolecules Parti-

tioning in Aqueous Two Phase Systems Using a

Semi - Empirical Approach”, 2nd Portuguese Bio-

molecular Modelling Meeting, Foz do Arelho, April

Boura J.S., Soland M., Yin W., Kuo C., Madeira C.,

da Silva C.L., Porada C., Almeida-Porada G., “Gene

Delivery Strategies to Efficiently Over-express Func-

tional HLA-G in Bone Marrow-Derived Mesenchymal

Stromal Cells” MicroBiotec´13, Aveiro, December

(selected from abstracts)

Carvalho, R.Jr., Woo, J., Aires-Barros, M.R., Cra-

mer, S.M., Azevedo, A.M., “Multimodal behavior of

phenylboronate chromatography”, 8º Encontro Naci-

onal de Cromatografia, Universidade da Beira Inte-

rior, Covilhã, December

Hatami, J., Andrade, P.Z., Cabral, J.M.S., da Silva,

C.L., Ferreira, F.C., “A two-phase protocol for the

expansion and megakaryocytic differentiation of

umbilical cord blood hematopoietic stem/progenitor

cells”, 8th International Meeting of the Portuguese

Society for Stem Cells and Cell Therapies, Faro,

May (Abstract awarded)

Monteiro, B.J.C., Guerreiro, J.D.T., dos Santos, F.,

Cabral, J.S.M., da Silva, C.L., Ferreira, F.C., “Study

of the effects of electrospun poly(epslon-

caprolactone)/gelatin matrices on human mesen-

chymal stem cell culture”, 3rd Portuguese Bioengi-

neering Meeting, Braga, February (Presentation

award: 3rd best Master Thesis)

Raiado-Pereira, L., de la Vega, J., Prazeres, D.M.F.,

Mateus, M., “Purification of pharmaceutical grade

plasmid DNA by HIC membrane chromatography –

Impact of plasmid size and process throughput”,

Portuguese Congress of Microbiology and Biotech-

nology | Microbiotec’2013, Aveiro, December

Silva, D.F.C., Azevedo, A.M., Fernandes, P., Chu,

V., Conde, J.P., Aires-Barros, M.R., “Aqueous two-

phase system in a microfluidic platform to accelerate

bioprocess design and optimization of monoclonal

antibodies”, Portuguese Congress of Microbiology

and Biotechnology | Microbiotec’2013, Aveiro, De-

cember

Šimčíková, M., Prather, K.L.J., Prazeres, D.M.F.,

Monteiro, G.A., “Development of a minicircle pro-

duction system based on ParA resolvase–mediated

in vivo recombination”, Portuguese Congress of

Microbiology and Biotechnology | Microbiotec’2013,

Aveiro, December

de Sousa, M.C. A, Rodrigues, C., Ferreira, I. F.,

Sirgado, T., Diogo, M., da Silva, C. L, Ferreira, F.C.

“Electrospun Nanofiber Based Scaffold Platform for

Stem Cell Alignment”, 1st CLUSTER Workshop in

Materials and Nanotechnology, IST, Lisbon, Decem-

ber

Poster Communications


Altas M.C., Fonseca L.P. Lourenço N.M.T., “Low

Temperature Enzymatic Resolution of 1-

Phenylethanol in Miniemulsion Media”, Biotrans

2013, Manchester, UK, July

Amador, M., Quesada-Hernández, E. Escacena, N.

Hmadcha, A. Ferreira, F.C., Heitor, M.V. Soria, B.


“Towards a new regulatory framework for cellular

medicaments manufacturing and clinical use in Eu-

rope”, I International Meeting on Stem Cells for Re-

generative Medicine and Drug Screening, Biocant,

Cantanhede, Portugal, July

Azevedo A.M., dos Santos, R., Rosa, S.A.S.L.,

Aires-Barros, M.R., “An Alternative Capture Step for

Monoclonal Antibodies: Phenyl Boronate as a New

Multi-modal Ligand”, 33th International Symposium

on the Separation of Proteins, Peptides and Polynu-

cleotides | ISPPP, Boston, MA/USA, July



M.M., Brüstle, O., Cabral, J.M.S., “Evaluation of mi-

crocarrier-based suspension cultures for human

induced pluripotent stem cells”, ECI Conference -

Scale-Up and Manufacturing of Cell-Based Thera-

pies II, San Diego, USA, January



M.M., Brüstle, O., Cabral, J.M.S., "Evaluation of Mi-

crocarrier-based Suspension Cultures for Human

Induced Pluripotent Stem Cells", International Socie-

ty for Stem Cell Research, 11th Annual Meeting,

Boston, USA, June

de Barros, D.P.C., Campos, S.R.R., Madeira, P.P.,

Azevedo, A.M., Baptista, A.M., Aires-Barros, M.R.,

“A semi-empirical model as a tool to predict bio-

molecular partitioning in aqueous two phase sys-

tem”, 20th Biennial meeting of the International So-

ciety for Molecular Recognition | Affinity 2013, Vien-

na, Austria, June

Boura, J.S., Soland, M., Yin W., Kuo, C., Madeira,

C., da Silva, C.L., Porada, C., Almeida-Porada, G.,

“Non-viral Gene Delivery of HLA-G to Bone Marrow

Stem Cells Using Minicircles”, Wake Forest Institute

for Regenerative Medicine Annual Retreat, Winston-

Salem, USA, March


J.D.T., de Almeida, M.C.M.D., Pollet, E., da Silva,

C.L., da Fonseca, M.M.R., Ferreira, F.C.

