Research Area Coordinator: Gabriel Monteiro

Microorganisms are critical for the biosynthesis of biomolecules. By harnessing the efficient and versatile capabilities of microorganisms such as bacteria and yeast, a wide range of valuable compounds can be produced.  We harness the efficient and versatile capabilities of microorganisms such as bacteria (e.g. Escherichia coli, Lactococcus lactis and Vibrio natriegens) and yeast for the biosynthesis of nucleic acids (mRNA, plasmid DNA, minicircles, single stranded DNA), recombinant proteins including enzymes (DNA polymerases, DNA helicases, chitinases), antibody fragments and nanocages. Other research avenues include the development of microbial factories that may play a crucial role in advancing sustainable economic practices (e.g. bio cementation, biorefineries).

Research Area Coordinator: Ana Rita Silva Santos

One of the keys to increasing access to life-saving biopharmaceuticals (e.g. antibodies, recombinant proteins, nucleic acids) is to increase their affordability. We contribute to increase the efficiency of downstream processing, the costliest segment of biomanufacturing, by tackling process bottlenecks and investigating continuous manufacturing solutions. This encompasses the development of efficient and affordable solutions for 1. the purification of monoclonal antibodies, antibody fragments, proteins, single-stranded DNA, plasmids, and plasmid-based vectors (e.g. minicircles), and bacteriophages, 2. the optimization of the production of mRNA and of dsRNA by in vitro transcription, of ssDNA templates by asymmetric PCR or bacteriophages, and of protein nanocages by E. coli cells and 3. the biomanufacturing of new generations of DNA modifying enzymes. We also explore new materials, technologies, and designs to implement unit operations such as lysis, (e.g. oscillatory reactors), chromatography (e.g. 3D-printed monoliths) and membrane filtration (e.g. centrifugal filters).

Research Area Coordinator: Ana Margarida Azevedo

Long development timelines and inefficient operation modes are two important bottlenecks of biologically based manufacturing. We explore miniaturization of platform technologies, continuous biomanufacturing and digitalization. Miniaturization is directed to the definition of upstream/downstream operating conditions, whereas continuous biomanufacturing is researched to improve efficiency, reduce costs, enhance product quality, and provide real-time control. The digitalization of biomanufacturing processes is crucial for enhancing efficiency, reducing costs, and ensuring precise quality control in the production of biopharmaceuticals and advanced therapy modalities. We specifically address the following research question “How to develop and incorporate a digitalization framework in the conceptual design, research and development of biomanufacturing processes?”.

Research Area Coordinator: Pedro Fonte

Encapsulation provides protection while enhancing functionality and bioavailability of small molecules and biomolecules. We study different types of nanocarriers, mainly polymer nanoparticles and lipid-based delivery systems as liposomes, solid lipid nanoparticles and nanostructured lipid carriers to deliver drugs, biopharmaceuticals, and food ingredients. Our efforts are directed towards the chemical modification of nanoparticles, the application of innovative polymers, the development of nano-based pharmaceutical formulations to enhance structural stability of loaded drugs and the performance of nanocarriers, and the lyophilization of biopharmaceuticals. Examples of research lines pursued include encapsulation of insulin for wound healing, probiotic cells for cancer therapy and CRISPR/Cas9 constructs for genome editing, development of compositions for dsRNA delivery, and exploration of DNA-origami based delivery methodologies.

Research Area Coordinator: Carla C.C.R. de Carvalho

The Marine Biotechnology area aims at the development of bioprocesses using bacterial cells and their enzymes. This involves sampling in marine biodiversity hotspots and extreme environments, the isolation of microorganisms under laboratorial conditions and the screening for enzyme activities, and the production of commercially interesting metabolites. The current library of bacterial isolates, has several strains able to convert industrial revelant substrates. The application of bioprocess engineering has allowed the development of bioprocesses based on whole cells and enzymes, at the L-scale, and suitable purification and analytical methods for the production of compounds, for e.g. the food, cosmetic, and textile industries. Bacterial strains for the bioremediation of toxic compounds have also been isolated and applied.

