Booklet H2020 by ITQB UNL

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Table of Contents 4 6 8 12

Foreword About us Horizon 2020 Areas of expertise Cellular and Molecular Biology Molecular and Structural Biology Biotechnology and System Biology Chemical Biology

18 Full list of labs 22 Expertise by lab

Foreword

Europe is facing momentous challenges. It needs to urgently overcome the economic stagnation and be prepared for the longterm challenges of our changing world: globalisation, pressure on resources, and ageing. In such a period of history, Science and Innovation play a key role in building a better and more sustainable society, and Academic Institutions and Companies are central players in this process. Europe does not have a long tradition of cooperation between the two different cultures of the academic and industrial world, in spite of the many attempts made in the last couple of decades. Therefore, a new paradigm needs to be adopted. Horizon 2020, the European Union’s new programme for research and innovation, aims at changing this scenario. It provides funding for every stage of the innovation process, from basic research to market uptake, stimulating Academia and Companies to work side by side to reach common objectives. At Instituto de Tecnologia Química e Biológica António Xavier from Universidade Nova de Lisboa (ITQB-UNL), we aim at reducing the gap between basic research and its translation to the productive sector. Horizon 2020, as other funding programmes, provides instruments to reach this objective, together with other players of the innovation system, including R&D intensive companies. Aiming to reach partners with which to bridge this gap, we hereby present a brief overview of ITQB-UNL’s research groups and areas of expertise.

About us

Instituto de Tecnologia Química e Biológica António Xavier is an academic research centre of Universidade Nova de Lisboa. Its mission is to carry out scientific research and postgraduate teaching in Chemistry, Life Sciences, and Associated Technologies, while also serving the community and promoting science and technology. With over 50 independent teams, ITQB hosts more than 400 researchers, including around 190 PhD holders and 120 PhD students, with different backgrounds and research interests. These numbers also include collaborators from our partner iBET – Instituto de Biologia Experimental e Tecnológica, a private not-for-

The strong expertise in Molecular Biosciences present at ITQB drives research in two strategic societal challenges, focused on the well-being of human societies (Molecular Basis of Health and Disease) and on the environment (Biological Resources and Sustainable Development). ITQB coordinates two Research Units –

profit institute which coordinates the more technological areas.

MOSTMICRO (Molecular, Structural and Cellular Microbiology) and

Researchers benefit from first-rate research facilities and

a third one – iNOVA4HEALTH.

GREEN-IT (Resources for Sustainability) - and is further involved in

equipment, some of which unique in the country. Available support structures include technical and administrative services (e.g., R&D Planning and Management Office, Communication Office, Research Manager, Industry Liaison Office, and Library), and scientific services (e.g., Analytical, Mass Spec, Crystallography and NMR). With a track-record of scientific excellence and a focus on internationalization, ITQB is also a leading centre for advanced training in Portugal.

Horizon 2020 an opportunity for innovative companies

Horizon 2020

What is Horizon 2020? Horizon 2020 is the European Union’s new programme for research and innovation. It provides funding for every stage of the innovation process from basic research to market uptake, in line with the EU’s

Excellent science

commitments under the “Innovation Union”, and will run from 2014

• • • •

to 2020 with an approximate budget just over EUR 70 000 M.

Horizon 2020 is built on three pillars

European Research Council Future and Emerging Technologies Marie Sklodowska-Curie Actions Research Infrastructures

Horizon 2020 is set on three major pillars: (i) Excellent science, which aims to strengthen EU’s position in science, providing a boost to top-level research in Europe; (ii) Strengthen industrial leadership in innovation, which includes major investment in key technologies, greater access to capital and support for SMEs; and (iii) Tackle societal challenges, helping to address major concerns

Industrial leadership

• • •

Leadership in enabling and industrial technologies Access to risk finance Innovation in SMEs

shared by all Europeans. Each of these pillars includes specific programmes and objectives.