“Polyhydroxyalkanoates: their production from crude

glycerol, electrospinning in fibrous scaffolds and use

to support mesenchymal stem cells culture”, 9th

European Congress of Chemical Engineering & 2nd

European Congress of Applied Biotechnology,

Hague, The Netherlands, April

Carvalho, R.Jr., Woo, J., Azevedo, A.M., Cramer,

S.M., Aires-Barros, M.R., “Phenylboronic acid as

ligand for a multimodal chromatography: characteri-

zation using protein library”, 20th Biennial meeting

of the International Society for Molecular Recogni-

tion | Affinity 2013, Vienna, Austria, June

Carvalho, R.Jr., Woo, J., Nakamura, K.A., Aires-

Barros, M.R., Azevedo, A.M., Cramer, S.M., “Phenyl

Boronic Acid as Ligand for a Multimodal Chromatog-

raphy: Adsorption Behavior Comparison between

Control Pore Glass and Agarose Matrixes” 33th In-

ternational Symposium on the Separation of Pro-

teins, Peptides and Polynucleotides | ISPPP, Bos-

ton, MA/USA, July

Carvalho, R.Jr., Woo, J., Parimal, S., Aires-Barros,

M.R., Cramer, S.M., Azevedo, A.M., “Phenylboronic

acid as ligand for a multimodal chromatography:

proof of concept”, 20th Biennial meeting of the Inter-

national Society for Molecular Recognition | Affinity

2013, Vienna, Austria, June

Dhadge, V., Azevedo, A., Hussain, A., Aires-Barros,

R., Roque, A.C.A., “Modified magnetic particles

coated with aminophenyl boronic acid for antibody

purification”, 20th Biennial meeting of the Interna-

tional Society for Molecular Recognition | Affinity

2013, Vienna, Austria, June

Hatami, J. Andrade, P.Z., Cabral, J.M.S., da Silva,

C.L, Ferreira, F.C., “Effective megakaryocytic differ-

entiation of umbilical cord blood hematopoietic stem/

progenitor cells using two-phase protocol”, Interna-

tional Twin Congress, 14th Congress on Reproduc-

tive Biomedicine and 9th Congress on Stem Cell

Biology & Technology, Tehran, Iran, September

Magalhães, S., Duarte, S., Monteiro, G.A., Prieto,

M., Fernandes, F., “Plasmid DNA delivery followed

through Förster Resonance Energy Transfer”, 9th

European Biophysics Congress EBSA, Lisbon, Por-

tugal, July

Monteiro, M.E., Raiado-Pereira, L., Prazeres,

D.M.F., Mateus, M., “FRAP as biophysical tool to

probe RNA and pDNA interaction with chromato-

graphic ligands in membrane adsorbers”, 20th Bien-

nial Meeting of the International Society for Molecu-

lar Recognition | Affinity 2013, Vienna, Austria, June

Monteiro, M.E., Raiado-Pereira, L., Prazeres,

D.M.F., Mateus, M., “FRAP Biophysical Tool to

Probe Nucleic Acids Membrane Ligand Interactions

in pDNA Purification in Membrane Adsorbers”, 9th

European Biophysics Congress- EBSA2013, Lisbon,

Portugal, July

Pinto-de-Oliveira, A., Coutinho, A., Ramos, C.G.,

Sousa, S.A., de Carvalho, C.C.C.R., Leitão, J.H., Sá

-Correia, I. “The Burkholderia cepacia small colony

variants (SC V) are a more pathogenic bacterial

form that may facilitate persistent respiratory infec-

tions in CF patients”, 36th European Cystic Fibrosis

Conference, Lisbon, Portugal, June





International Society for Stem Cell Research, 11th

Annual Meeting, Boston, USA, June





International Conference on Stem Cells for Drug

Screening and Regenerative Medicine, Cantan-

hede, Portugal, July

Sanches, S., Nunes, C., Passarinho, P., Ferreira, F.,

Rodrigues, A., Cardoso, V.V., Ferreira, E., Benoliel,

M.J., Crespo, M.T.B., Pereira, V.J., Crespo, J.G.,

“Evaluation of an Hybrid Process that Combines LP/

UV Photocatalysis with Nanofiltration for Water

Treatment”, 8th Micropol & Ecohazard 2013, Zurich,

Switzerland, June

dos Santos D.J.V.A., Leitão, J.H., Guedes, R.C.,

“Development and validation of a homology model

of Type II phosphomannose isomerase”, 6th Inter-

national Theoretical Biophysics Symposium

(TheoBio 2013), Gothenburg, Sweden, June

dos Santos, F., Costa, R., Burnouf, T., Tseng, Y-H.,

Liu, S-H., Ku, C-P., da Silva, C.L., Cabral, J.M.S.,

“Scalable expansion of human mesenchymal stem

cells using a microcarrier-based system under se-

rum-free and xeno-free conditions”, Scale-Up and

Manufacturing of Cell-Based Therapies, San Diego,

USA, January

da Silva, C.L., dos Santos, F., Campbell, A., An-

drade, P.Z., Wen, Y., Boucher, S., Roos, E., Kuli-

gowski, S., Vemuri, M., Cabral, J.M.S., “A High Den-

sity Xeno-Free Bioreactor Culture System for the

Clinical-Scale Expansion of Human Mesenchymal

Stem/Stromal Cells”, Scale-Up and Manufacturing of

Cell-Based Therapies, San Diego, USA, January

Szekely, Gy., Ferreira, F.C., Heggie, W., Livingston,

A.G., “Process intensification by organic solvent

nanofiltration: removal of genotoxic impurities from

pharmaceutical products”, 4th International Confer-

ence on Organic Solvent Nanofiltration, Aachen,

Germany, March

Trabuco, J.R.C., Willson, R.C, Prazeres, D.M.F.,

“Miniaturization of Capture Assays for Dengue De-

tection in Airports: A Comparative Evaluation of

Available Technologies”, Affinity 2013, Vienna, Aus-

tria, June

Weber, J.L, Carmelo, J.G., Bear, M., Hervy M., Di-

ogo, M.M., da Silva, C.L., Cabral, J.M.S.,

“Evaluation of microcarrier-based suspension cul-

tures for human mesenchymal stem cells”, Biopro-

cess International Conference & Exposition, Boston,

USA, September



J.D.T., de Almeida, M.C.M.D., Pollet, E., Lobato da

Silva, C., da Fonseca, M.M.R., Ferreira, F.C.,

“Polyhydroxyalkanoates Fibrous Scaffolds for Sup-

port of Mesenchymal Stem cells”, 1st CLUSTER

Workshop in Materials and Nanotechnology, IST

Lisbon, December

Carvalho, F.D.R., Paradiso, P., Saramago, B., do

Rego, A.M.B., Fernandes, P., Towards a rational

approach for enzyme immobilization in a microreac-

tor framework, Portuguese Congress of Microbiolo-

gy and Biotechnology | Microbiotec’2013, Aveiro,

December.

Duarte, S., Rodrigues, L., Monteiro, G.,

“Heterologous production of curcumin by probiotic

lactic acid bacteria towards gastrointestinal cancer

therapy”, E3 Forum 2013, Lisbon, June

Duarte, S.O.D., Paulo, J., Machado, D., Rocha, I.,

Mergulhão, F.J.M., Rodrigues, L.R., Monteiro, G.A.,

“A synthetic biology approach to engineer

"therapeutic" bacteria”, Portuguese Congress of


Aveiro, December

Faria, N.T., Ferreira, C., Santos, M., Marques, S.,

Fonseca, C., Ferreira, F.C., “Sustainable glycolipids:

yeast conversion of lignocellulosic biomass into

mannosylerythritol lipids”, Portuguese Congress of


Aveiro, December

Magalhães, S., Duarte, S., Monteiro, G.A., Prieto,

M., Fernandes, F. “Trafficking studies of plasmid

DNA through Förster Resonance Energy Transfer”,

Portuguese Congress of Microbiology and Biotech-

nology | Microbiotec’2013, Aveiro, December

Magalhães, S., Nilsen, I.W., Monteiro, G.A.,

“Improvement of DNA vaccines”, E3 Forum 2013,

Lisbon, June

de Miguel, M., Ferreira, F.C., Baleizão, C., Farinha,

J.P., “Stimuli-Responsive Fiber Scaffolds for Stem

Cell Cultivation”, 1st CLUSTER Workshop in Materi-

als and Nanotechnology, Lisbon, December

Monteiro, M., Lourenço, N.M.T., Afonso, C.A.M.,

“Simple and more sustainable approaches for one

pot enzymatic resolution of sec-alcohols”, PC 87,

10th Portuguese National Meeting of Organic

Chemistry, Lisbon, September

Rocha, A., Lourenço, N.M.T., “Novel room-

temperature choline carboxylate zwitterionic ionic

liquids as potential electrolytes”, PC 1, 10th Portu-

guese National Meeting of Organic Chemistry, Lis-

bon, September


Rosa, A.M.M., Louro, A.F.D., Martins, S.A.M.,

Inácio, J.J., Azevedo, A.M., Prazeres, D.M.F.,

“Molecular Recognition of DNA Hybrids on Paper

Via the Anchoring of Antibodies With a Fusion of ZZ

-Domain With Carbohydrate-Binding Modules”, Por-

tuguese Congress of Microbiology and Biotechnolo-

gy | Microbiotec’2013, Aveiro, December

Šimčíková, M., Carreira, L., Gonçalves, G., Prather,

K.L.J., Prazeres, D.M.F., Monteiro, G.A., “The effect

of rpiA overexpression on plasmid biopharmaceuti-

cal production by Escherichia coli galg20, a pgi-

gene knockout strain”, Portuguese Congress of Mi-

crobiology and Biotechnology | Microbiotec’2013,

Aveiro, December

Simões, I.N., Vale, P., Soker, S., Atala, A., Cabral,

J.M.S., da Silva, C.L., Baptista, P.M., “Urinary

Rhabdosphincter Bioengineering – A Decellularized

Urethra Matrix for Modeling Stress Urinary Inconti-

nence In vitro and Tissue Engineering Applications”,

8th International Meeting of the Portuguese Society

for Stem Cells and Cell Therapies, Faro, May

Soares, R., Azevedo, A.M., Fernandes, P., Chu, V.,

Aires-Barros, M.R., Conde, J.P., “Integrated Extrac-

tion, Concentration and Quantification of Ochratoxin

A in Wines using a Microfluidic Aqueous Two Phase

Extraction coupled to a Fluorescence Linked Im-

munosorbent Assay”, Portuguese Congress of Mi-

crobiology and Biotechnology | Microbiotec’2013,

Aveiro, December

Szekely, Gy., Bandarra, J., Heggie, W., Sellergren,

B., Ferreira, F.C., “Scavenging Genotoxics from

Active Pharmaceutical Ingredients Streams by Mo-

lecular Imprinting and Nanofiltration”, 1st CLUSTER

Workshop in Materials and Nanotechnology, Lisbon,

December

Teixeira, R., Lourenço, N.M.T., “Synthesis of Novel

Task-Specific Ionic Liquids Bearing an Anhydride

Moiety”, PC 68, 10th Portuguese National Meeting

of Organic Chemistry, Lisbon, September

Trabuco, J.R.C., Martins, S.A.M., Monteiro, G.A.,

Chu, V., Conde, J.P., Prazeres, D.M.F., “Towards

the miniaturization of cell assays for GPCR monitor-

ing”, Portuguese Congress of Microbiology and Bio-

technology | Microbiotec’2013, Aveiro, December

Dissertations

Ph.D. Theses

Carlos Monteiro, PhD in Pharmaceutical and

Medicinal Chemistry, “Development of new synthet-

ic methodologies for organic synthesis based on

biocatalysis”, FF/UL (Supervisors: C.A.M. Afonso,

N.M.T. Lourenço)

Geisa Gonçalves, PhD in Bioengineering,

“Rational engineering of E. coli strains and vectors

for improved manufacturing of plasmid biopharma-

ceuticals”, IST/UL (Supervisors: D.M.F. Prazeres,

K.L.J. Prather, G.A. Monteiro)

João Cavalheiro, PhD in Biotechnology, “From

biodiesel glycerol to co- and ter- bacterial polyes-

ters”, IST/UL (Supervisors: M.M.R. Fonseca, M.C.M.

de Almeida)

Jonathan de la Vega, PhD in Biotechnology,

“Impact of plasmid downstream processing on tran-

sient transfection”, IST/UL (Supervisor: D.M.F.

Prazeres, G.A. Monteiro)

Michaela Simcíková, PhD in Bioengineering,

“Development of a process for the production and

purification of minicircles for biopharmaceutical ap-

plications”, IST/UL (Supervisor: G.A. Monteiro,

D.M.F. Prazeres)

Rimenys Jr Carvalho, PhD in Bioengineering,

“Phenylboronic Acid as Ligand for Multimodal Chro-

matography”, IST/UL (Supervisors: A.M. Azevedo,

S.M. Cramer, M.R. Aires-Barros)

Sezin Aday, PhD in Bioengineering, “Platforms to

modulate the activity of hematopoietic stem cells

and their progenies”, IST/UL (Supervisors: L. Fer-

reira, C. Lobato da Silva)

M.Sc. Theses

Alice Goudjil Portela, MSc in Biotechnology, “Ex-

vivo expansion of human Pluripotent Stem Cells

using alginate based culture systems, IST/UL

(Supervisors: F.C. Ferreira, J.M.S. Cabral)

Ana Filipa Pires, MSc in Bioenginneering,

“Assessing the use of conjugated polymers and

electric fields for cell culture”, IST/UL (Supervisors:

J. Morgado, F.C. Ferreira)

Ana Raquel Fortuna, MSc in Biological Engineer-

ing, “Early Breakthrough Detection during Chroma-

tographic Separation - a study directed to the mAbs

downstream process”, IST/UL (Supervisors: M. Ma-

teus, L. Villain)

Ana Teresa Bento, MSc in Biological Engineer-

ing, “Role of RET signals in human hematopoietic

stem cell transplantation, IST/UL (Supervisors: C.