Research Area Coordinator: Maria Teresa Cesário

In the perspective of a Circular Economy, residual biomass, marine or terrestrial, owe to be processed to new end-products or as raw materials to be reincorporated into production cycles.  Aiming at this, our group is using fractionation and/or fermentation technologies to upgrade biomass or their fractions to value-added products.

The carbohydrate fraction of lignocellulosic agricultural residues, vegetable kitchen waste and of macroalgae has been used as carbon source in biological processes to produce bacterial metabolites namely biodegradable polyesters – polyhydroxyalkanoates (PHAs) and organic acids (gluconic or xylonic acids). Bioreactor cultivations operating either in fed-batch or in continuous mode have been developed aiming at high sugar conversions and productivities. Both terrestrial and marine PHA-producing bacteria have been used as biocatalysts.

Besides the carbohydrate fraction, macroalgae (seaweed) are rich in proteins and bioactive molecules like peptides, polyphenols and carotenoids. Biorefinery processes aiming at the cascade extraction of these fractions are being developed. In particular, the extraction of the protein fraction using aqueous solutions and more recently green solvents is being assessed to being used as ALTERNATIVE PROTEINS for aquafeed. Besides extraction, microbial protein ingredients obtained through the fermentation of macroalgae have been targeted as Alternative Proteins. Fermentation decreases crude fibre and improves algal protein bio-accessibility, content and quality. Further, the nutritional and bioactive properties of these products are improved due to microbial vitamins, proteins and essential amino acids.

Recently, underexploited residual marine biomass such as marine invertebrate castoffs from bivalve molluscs and cephalopod is being upgraded through fermentation by yeasts and/or bacteria into microbial protein biomasses for more nutritious, high-value and sustainable food, feed and non-food products.

Research Area Coordinator: Luis P. Fonseca

Polymers via Biocatalysis and Green Chemistry like polyesters (IST-patent) and polyamides with pendent functional groups (e.g., hydroxy, carboxylic, amine, epoxy, thiol, vinyl, others) that meet the manufacturers’ performance requirements and add functionality for textile, automotive, furniture, and polymeric resins applications. Additionally, the novel polymers also include eco-design principles, i.e., incorporate strategic points in the polymer backbone chain that allow faster biodegradability/compostability and/or hydrolysis of cleavage bonds particularly -C-O- and/or -C-N- with the release of monomers, oligomers, and/or small polymer fractions that are fed to a new cycle of polymer production on the development of closed-loop recycling technologies contributing for an innovative plastic circular economy.

Research Area Coordinator:  Ana Lanham

Bioprocesses for wastewater treatment is the largest biotechnological application by volume in the world. These processes rely on the microbial, metabolic and eco-physiological diversity and resilience of open microbiomes applied to engineered systems to treat water, waste and wastewater and to recover valuable resources such as fine chemicals, polymers, nutrients and energy.

This area aims to understand these systems and their microbiomes, so that we can optimise, or design, new and more fitting processes underpinned by the concepts of circular, sustainable and zero-waste systems.

Our team’s expertise includes designing experimental and modelling studies both at lab and full scale using various microbiological techniques, from microscopy to metagenomics, and combining this with bioprocess engineering skills in various bioreactor designs. We have worked with a wide range of partners, from academia to water utilities and industrial partners, at national and international level. Our interests cover microbial, and microalgae-bacteria consortia systems and more recently the impact of viromes (phage) on open microbiomes for the purpose of organic feedstock fermentation into chemical building blocks, and wastewater treatment, namely advanced biological phosphorus removal and textile dye bioconversion.

Research Area Coordinator:  Frederico Ferreira

The focus areas pMESH at 2BRG and dMESH at SCERG operate synergistically to foster collaborative research at Alameda and Tagus Park.