Societal challenges

• •

Health, demographic change and well-being

• • •

Secure, clean and efficient energy

•

Europe in a changing world

•

Secure societies

Food security, sustainable agriculture and forestry, marine and maritime and inland water research, and the bioeconomy Smart, green and integrated transport Climate action, environment, resource efficiency and raw materials inclusive, innovative and reflective societies protecting freedom and security of Europe and its citizens

Horizon 2020

Innovative companies and Academia a marriage sponsored by Horizon 2020

Horizon 2020 requires that Academia and innovative companies find areas of common interest and share their expertise, in particular in the following initiatives:

Innovative companies and the public funds Innovative companies create over 80% of the net new jobs, therefore being very important economic drivers. However, industrial partners, in particular SMEs, do not take full advantage of available public funds.

How will Horizon 2020 support innovative companies? In Horizon 2020, SMEs will receive money to cover the whole

The objective of these actions is to ensure the optimum

innovation chain from basic research to innovative products, from

development and dynamic use of Europe’s intellectual capital in

lab to market. Funds will be available for testing, prototyping,

order to generate new skills and innovation, with the objective of:

demonstration and pilot type activities, for business-driven R&D, for promoting entrepreneurship and risk-taking and for shaping demand for innovative products and services. SMEs will receive around 20% of the combined budgets of the “Societal Challenges”-pillar, and of the specific objective “Leadership in Enabling and Industrial Technologies”, part of the “Industrial Leadership”-pillar, which in practice will mean about EUR 8 650 M in EU support for Research and Innovation activities going to SMEs.

Marie Sklodowska-Curie Actions

• Foster new skills through excellent initial training of researchers Innovative Training Networks

• Nurture excellence through cross-border and cross-sector mobility Individual Fellowships

• Stimulate innovation through cross-fertilisation of knowledge Research and Innovation Staff Exchange

Horizon 2020

ITQB and pioneering companies: working together for the Innovation Union ITQB stands out for its unique expertise in Molecular Biosciences, covered by four broad scientific disciplines: Cellular and Molecular Biology, Molecular and Structural Biology, Biotechnology and Systems Biology, and Chemical Biology. These scientific fields strongly contribute to address strategic societal challenges focusing the well being of human societies and on the environment. ITQB has a long tradition of national and international cooperation. Since our very beginning, we are an open institution with longstanding agreements with other organisations to host members performing research with us. We have also a strong participation in international projects, and foreign scientists visiting regularly to spend periods of time at ITQB. Moreover, our researchers are partners in national, European and other international collaborative

Collaborative projects

projects and participate in scientific and technological networks.

As already happened in the previous European framework

Along our history of over two decades, we have gained some expe-

programmes, most of the collaborative projects will require

rience in collaborating with companies, in many cases via Instituto

the participation of companies. In addition, dedicated calls for

de Biologia Experimental e Tecnológica (iBET), a private not-for-

collaborative projects targeted to SMEs will be implemented

profit research organisation that bridges university and industry

in specific areas with the aim of reinforcing the scientific and

research. We recognise that partnering with companies is increas-

technological base of SMEs and of validating innovative solutions.

ingly fundamental to reach EU’s aims of making Europe a world-

These projects should be led by SMEs with R&D capacities

class science performer, removing obstacles to innovation, and

and include the participation of universities, research centres

revolutionising the way public and private sectors work together.

and other industries or industrial associations as appropriate. Importantly, funded projects will be outcome oriented.

Horizon 2020 is the perfect opportunity for us to work together. We invite you to get to know us better, and look at our diverse expertise.

Areas of expertise with list of labs by area

Areas of expertise

Molecular and Structural Biology

Molecular and structural biology allows a mechanistic understanding of how different molecular components work together for particular biological processes. Learning about the structure and function of different biological processes is useful for many applications ranging from drug design and materials development to energy production and bioremediation. There are 18 laboratories with expertise in this area. laboratories in this area are listed on page 12

Cellular and Molecular Biology

Cell and Molecular Biology aims to understand life by looking into how molecules organize themselves within cells. The concerted action of different molecules allows cells to grow, differentiate, divide, and coordinate all the activities that are essential in living systems. This approach is particularly important for understanding the basis of health and disease in different organisms and may have applications in diverse areas from medicine to plant breeding. There are 16 laboratories with expertise in this area. laboratories in this area are listed on page 13