Lobato da Silva, J.H. Veiga)

Ângelo Miguel Rocha, MSc in Química Farma-

cêutica e Terapêutica, “Desenvolvimento de meto-

dologias para síntese de fármacos metálicos e não-

metálicos, FF/UL, IST/UL (Supervisor: C.A.M. Afon-

so, N.M.T. Lourenço)

Antonio Lima Grilo, MSc in Biological Engineer-

ing, “Aqueous Two-Phase Systems for Large Scale

Purification of Monoclonal Antibodies”, IST/UL

(Supervisors: A.M. Azevedo, G. Vedantham)

André Nascimento, MSc in Biotechnology,

“Polishing of Monoclonal Antibodies Stream through

Convective Flow Devices, IST/UL (Supervisors:

A.M. Azevedo, M. Mateus)

André Fernandes, MSc in Biological Engineer-

ing, “Ozonation or evaporation as a wastewater

treatment after aneorobic methanization for its recir-

culation to bioethanol production process”, IST/UL

(Supervisors: D.M.F. Prazeres, M. Kamiński)

Bárbara Silva, MSc in Biological Engineering,

“New sparse modelling tools in flavour research”,

IST/UL (Supervisors: J.M.C. Menezes, R. Bro)

Bernardo Abecasis, MSc in Biological Engineer-

ing, “Developing an Advanced Therapy Medicinal

Product (ATMP) for regulatory approval: optimiza-

tion of product release and shelf life”, IST/UL

(Supervisors: C. Lobato da Silva, F. Santos)

Bruno Santos Raquel, MSc in Biological Engine-

ering, “Desenvolvimento de uma metodologia de

avaliação de riscos para planeamento de activida-

des de manutenção numa indústria farmacêutica”,

IST/UL (Supervisors: M.C. Fernandes, L.P. Fonse-

ca)

Catarina Marciano Alves, MSc in Biological Engi-

neering, “Evaluation of alternative feedstocks for

succinic acid production”, IST/UL (Supervisors:

J.A.L Santos, M. Jansen)

Catarina Sanches Seita, MSc in Biological Engi-

neering, “Flexible Modular Process Design for Enzy-

matic Biodiesel Production”, IST/UL (Supervisors:

L.P. Fonseca, J.M. Woodley)

Cristiana Pardal, MSc in Pharmaceutical Engine-

ering, “Otimização do processo de produção de

uma formulação de comprimidos revestidos”, IST/

UL (Supervisors: J.M.C. Menezes, P. Salústio)

Daniel Pais, MSc in Biological Engineering,

“Towards a Microfluidic Chemoenzymatic Reactor”,

IST/UL (Supervisors: D.M.F. Prazeres, N. Szita)

Diana Santos, MSc in Biomedical Engineering,

“Culture Platform for Induction of Human Induced

Pluripotent Stem Cells into Cortical Neural Stem and

Progenitor Cells under Chemically Defined Condi-

tions”, IST/UL (Supervisors: M.M. Diogo, J.M.S. Ca-

bral)

Diogo Valente, MSc in Biological Engineering,

“cGMP activities in the context of a Contract Manu-

facturing Organization (CMO)”, IST/UL (Supervisors:

D.M.F. Prazeres, R. Fortunato)

Diogo Sebastião, MSc in Biological Engineering,

“Photosynthetic algal microbial fuel cell: Bacteria

and microalgae as biocatalysts for energy produc-

tion and byproducts valorization”, IST/UL

(Supervisors: F.C. Ferreira, C. Matos)

Diogo de Sousa Pinto, MSc in Biotechnology,

“Maximizing human mesenchymal stem/stromal

cells therapeutic potential through 3-D cell cultiva-

tion, IST/UL (Supervisors: C. Lobato da Silva,

J.M.S. Cabral)

Fábio Lampreia, MSc in Biotechnology,

“Overexpressing BDNF in Neural Stem Cells using

non-viral gene delivery strategies, FCT/UNL

(Supervisor: C. Madeira)

Inês Ferreira, MSc in Bioenginneering,

“Biofunctionalization of electrospun poly(epslon-

caprolactone) nanofibers to promote neural stem

cell adhesion, alignment and expansion”, IST/UL

(Supervisors: F.C. Ferreira, M.M. Diogo)

Inês Nunes, MSc in Pharmaceutical Engineering,

“Formulation and Analytical Methods Development

of Feminine Hygiene Specific Products”, IST/UL

(Supervisors: J.M.C. Menezes, H. Marques)

Inês Fernandes Pinto, MSc in Biological Engi-

neering, “Novel capture processes for monoclonal

antibodies purification”, IST/UL (Supervisors: A.M.