Aligned with 2BRG mission, pMESH contributes to foster circular and bioeconomy by (i) developing new processes to valorises agro-industrial effluents into added value products, such as biosurfactants, fuels and enzymes exploiting non-conventional yeasts and designing environmentally friendly solutions for the cosmetics, detergents and bioremediation industries, (ii) developing novel nanostructures materials to support health applications as well as size and molecular recognition based separations, and (iii) optimization of novel (bio)reactors and processes to enhance food and pharma production  sustainability. pMESH holds proprietary knowledge on processes, bioreactors, separations, as well as new materials such as functional nanoparticles, molecular imprinted polymers and membranes (PT106959, PT107637, PT109480, PT117220, PT117583 PT118115, PT118493).

Ongoing and past pMESH’s projects include mannosylerythritol lipid production and applications to cosmetics and fuels, (SURFsUp, Cruise, Mero), genotoxic removal of active pharmaceutical ingredients (GenoSep, SelectHost), water reuse and added value products within lupin beans processing (Biorg4WasteWaterVal+).

pMESH holds labs on Biosurfactants and Biofuels, Nanomaterials for Bioeconomy and Processes for Sustainable Food and Pharma.

Laboratories:

Processes for Sustainable Food and Pharma (Pro-Sus) (PI: Frederico Ferreira).

Biosurfactants and Biofuels (BioSurfuel) (PI: Nuno Faria)

Nanomaterials for Bioeconomy (NanoBio) (PI: Teresa Esteves)

Research Area Coordinator: Margarida Diogo

BEPStem holds labs on: Stem Cell Advanced Tissue Models (PI Margarida Diogo), Stem Cell Biosystems Engineering (PI Tiago Fernandes) and Stem Cell Epigenetics (Simão Rocha).

We are using human pluripotent stem cells (hPSCs) to develop advanced models of healthy and diseased human tissues, including neural, cardiac, and hepatic tissues. By combining stem cell biology with engineering approaches, we are advancing applications in disease modeling, drug screening, toxicology assays, and regenerative medicine. Our improved reprogramming techniques and innovative gene editing strategies enable us to create disease-specific human induced pluripotent stem cell (hiPSC) lines and their isogenic controls. We are actively studying the consequences of epigenetic dysfunction in hiPSC fate. Additionally, we are using innovative genome editing strategies to generate hPSCs with genetic compatibility for patient-specific regenerative medicine applications. Through novel biosystems engineering approaches, we are uncovering molecular mechanisms that influence hiPSC pluripotency and differentiation. We apply this knowledge to create artificial niches for more controlled hiPSC differentiation using bioengineering strategies like micropatterning, microfluidics, and microencapsulation. Among other applications, these tools will enhance the vascularization of our hiPSC-based 3D tissue models.

Laboratories:

Stem Cell Advanced Tissue Models Lab

Stem Cell Biosystems Engineering Lab

Stem Cell Epigenetics Lab

Research Area Coordinator: Cláudia Lobato da Silva

DMCMT holds labs on : Modulation of the Stem Cell Niche (PI Cláudia Lobato da Silva) and Smart Bioprocess Design for Cellular and Molecular Therapies (PI Ana Fernandes-Platzgummer)

We are dedicated to advancing Regenerative Medicine through innovative, collaborative research to address the critical manufacturing challenges of cell-based therapeutics. In the field of umbilical cord blood-derived hematopoietic stem/progenitor cells (HSPC), we are developing customized bioreactors and studying the interactions between HSPC and their niche to enhance their expansion. For mesenchymal stromal cells (MSC) and their extracellular vesicles (EVs), we have been establishing scalable and controlled manufacturing processes, while aiming to improve the therapeutic functionality of these cell-based products. We are also advancing the manufacturing of chimeric antigen receptor natural killer (CAR-NK) cells and their EVs through innovative transduction techniques and precise quality control methods. Moreover, to address the challenges of cell storage and transportation in a therapeutic context, we are studying encapsulation technologies to preserve cell viability and functionality. Importantly, we participate in EU-funded collaborative projects to scale-up the production of human skeletal and smooth muscle cells for Tissue Engineering settings. More recently, in the context of cellular agriculture, we are establishing manufacturing platforms for expanding and differentiating cells from relevant species for cell-based food production (pig, bovine and chicken).