Biotechnology and Systems Biology

Exploiting biological processes, molecules or organisms for developing new products and technologies is the objective of biotechnology. Systems biology takes this idea one step further in the sense that the complex interaction and the dynamics of all the components are taken into account. Applications include plant biotech, food and feed industry, biocatalysis, bioremediation, and biopharmaceuticals. There are 14 laboratories with expertise in these areas. laboratories in this area are listed on page 14

Chemical Biology

This area applies chemical techniques, tools, and analysis to produce synthetic compounds with biological applications or to study biological systems. The broad nature of this discipline is paralleled by the extent of possible applications in the chemical industry, food and feed industry, new materials, waste water treatment, pharmaceutical and cosmetic industry, energy production, and environmental protection (green chemistry). There are 14 laboratories with expertise in this area. laboratories in this area are listed on page 15

Areas of expertise

Molecular and Structural Biology

Applied and Environmental Mycology (Cristina Silva Pereira)

Bacterial Energy Metabolism (Inês Cardoso Pereira)

Biological Energy Transduction (Manuela Pereira)

Biomolecular NMR (Manolis Matzapetakis)

Cell Physiology & NMR (Helena Santos)

CERMAX Facility (Pedro Lamosa)

Industry and Medicine Applied Crystallography (Pedro Matias)

Inorganic Biochemistry and NMR (Ricardo Louro)

Mass Spectrometry (Ana Coelho)

Membrane Protein Crystallography (Margarida Archer)

Microbial & Enzyme Technology (Lígia Martins)

Molecular Genetics of Microbial Resistance (Lígia Saraiva)

Molecular Simulation (António Baptista)

Protein Modelling (Cláudio Soares)

Proteomics Unit (Pedro Matias)

Raman Spectroscopy of Metalloproteins (Smilja Todorovic)

Structural Biology (Carlos Frazão)

Structural Genomics (Maria Arménia Carrondo)

Areas of expertise

Cellular and Molecular Biology Bacterial Cell Biology (Mariana Pinho)

Bacterial Cell Surfaces and Pathogenesis (Sérgio Raposo Filipe)

Cell Physiology & NMR (Helena Santos)

Cell Signalling in Drosophila (Pedro Domingos)

Cellular Neurobiology (Federico Herrera)

Genomics and Stress (Claudina Pousada)

Glycobiology (Júlia Costa) 39 GPlantS (Margarida Oliveira) 40 Microbial Development (Adriano Henriques)

Molecular Genetics of Microbial Resistance (Lígia Saraiva)

Molecular Microbiology of Human Pathogens (Raquel Sá Leão)

Plant Cell Biology (Rita Abranches)

Plant Cell Biotechnology (Pedro Fevereiro)

Plant Gene Regulation (Nelson Saibo)

Plant Metabolomics (Carla António)

Plant Molecular Ecophysiology (Manuela Chaves)

Plant Quantitative Genetics (Carlota Vaz Patto)

Areas of expertise

Biotechnology and Systems Biology Animal Cell Technology UNIT (Paula M. Alves)

Applied and Environmental Mycology (Cristina Silva Pereira)

Biomolecular Diagnostics (Abel Oliva)

Equilibrium and Transport Properties (José Esperança)

GPlantS (Margarida Oliveira) 40 Microbial & Enzyme Technology (Lígia Martins)

Molecular Thermodynamics I (Luis Paulo Rebelo)

Nutraceuticals and Delivery Lab (Catarina Duarte)

Pharmacokinetics and Biopharmaceutical Analysis (Ana Simplício)

Pilot Plant (António Cunha) 55

Plant Cell Biology (Rita Abranches)

Plant Cell Biotechnology (Pedro Fevereiro)

Plant Quantitative Genetics (Carlota Vaz Patto)

Sustainable Separation Technologies (Isabel Marrucho)

Areas of expertise

Chemical Biology Biological Energy Transduction (Manuela Pereira)