Azevedo, M.R. Aires Barros)

Inês Filipa Louro, MSc in Biological Engineer-

ing, “Mesenchymal stem/stromal cells: comparative

study in four cell types on their expandability in cul-

ture and on their safety profiles”, IST/UL

(Supervisors: C. Lobato da Silva, H. Cruz)

Joana Cecilio, MSc in Pharmaceutical Enginee-

ring, “Desenvolvimento de Métodos de Espectrosco-

pia de Infravermelho Próximo com Aplicação na

Industria Farmacêutica”, IST/UL (Supervisors:

J.M.C. Menezes, S. Rosa)

Inês Clemente, MSc in Biological Engineering,

“Encapsulation of Lactobacillus casei and its stability

in model foods”, IST/UL (Supervisors: M. Mateus, S.

Horáčková)

Joana Faustino, MSc in Biological Engineering,

“Off-line Dynamic Image Analysis vs PAT Monitoring

Tools on a Lab-Scale Hot Melt Coating Process”,

IST/UL (Supervisors: J.M.C. Menezes, S. Sacher)


Joana Carmelo, MSc in Biological Engineering,

“Optimizing the production of human mesenchymal

stem/stromal cells in xeno-free microcarrier-based

reactor systems”, IST/UL (Supervisors: C. Lobato

da Silva, J.M.S. Cabral)

Joana da Silva, MSc in Biological Engineering,

“Characterization and modulation of central nervous

system immune response following transplantation

of mesenchymal stem cells into the mouse brain,

IST/UL (Supervisors: C. Lobato da Silva, P.

Ponsaerts)

Joana Galante, MSc in Biological Engineering,

“Vegetable Protein Functionality. From Milk Ana-

logue to Fiber”, IST/UL (Supervisors: M. Mateus, F.

van de Velde)

João Carlos da Silva, MSc in Biomedical Engi-

neering, “Genetic engineering of synovial-derived

mesenchymal stem cells for cartilage regeneration,

IST/UL (Supervisors: C. Madeira, J.M.S. Cabral)

João Belchior, MSc in Biotechnology, “Screening

and evaluation of synthetic protein-mimic affinity

ligands for the purification of plasmid DNA, IST/UL

(Supervisors: M.A. Taipa, D.M.F. Prazeres)

João Crispim, MSc in Biological Engineering,

“High throughput screening platform for embryonic

development in vitro”, IST/UL (Supervisors: C. Lo-

bato da Silva, E. Vrij)

João Monteiro, MSc in Biotechnology,

“Establishment of a novel process for the purifica-

tion of cutinase with triazine-scaffolded synthetic

affinity ligands, IST/UL (Supervisor: M.A. Taipa)

Leonor Serra, MSc in Biological Engineering,

“Simultaneous Saccharification and Fermentation

for the Production of Itaconic Acid with Ustilago

maydis, IST/UL (Supervisors: J.A.L. Santos, D.

Kreyenschulte)

Liliana Agostinho, MSc in Biomedical Engineer-

ing, “Strategies for optimization of ex-vivo expansion

of human hematopoietic stem/progenitor cells from

the umbilical cord blood”, IST/UL (Supervisors: C.

Lobato da Silva, J.M.S. Cabral)

Luana Cardoso Grangeiro, MSc in Biotechnolo-

gy, “Preparation, characterization and performance

of chromatographic membrane with phenylboronate

ligands for biomolecules purification, IST/UL

(Supervisors: M. Mateus, A.M. Azevedo)

Luís Carreira, MSc in Biotechnology, “Evaluation of

rpiA promoter strength in plasmid DNA production”,

IST/UL (Supervisor: G.A. Monteiro)

Luís Carreira, MSc in Biological Engineering,

“Handling complex GC-MS-based metabolomics

data: A uni- and multivariate statistical analysis ap-

proach”, IST/UL (Supervisors: J.M.C. Menezes, R.

Duarte)

Mafalda dos Santos, MSc in Biological Enginee-

ring, “Implementação de normas específicas para o

desenvolvimento e produção de dispositivos médi-

cos e o seu impacto qualitativo nas atividades de

IDI num contexto de "start-up" tecnológica”, IST/UL

(Supervisors: D.M.F. Prazeres, A. Soares)

Marcelo da Silva, MSc in Biological Engineering,

“Advanced numerical techniques for optimal experi-

mental design applied to microbial kinetics”, IST/UL

(Supervisors: A.M. Azevedo, J. Van Impe)

Márcia Antunes, MSc in Biological Engineering,

“Production of recombinant human xanthine oxidase

in E. coli and optimization of its application for pre-

parative synthesis of oxidized drug metabolites, IST/

UL (Supervisors: A.M. Azevedo, M. Kittelmann)

Margarida Braga, MSc in Biological Engineering,

“Análise instrumental da textura em produtos de

panificação”, IST/UL (Supervisors: M. Mateus, M.