Laboratories:

Modulation of the Stem Cell Niche Lab

Smart Bioprocess Design for Cellular and Molecular Therapies Lab

Research Area Coordinator: Frederico Ferreira

The focus areas dMESH at SERG and pMESH at 2BRG operate synergistically to foster collaborative research at Tagus Park and Alameda.

dMESH holds labs on: Bioelectronics for Cancer Therapies, Biomimetic and Functional Regenerative Biomaterials, Bioreactor and Biomaterial Technologies for Stem Cell Manufacturing  and Sustainable Tissue Engineering, Materials and Processes. 

Aligned with SCERG mission, dMESH contributes to develop advanced health and food products, fostering the fields of (i) additive manufacturing and biomaterials, developing new stimuli responsive biomaterials, nanoparticles, scaffolds, and bioinks for the regeneration of bone, cartilage, osteochondral, neural, cardiac, among other tissues as well as wireless strategies for regenerative and cancer therapies; (ii) modelling and machine learning/artificial intelligence approaches to generate digital twins of novel bioreactors, scaffolds, devices and processes and (iii) sustainable development of cellular agriculture, including optimization studies on fish tissue formation and bioreactor-based processes, designing novel vegan and edible scaffolds, bioinks, microcarriers, and structured food; and exploiting electrical and physical stimulation to enhance tissue maturation.

Ongoing and past dMESH’s projects are on cell agriculture, bioreactors, vascularization, cancer therapies, and neural and osteochondral regeneration.

Laboratories:

Sustainable Tissue Engineering, Materials and Processes (STEM-P) (PI: Frederico Ferreira)

Bioreactor and Biomaterial Technologies for Stem Cell Manufacturing Lab (PI: Carlos Rodrigues)

Bioelectronics for Cancer Therapies (PI: Paola Alberte)

Biomimetic and Functional Regenerative Biomaterials (PI: João Silva)

Research Area Coordinator: Isabel Sá-Correia

The new Bio-based Economy requires the development of large-scale economically viable yeast-based-processes for efficient valorisation of residues and low-cost feedstocks to produce biofuels, chemicals, and materials. Our research programs explore yeast diversity, molecular and cellular biology, and functional and comparative genomics to understand and improve yeast bioconversion.  Special emphasis is given to the holistic understanding of molecular targets and mechanisms underlying yeast response and tolerance to stresses of biotechnological relevance, in particular acetic acid and other short- and medium chain monocarboxylic acids, methanol, and other inhibitors present in lignocellulosic hydrolysates. The role in multistress tolerance of yeast cell envelope, including the cell wall and plasma membrane embedded multidrug/multixenobiotic resistance transporters, H+-ATPase and other transporters involved in ion homeostasis and its regulation, is under study, especially in the model yeast Saccharomyces cerevisiae. Non-conventional yeast species/strains that can efficiently consume all the major carbon sources present in promising feedstocks, exhibit a robust phenotype and interesting biosynthetic pathways, are being isolated in association with commercial (micro)algae cultivation, molecularly identified, and screened for efficient production of lipids, carotenoids, and biosurfactants. Attention is given to the frequently isolated oleaginous red yeasts of the genus Rhodothorula and other yeasts also with potential as probiotics.

Research Area Coordinator: Nuno Mira

The SynthYeasts’ team explores the development of metabolic engineering approaches (supported by computational metabolic modelling) to improve production of add-value bulk chemicals in Yeasts,  including of molecules that are “new-to-nature” and for which synthetic biochemical pathways are designed and customized. Another strong focus is the work on the biology, physiology of wine Yeasts (specially those belonging to the Saccharomycodeacea family) to be used in the industry as starter cultures with multi-functional purposes including bio-flavourants and biocontrol agents. The third vector of our lab is the development of non-conventional treatments, based on probiotic lactobacilii species of the human microbiome, for the treatment of infections caused by Candida species.