Bioorganic Chemistry (Rita Ventura) 31 Cell Physiology & NMR (Helena Santos)

CERMAX Facility (Pedro Lamosa) 35 Coordination and Supramolecular Chemistry (Rita Delgado)

Equilibrium and Transport Properties (José Esperança)

Homogeneous Catalysis (Beatriz Royo)

Inorganic Biochemistry and NMR (Ricardo Louro)

Molecular Simulation (António Baptista)

Molecular Thermodynamics (Luis Paulo Rebelo)

Organometallic Chemistry (Carlos Romão)

Protein Modelling (Cláudio Soares)

Raman Spectroscopy of Metalloproteins (Smilja Todorovic)

Sustainable Separation Technologies (Isabel Marrucho)

Full list of Labs in labâ&#x20AC;&#x2122;s alphabetical order

Full list of labs

Animal Cell Technology UNIT (Paula M. Alves)

Applied and Environmental Mycology (Cristina Silva Pereira)

Bacterial Cell Biology (Mariana Pinho)

Bacterial Cell Surfaces and Pathogenesis (Sérgio Raposo Filipe)

Bacterial Energy Metabolism (Inês Cardoso Pereira)

Biological Energy Transduction (Manuela Pereira)

Biomolecular Diagnostics (Abel Oliva)

Biomolecular NMR (Manolis Matzapetakis)

Bioorganic Chemistry (Rita Ventura) 31

Molecular and Structural Biology

Cell Physiology & NMR (Helena Santos)

Cell Signalling in Drosophila (Pedro Domingos)

Cellular Neurobiology (Federico Herrera)

CERMAX Facility (Pedro Lamosa)

Coordination and Supramolecular Chemistry (Rita Delgado)

Equilibrium and Transport Properties (José Esperança)

Cellular and Molecular Biology

Biotechnology and Systems Biology

Chemical Biology 19

Full list of Labs

Genomics and Stress (Claudina Pousada)

Glycobiology (Júlia Costa) 39 GPlantS (Margarida Oliveira) 40

Molecular and Structural Biology 20

Homogeneous Catalysis (Beatriz Royo)

Industry and Medicine Applied Crystallography (Pedro Matias)

Inorganic Biochemistry and NMR (Ricardo Louro)

Mass Spectrometry (Ana Coelho)

Membrane Protein Crystallography (Margarida Archer)

Microbial & Enzyme Technology (Lígia Martins)

Microbial Development (Adriano Henriques)

Molecular Genetics of Microbial Resistance (Lígia Saraiva)

Molecular Microbiology of Human Pathogens (Raquel Sá Leão)

Molecular Simulation (António Baptista)

Molecular Thermodynamics (Luis Paulo Rebelo)

Nutraceuticals and Delivery Lab (Catarina Duarte)

Cellular and Molecular Biology

Biotechnology and Systems Biology

Chemical Biology

Full list of labs

Organometallic Chemistry (Carlos Romão)

Pharmacokinetics and Biopharmaceutical Analysis (Ana Simplício)

Pilot Plant (António Cunha) 55

Molecular and Structural Biology

Plant Cell Biology (Rita Abranches)

Plant Cell Biotechnology (Pedro Fevereiro)

Plant Gene Regulation (Nelson Saibo)

Plant Metabolomics (Carla António)

Plant Molecular Ecophysiology (Manuela Chaves)

Plant Quantitative Genetics (Carlota Vaz Patto)

Protein Modelling (Cláudio Soares)

Proteomics Unit (Pedro Matias)

Raman Spectroscopy of Metalloproteins (Smilja Todorovic)

Structural Biology (Carlos Frazão)

Structural Genomics (Maria Arménia Carrondo)

Sustainable Separation Technologies (Isabel Marrucho)

Cellular and Molecular Biology

Biotechnology and Systems Biology

Chemical Biology 21

Expertise by lab in labâ&#x20AC;&#x2122;s alphabetical order

Expertise by lab

Animal Cell Technology UNIT Paula M. Alves

What do we do? Our research is centred on the development of bioprocesses and engineering tools for the production of complex biopharmaceuticals. Through this synergy we have gained a significant track record in the production of several human and veterinary virus-based vaccines, recombinant proteins and viral vectors for gene therapy, all with recognized know-how spanning from the initial vector design and cell line development, through all stages of process development and scale-up. A great effort has also been employed in the development of new tools and methodologies for cell therapy applications and also into pre-clinical research involving novel 3D in vitro cellular models either from Stem Cells or from primary cultures of human hepatocytes, cancer and brain cells.