Esquível)

Margarida Azevedo, MSc in Biotechnology,

“Improvement of avian influenza DNA vaccine can-

didates: The impact of antigen-targeting sequences,

IST/UL (Supervisors: G.A. Monteiro, M. Fevereiro)

Maria Gonçalves Fernandes, MSc in Biological

Engineering, “Study of autophagy in Tauopathies,

IST/UL (Supervisors: F.C. Ferreira, H. Vieira)

Maria João Sebastião, MSc in Biotechnology,

“Expansion of human Neural Stem Cells in micro-

carrier-based spinner flask culture systems, IST/UL

(Supervisors: M.M. Diogo, C.A.V. Rodrigues

Marilena Ornelas, MSc in Biological Engineer-

ing, “Aggregation behaviour of globular proteins”,

IST/UL (Supervisors: M. Mateus, F. Van de Velde)

Marta dos Santos Matias, MSc in Biological En-

gineering, “Estratégias de Melhoria Contínua de

Processos: Monitorização e Optimização em Linhas

de Produção Alimentar”, IST/UL (Supervisors: M.

Mateus, C. Faustino)

Miguel Luís Ribeiro, MSc in Pharmaceutical En-

gineering, “Implementation of an anti-counterfeiting

device - enhancing supply chain robustness by a

Risk management approach”, IST/UL (Supervisors:

J.M.C. Menezes, J. Moreira)

Mónica Inês Peralta, MSc in Biological Enginee-

ring, “Validação de Sistemas informatizados”, IST/

UL (Supervisors: L.P. Fonseca, D. Silva)

Olga Sofia Reis, MSc in Pharmaceutical Engi-

neering, “Evaluation of a Fluidized Bed Wet Granu-

lation Process using a QbD approach”, IST/UL

(Supervisors: J.M.C. Menezes, J. Abreu Pinto)

PedroSilva, MSc in Biomedical Engineering,

“Purification of Human Induced Pluripotent Stem

Cell-Derived Cells for Regenerative Medicine Appli-

cations”, IST/UL (Supervisors: M.M. Diogo, J.M.S.

Cabral)

Pedro Pereira, MSc in Biological Engineering,

“Biomimetic replicas - Transfer of complex architec-

tures from plant surfaces onto polymeric materials”,

IST/UL (Supervisors: D.M.F. Prazeres, G.A. Mon-

teiro)

Pedro Couto, MSc in Biological Engineering,

“Comparative Analysis of Two Different Isolation

and Cryopreservation protocols of Human Mesen-

chymal Stem/Stromal Cells from the Umbilical Cord

Matrix”, IST/UL (Supervisors: C. Lobato da Silva, C.

Cardoso)

Raquel Santos, MSc in Biotechnology, “An alterna-

tive capture step for monoclonal antibodies: phenyl-

boronate as a new multi-modal ligand”, IST/UL

(Supervisors: A.M. Azevedo, M.R. Aires Barros)

Rita Pais, MSc in Biological Engineering, “Estudo

da complexação do limoneno com ciclodextrinas

estruturalmente diferentes”, IST/UL (Supervisors: M.

Mateus, C.M.M. Duarte)

Rúben Soares, MSc in Biotechnology, “Integrated

Extraction, Concentration and Quantification of

Ochratoxin A in Wines using a Microfluidic Aqueous

Two Phase Extraction coupled to a Fluorescence

Linked Immunosorbent Assay, IST/UL (Supervisors:

M.R. Aires Barros, J.P Conde)

Sandra Bernardo, MSc in Biotechnology,

“LYTAG-driven Integrative Platform for Purification

of Monoclonal Antibodies by Aqueous Two-phase

Systems, IST/UL (Supervisors: M.R. Aires Barros,

A.M. Azevedo)

Sandra Margarido, MSc in Biological Enginee-

ring, “Implementação de uma metodologia de análi-

se sensorial no plano de controlo de qualidade dos

xaropes de glucose-frutose”, IST/UL (Supervisors:

J.A.L. Santos, M.R. Oliveira)

Sara Cardoso, MSc in Biological Engineering,

“Testing of CIM™ monolithic chromatographic sup-

ports for plasmid DNA purification, IST/UL

(Supervisors: D.M.F. Prazeres, U. Černigoj)

Susana Santos, MSc in Biological Engineering,

“Growth and cell cycle kinetics of AML and CLL cell

lines in a 3D bone marrow biomimicry under oxida-

tive and starvation stresses”, IST/UL (Supervisors:

F.C. Ferreira, A. Mantalaris)