Research Area Coordinator: Miguel Teixeira

The FunPath Lab is focused on understanding fungal infections caused by human pathogenic yeasts of the Candida genus, from a genome-wide perspective, and on using this information to improve therapeutic options.

Our current projects within this subject include:

–  The use of genomics, transcriptomics, proteomics and chemogenomics to unravel the evolution of Candida clinical isolates towards clinically-relevant phenotypes.

–  The development of computational tools and models to study transcriptional regulation and metabolism in Candida and Cryptococcus at a genomic scale, including particularly the Yeastract+ database.

– The characterization of the large array of multidrug resistance transporters and of the transcription regulatory networks controlling Candida response to clinically-relevant stresses and conditions.

Altogether, the gathered knowledge is expected to aid in the design of novel tools for: i) the diagnosis of drug resistance in clinical isolates; ii) identification of new drug targets that may act as determinants of biofilm formation, drug resistance or virulence; iii) the design of more effective drugs, to be used alone or in combination therapy with currently existing antifungals.

Research Area Coordinators: Rodrigo Costa / Tina Keller-Costa 

Life as we know is strongly underpinned by inter-domain symbiotic relationships (Bacteria-Archaea-Eukarya). Ranging from simple associations dominated by a single or few mutualist(s), such as the squid-Vibrio and gutless worm symbioses, to the complex “microbiomes” associated with the human gut, plant roots or marine corals and sponges, it seems indisputable that microorganisms in the three domains of life are capable of populating every micro-niche offered for colonization by their animal and plant hosts.

The Microbial Ecology and Evolution Research Group (MicroEcoEvo) at BSRG addresses the causes and consequences of microbial diversity and function in natural and fabricated biomes – with emphasis on Eukaryote-Prokaryote symbioses in the marine realm -, their implications to host/ecosystem health and climate regulation, and potential use as renewable sources of innovative biotechnologies. Research projects focus on harnessing the metabolism of cultured and uncultured (“microbial dark matter”) bacterial symbionts to develop microbiome engineering approaches to (i) suppress microbial diseases and mitigate climate change stressors in aquaculture and coral reef ecosystems, and (ii) design marine-based bioproducts of application across multiple sectors (e.g., health, environment, food, and feed) to leverage the circular blue bioeconomy. Model study systems include the microbiomes of marine sponges, corals, algae, and fish, as well as polar microbiomes.

Research Area Coordinators: Jorge Leitão / Sílvia Sousa / Joana Feliciano

Our research group is dedicated to the uncovering of the still enigmatic roles played by non-coding RNAs (sRNAs) in the biology and pathogenesis of bacteria of the Burkholderia cepacia complex (Bcc). Despite their critical role in post-transcriptional regulation of gene expression and fast adaptation to ever changing environments, the functions of these sRNAs remain largely unexplored. We have recently identified over a hundred of virulence-related novel sRNAs, and our current research focuses on understanding their biological roles, especially those expressed under infection-like conditions. Our work also delves into the functional analysis of sRNAs within extracellular vesicles secreted by Bcc during infection-like conditions, investigating their potential role as modulators of host responses. Additionally, we are identifying and characterizing immunogenic surface-exposed proteins, aiming to develop new immune-based strategies to combat Bcc infections. We value our research collaborations, and we particularly keen on the characterization of novel antimicrobial molecules with therapeutic potential. We are also trying to push the boundaries of microbial pathogenesis and immune response, striving to develop innovative solutions to combat Bcc infections.

Research Area Coordinator: Leonilde Moreira

In our research at the Bacterial Pathogenomics Lab, we study the molecular mechanisms that enable the opportunistic pathogen Burkholderia multivorans to adapt to the cystic fibrosis (CF) lung, a condition that frequently leads to chronic respiratory infections. Comparative genomics studies of isolates recovered from chronic CF infections over time have identified a number of relevant genes and pathways that are currently under investigation. Our findings indicate that the development of multicellular aggregates, also referred to as non-surface attached biofilms, is a common feature that likely plays a crucial role in bacterial adaptation and long-term survival in the host. By employing genetic and genomic approaches, we have pinpointed a number of genes that play a role in the formation of aggregates, and we are currently investigating them further. Specifically, the bep genes are currently being studied as they are involved in the production of the main polysaccharide found in the extracellular matrix. Additionally, efforts are underway to hinder the formation of aggregates in B. multivorans. To accomplish this, we primarily rely on the utilization of glycoside hydrolase (GH) enzymes that are naturally produced by these bacteria. The testing of GHs enzymatic activities to disrupt biofilms and aggregates formed by single and multiple species involves a combination of biochemistry, genetics, and microscopy analysis.