Which expertise can you get from us? Bioprocess engineering, biopharmaceuticals, vaccines, proteins, viral vectors, virus-like particles, gene therapy, cell therapy, cellular models, stem cells, hepatocytes, cell line development

Main fields for collaboration Biopharmaceutical Industry

Paula M. Alves, PhD | marques@itqb.unl.pt

Expertise by lab

Applied and Environmental Mycology Cristina Silva Pereira What do we do? We established a method to recover plant suberin with film forming abilities. The biopolyester films display antimicrobial and antibiofouling properties. We are now investigating their biological properties, crucial for clinical usages. We are elucidating the superior catabolic capacities of fungi\ for degrading hazard halogenated pollutants in soils, analysing individual strains and communities. Data raise new questions on the ecological and environmental roles of fungi. We elucidated how structure rules the toxicity of ionic liquids in filamentous fungi. Even at sub-inhibitory concentrations, they alter the metabolic footprint and activate the biosynthesis of osmolytes and unusual metabolites. We are using ionic liquids in fungal biology, for altering the expression of genes involved in morphogenesis, signalling, secondary metabolism and allergen production.

Which expertise can you get from us? Fungi; fungal biology; bioremediation; biocatalysis; ionic-liquids; eco-toxicity; suberin; secondary-metabolism; proteomics; transcriptomics

Main fields for collaboration Pharmaceutical Industry; Materials; Bioremediation

Cristina Silva Pereira, PhD | spereira@itqb.unl.pt

Expertise by lab

Bacterial Cell Biology Mariana Pinho

What do we do? We study the cell division in cocci, with the aim of identifying mechanisms required for chromosome segregation and selection of the division plane in Staphylococcus aureus, as well as the resistance mechanisms of this bacteria to antibiotics that target the synthesis of the peptidoglycan (the major component of the bacteria cell wall). We also study the mechanisms of localization of Staphylococcus aureus proteins involved in the synthesis of the bacterial surface. This line of work will lead to the construction of a library of reporter strains which express fluorescent derivatives of proteins required for the synthesis of the cell surface. These strains can be used to study the mode of action of new antimicrobial compounds.

Which expertise can you get from us? Bacterial cell biology, antibiotic resistance, Staphylococcus aureus, cell wall synthesis, protein localization

Main fields for collaboration Pharmaceutical Industry

Mariana Pinho, PhD | mgpinho@itqb.unl.pt

Expertise by lab

Bacterial Cell Surfaces and Pathogenesis SĂŠrgio Raposo Filipe What do we do? Peptidoglycan (PGN) is a major component of the cell surface of most bacteria that protects them from substantial osmotic forces, defines their shape and flags their presence to an infected host. In order to understand how the bacteria cell wall is synthesized, organised, modified and degraded during the bacterial cell cycle, our research lines try to answer the following questions: 1. How is the synthesis of PGN coordinated with the assembly of other components of the cell surface in Gram-positive bacteria? 2. Are the various components at the bacterial surface capable of hiding the PGN from the infected host? 3. Do different bacteria rely on distinct strategies to hide the inflammatory PGN macromolecule in different hosts?