Tânia Baltazar, MSc in Biotechnology,

“Monolayer Differentiation of Human Induced Plu-

ripotent Stem Cells (hiPSC) into Cardiomyocytes,

IST/UL (Supervisors: M.M. Diogo, J.M.S. Cabral)

Tatiana Sirgado, MSc in Biomedical Engineering,

“Human Mesenchymal stem cells cultivation on nat-

ural/synthetic polymeric supports, IST/UL

(Supervisors: F.C. Ferreira, C. Lobato da Silva)

Teresa Pereira, MSc in Biological Engineering,

“Non-viral engineered human mesenchymal stem/

stromal cells to promote angiogenesis”, IST/UL

(Supervisors: C. Lobato da Silva, G.A. Monteiro)

Tiago Ferro, MSc in Biomedical Engineering and

Biophysics, “Isolation, characterization and ex-vivo

expansion of human synovial tissue derived-

mesenchymal stem/stromal cells”, FC/UL

(Supervisors: J.M.S. Cabral, Hugo Ferreira (FC/UL))

Tiago Pinto, MSc in Biological Engineering,

“Production of biohydrogen through the fermentation

of Spirogyra sp. biomass by Clostridium butyricum,

IST/UL (Supervisors: C.C.C.R. de Carvalho, P. Silva

Moura)

Vanessa Silva, MSc in Biological Engineering,

“Fed-batch production of FAME-biodiesel from rape-

seed oil catalysed by a liquid lipase formulation –

optimizing process parameters to maximize catalyst

productivity”, IST/UL (Supervisors: L.P. Fonseca,

J.M. Woodley)

Vasco Silva, MSc in Biotechnology, “Preparation

and characterization of chitosan nanoparticles for

gene delivery, IST/UL (Supervisor: M. Mateus)

Vera André, MSc in Biological Engineering,

“Monitorização e Controlo da Segurança Alimentar

na Produção Industrial de Snacks”, IST/UL

(Supervisors: M. Mateus, A. Parreira)


Staff Faculty

Joaquim M.S. Cabral

Maria Raquel Aires-Barros

Duarte Miguel Prazeres

Luís Fonseca

José Menezes

Cláudia Lobato da Silva

Gabriel Monteiro

José Santos

Maria Ângela Taipa

M. Margarida Diogo

Marília Mateus

Research Scientists

Carla C.C.R. de Carvalho

Frederico Ferreira

Ana Azevedo

Pedro Fernandes

Teresa Catarina Madeira

Post-doctoral Fellows

Ana Fernandes-Platzgummer

Carlos Rodrigues

Dragana de Barros

Marisa Salgueiro

Nuno Lourenço

Sara Badenes

Sofia Martins

Sudarsu Ramanaiah

Tiago Fernandes

PhD Students

Alexandra Hertrampf

Ana Rosa

António Soure

Aruna Santhagunam

Cláudia Miranda

Daniel Camarneiro Silva

Filipe Carvalho

Francisco Moreira

Geisa Gonçalves

Gonçalo Rodrigues

Inês Fernandes Pinto

Irina Simões

Javad Hatami

Joana Boura

João Guerreiro

João Trabuco

Jonhathan de la Vega

Jorge Pascoal

Luís Raiado Pereira

Lúcia Volta e Sousa

Márcia Mata

Marisa Santos

Marta Costa

Michaela Simcikova

Miriam Sousa

Nuno Faria

Rimenys Carvalho

Rui Carvalho

Salomé Magalhães

Sofia Duarte

Tiago Dias

Tomás Dias

Master Students

Alice Portela

André Nascimento

Carlos Rodrigues

Cátia Jorge

Diana Marques

Diana Santos

Dina Antunes

Diogo Pinto

Fábio Gonçalves

Fábio Lampreia

Inês Ferreira

Inês Pimentel

Isabel Pinto

João Belchior

João Monteiro

João Silva

Liliana Agostinho

Liliana Brito

Luana Grangeiro

Luis Carreira

Margarida Azevedo

Maria João Sebastião

Mariana Pina

Raquel Santos

Rita Fernandes

Samuel Jorge

Sandra Bernardo

Sara Mateus

Tânia Baltazar

Tatiana Sirgado

Teresa Trindade

Tiago Ferro

Vasco Silva

Research Assistants

Andreia Fernandes

Fátima Cristina Pinto

Joana Carmelo

Joana Serra

Jorge Paulo

Maria João Jacinto

Marina Monteiro

Pedro Prereira

Ruben Soares

Sara Matias

Sara Rosa

Technician

Ricardo Pereira

BERG

BioEngineering Research Group

Institute for Biotechnology and Bioengineering

Instituto Superior Técnico

Av. Rovisco Pais

1049-001 Lisbon

Portugal

www.ibb.pt/berg

berg 2013

Documents

research activities

biocatalysis laboratory

research scientists

research team

stem cell bioengineering

research group main

bioprocess engineering

main research topics