Research Area Coordinators: Arsénio M. Fialho / Dalila Mil-Homens

Antibiotic resistance in bacteria is rampant and has created major problems in health care worldwide. Of particular concern is the emergence of multi-drug-resistant bacteria, such as the ones belong to the Burkholderia cenocepacia complex (Bcc) group. These bacteria are opportunistic and prevalent in intensive care units. In addition, they appear to be highly adapted to the respiratory tract and are problematic pathogens in cystic fibrosis patients. In our lab (Bioadhesion Lab), we study the phenomena of bacterial adhesion to host cells and its significance in Bcc pathogenesis. We address this issue from two different perspectives:

1) – The identification and functional characterization of adhesin determinants, particularly those belonging to the class of trimeric autotransporter adhesins (TAAs). To study the contribution of adhesins to pathogenesis, we employ a multidisciplinary approach that includes molecular and cell biology, genomics and transcriptomics, biochemistry, and biophysics.

2)  – Investigate the effectiveness of anti-adhesion therapy in Bcc infection control. To achieve this, we study the anti-adhesive properties of a selected panel of host glycans.

Finally, we focused on the development of a non-mammalian animal model (the larvae of the greater wax moth Galleria mellonella) to dissect Bcc virulence and to evaluate drug efficacy and toxicity. We made available a facility at iBB including an insectarium for breeding and maintenance of larvae for in vivo studies. This model system has significant logistical and ethical advantages over mammalian models.

Research Area Coordinator: Nuno Bernardes

Our work is focused on: i) protein- and peptide-based strategies to enhance tumor-targeted delivery and retention of nanosized drug delivery systems, such as polymeric nanoparticles and extracellular vesicles (EVs); and (ii) cell-based theranostics for cancer with clinically relevant therapeutic cells. Currently, we are exploring different technical approaches and 3D cellular models to increase therapeutic efficacies by studying peptide-cell interactions in the tumor microenvironment which can improve the release of cargoes from the carriers and modulate the communication of cancer cells with their microenvironment.

Specifically, our research topics include:

1. Mapping the proximity proteome of the anti-cancer peptide p28 in breast and lung cancer cells to identify uptake mechanisms and new putative drug targets for new drug combinatorial approaches.
2. Improved diffusion and cellular uptake of functionalized nanomedicines, exploring p28-functionalized biomaterials for drug delivery in 2D and 3D models of cancer, such as spheroids.
3. 3D cancer spheroids and organoids to understand mechanisms of drug resistance, provide putative new therapeutic targets, and optimize drug screening protocols.

Research Area Coordinator: Teresa Pinheiro

The two main pillars of current research activities are I) Cellular uptake of nanoplataforms for radiosensitisation; ii) Multimodal imaging based on ion microbeams, mass spectrometry and optical microscopy.

Specifically, new radiosensitizers, such as B/Fe/Au/nanodiamonds platforms are being used and synthesized.  Cell culture models are used to investigate cellular uptake and cellular responses following incubation with the nanoplatforms and irradiation with photon/proton beams. Cell responses include lipidomic/metabolomic changes and genomic instability, whereas cellular targets are being investigated using multimodal correlative imaging approaches.

In order to go beyond the use of 2D cell culture models and to further investigate the cellular radiation response, it is envisaged to develop 3D cell models. This will provide a common basis for investigating radiation effects, which can be used as a model for metastasis simulation and for enhanced precision in subcellular dose distribution.