Which expertise can you get from us? Gram-positive bacteria, Staphylococcus aureus, Streptococcus pneumoniae, Bacterial cell biology, Bacterial cell surfaces, Peptidoglycan, Pathogen-associated molecular pattern (PAMPs), Innate immunity, HPLC, Fluorescence microscopy

Main fields for collaboration Pharmaceutical Industry and Plants

SĂŠrgio Filipe, PhD | sfilipe@itqb.unl.pt

Expertise by lab

Bacterial Energy Metabolism InĂŞs Cardoso Pereira What do we do? We study the energy metabolism of a group of anaerobic bacteria that use sulphur compounds for respiration. These organisms are of great environmental importance given their key role in the global Sulphur cycle, and are especially relevant in marine environments and/or the human or animal gut. At a fundamental level we are interested in how these organisms derive energy from the respiration of Sulphur compounds, and have focused particularly in their membranebound respiratory complexes. At an applied level we study the potential use of these organisms for biological hydrogen production and bioremediarion of metals and pharmaceutical compounds, and also the use of individual enzymes (hydrogenases and formate dehydrogenases) for bioelectrochemical applications (H2 sensor; H2 production; CO2 sequestration).

Which expertise can you get from us? Biological hydrogen production; Bioremediation; Environmental microbiology; Sulphur Metabolism; Marine bacteria; Bioenergetics; Membrane-bound Proteins; Sulphate and Nitrate Reducing Bacteria; Sulphur Cycle

Main fields for collaboration Energy, Bioremediation, Waste water treatment, Petroleum industry

Expertise by lab

Biological Energy Transduction Manuela Pereira What do we do? In our group we study the molecular mechanisms of electron transfer, ion translocation and their coupling. As model systems we use respiratory chains and their components. The research involves isolated proteins (wild type and recombinants) as well as reconstituted proteins or even membrane vesicles. We perform a multidisciplinary approach using a wide range of biochemical and biophysical techniques applied to different proteins, with focus on membrane proteins, involved in energy transduction and transport.

Which expertise can you get from us? Bioenergetics, membrane proteins, electron transfer proteins, proton pumps

Main fields for collaboration Pharmaceutical Industry, Devices (Oxygen detection)

Manuela Pereira, PhD | mpereira@itqb.unl.pt

Expertise by lab

Biomolecular Diagnostics Abel Oliva

What do we do? Our research is focused on immunosensor and microfluidic chip development, tick born diseases studies, in vitro parasites culture and veterinary diagnostics; nanoparticle (quantum dots) development, functionalisation and conjugation towards biological application; cell handling and electrical and optical characterisation in microfluidic devices.

Which expertise can you get from us? Biosensors, optical sensors, microfluidics, microfabrication, tick born diseases, babesia spp, theileria spp, nanoparticles, quantum dots

Main fields for collaboration Development of diagnostics and vaccines for veterinary

Abel Oliva, PhD | oliva@itqb.unl.pt

Expertise by lab

Biomolecular NMR Manolis Matzapetakis What do we do? We specialise in applications of Nuclear Magnetic Resonance (NMR) to an array of biological problems such as the structure determination of proteins and protein-drug complexes, the study of protein-protein and protein-nucleic acid interactions, as well as a complex small molecule biological mixture analysis with applications to metabolomics. Our specific interests involve the study of the mechanism of allosteric regulation of the human soluble guanylate cyclase by its NO sensing domain, the study of the structure and function of proteins involvement in bacterial morphogenesis, and the identification of biomarkers via metabolomics studies for the identification of tuberculosis infections and, in a separate project, specific traits in animals to be used in selective breeding.

Which expertise can you get from us? NMR, Structural biology, metabolomics

Main fields for collaboration Pharmaceutical Industry; Analytical Services (Metabolomics)

Manolis Matzapetakis, PhD | matzman@itqb.unl.pt

Expertise by lab

Bioorganic Chemistry Rita Ventura

What do we do? We have a strong expertise in the enantioselective total synthesis of a wide range of natural compounds and their analogues in order to improve or modify their biological properties. We have a large experience in carbohydrate chemistry, especially in the development of efficient methods for the obtention of challenging 1,2-cis glycosides, important intermediates in the synthesis of di- and higher saccharides. Other expertise includes solid supported synthesis, development and application of new organocatalysts and synthesis of molecules as important tools for diverse biological studies.

Which expertise can you get from us? Organic Chemistry, enantio-selective synthesis, synthesis of biologically active compounds and analogues, carbohydrate chemistry, organo-catalysis

Main fields for collaboration Pharmaceutical industry, chemical industry, biotech companies, agrochemicals, materials, etc

Rita Ventura, PhD | rventura@itqb.unl.pt

Expertise by lab

Cell Physiology & NMR Helena Santos

What do we do? Our research is focused on beneficial microbes, i.e., microorganisms that promote human health or well-being, or are sources of new metabolites and enzymes with potential application in biotechnology. We perform the Metabolic Engineering of Bacteria with Industrial Relevance (Lactococcus lactis and Corynebacterium glutamicum) for acquisition of useful traits such as increased acid resistance and production of added-value compounds (butanediol, mannitol, erythritol). We use in vivo NMR to monitor the dynamics of intracellular metabolite pools. We also study the strategies of Osmo- and Thermo-Adaptation in Hyperthermophilic Organisms with a focus on ionic osmolytes: biosynthetic pathways and regulation, physiological role, molecular basis for protein stabilization, and novel applications. This research line unfolded from our findings that hyperthermophiles accumulate unique ionic osmolytes with excellent stabilizing properties of biomaterials. Applications in the cosmetics and pharmaceutics industries have been proposed, namely as ingredients in hydration creams and stabilizing agents of vaccines.

Which expertise can you get from us? Metabolic Engineering, Microbiology, Biotechnology of Extremophiles, Hyperthermophiles, heat stress response, thermoprotection, thermolytes

Main fields for collaboration Cosmetics Industry, Protein stabilizers, Nutraceuticals, Food Industry (Dairy products), Biofuels and chemicals from biomass (Bioeconomy)

Helena Santos, PhD | santos@itqb.unl.pt 32

Expertise by lab

Cell Signalling in Drosophila Pedro Domingos What do we do? Retinitis pigmentosa (RP) is a major cause of human blindness. In this disease, the photoreceptor cells in the eye progressively degenerate over time. About 30% of autosomal dominant RP cases are caused by mutations in Rhodopsin, the light sensitive protein of photoreceptors. In Drosophila, equivalent mutations in ninaE (the gene encoding Rhodopsin 1), also cause dominant degeneration of the retina and most of these mutations produce misfolded forms of Rhodopsin 1, which are not properly processed and accumulate in the endoplasmic reticulum. Our goal is to identify the molecular mechanisms mediating the cell death process in RP. We use the tools of modern Drosophila genetics, cell biology and imaging to investigate the role of the IRE1/Xbp1 signaling pathway and downstream genes in the regulation photoreceptor degeneration.

Which expertise can you get from us? Vision; photoreceptor; retinitis pigmentosa; Drosophila; Ire1/Xbp1

Main fields for collaboration Pharmaceutical Industry

Pedro Domingos, PhD | domingp@itqb.unl.pt

Expertise by lab

Cellular Neurobiology Federico Herrera What do we do? The overall aim of my laboratory is to lay the groundwork for the application of regenerative medicine on central nervous system (CNS) disorders. We are interested in the mechanisms involved in the production of CNS cells, both neurons and glia. The adult CNS has neural precursor cells with potential to produce new neurons and glia, and thus repair damaged tissue. However, in practice, the adult CNS does not support this regeneration process. If we could understand how neurons and glia are produced, we could promote CNS repair in a wide range of human pathologies involving neuronal loss, such as Alzheimer, Parkinson, spinal cord injury or stroke. We are also developing new molecular tools to control cell function and fate by means of light (optogenetics). Some CNS cells promote tissue repair, while others are an obstacle for regeneration. If we were able to activate, inactivate or kill specific subpopulations of CNS cells by simply stimulating them with a source of light at a particular wavelength, we could control the regeneration process. Additionally, these tools could have applications in cancer therapeutics.

Which expertise can you get from us? Cell and molecular biology of the central nervous system in normal and pathological conditions, neural stem cells, live cell imaging, in vivo models of regeneration (planaria), optogenetics

Main fields for collaboration Health science research, Biopharmaceutical industry

Federico Herrera, PhD | fherrera@itqb.unl.pt

Expertise by lab

CERMAX Facility Pedro Lamosa

What do we do?

Our main expertise is the use of NMR spectroscopy as a tool to address several biologically related studies. These studies have focused in the discovery of novel compatible solutes accumulated by hyperthermophiles, their structure determination, and their action upon protein structure and protein dynamics applied to protein stabilisation; expertise in 3D protein structure determination, protein dynamics studies using H/D exchange and 15N relaxation studies, and the determination of the structure of small molecules using conventional 2D NMR techniques; and also the discovery of new metabolic pathways in prokaryotes.

Which expertise can you get from us? NMR spectroscopy, structure determination, small molecule identification, metabolic pathways

Main fields for collaboration All fields

Pedro Lamosa, PhD | lamosa@itqb.unl.pt

Expertise by lab

Coordination and Supramolecular Chemistry Delgado

What do we do? We synthesise macrocycles and cryptands, and determine thermodynamic equilibrium constants: acid-base equilibrium, complex formation; association constants of species bound by weak interactions. We perform coordination chemistry studies in solution and study or characterise entities (metal complexes; supramolecular associations, etc.) by several spectroscopic techniques (NMR, UV-vis, epr, etc.). We also study the stability of complexes, including kinetics of dissociation in solution.

Which expertise can you get from us? Metal complexes for image and therapy of tumours, Molecular recognition of anions and zwitterions, Inhibitors of protein-protein interactions

Main fields for collaboration Pharmaceutical industry, Environment

Rita Delgado, PhD | delgado@itqb.unl.pt

Expertise by lab

Equilibrium and Transport Properties José Esperança

What do we do? Our research focuses mainly on the synthesis, characterisation and applications of ionic liquids (ILs). We synthesise novel ILs and perform the thermophysical and phase equilibria characterisation of ILs and their mixtures with conventional solvents, polymers and inorganic salts. We study ILs under metastable regimes, namely negative pressures to obtain knowledge about the morphology/structure and interactions of ILs. Our more applied activity involves the development of novel materials based on ionic liquids and nanomaterials, of novel techniques for successful crystallization of proteins and of new purification routes for enzymes and proteins using ILs.

Which expertise can you get from us? Ionic liquid; separation processes; phase equilibria; thermophysical properties; negative pressures; structure; nanomaterials; enzymes

Main fields for collaboration Chemical Industry, Pharmaceutical Industry (Process)

José Esperança, PhD | jmesp@itqb.unl.pt

Expertise by lab

Genomics and Stress Claudina Pousada What do we do? Our laboratory has a long expertise in dealing with the yeast Saccharomyces cerevisiae and the sulphate-reducer bacterium, Desulfovibrio gigas. Yeast is largely being used as a model system for drug discovery. Indeed, yeast assays for the identification of inhibitors/activators of several cellular processes are well established. We have implemented the TALEN-based technology for gene editing that may have many applications in several fields. Moreover we are currently interested in the constructions of yeast-based biosensors for the detection of metals in contaminated environments. Several yeast mutants will be genetically modified in order to detect metal levels in the contaminated water by means of simple and cost-efficient assays. D. gigas possesses a wide biotechnology potential in bioremediation by helping removal of sulphate and heavy metals from natural environments and of industrial waste liquids and sewage. We have recently sequenced and analyzed the genome of this bacterium having found several genes that might be relevant for biotechnology applications.

Which expertise can you get from us? Stress, Environment, Metals, talens (gene editing), Drug screening, Genome sequencing

Main fields for collaboration Water waste treatment and Health/Medicine

Claudina Rodrigues-Pousada, PhD | claudina@itqb.unl.pt

Expertise by lab

Glycobiology JĂşlia Costa

What do we do? Our research is focusing on protein glycosylation. We use methodologies in biochemistry, molecular biology and cell biology, having in view the structural elucidation of protein glycosylation, the production of glycosyltransferases to explore their synthetic potential, and the study of biological roles of glycans. Currently, we are studying the following topics: functional roles of glycans in the central nervous system; protein glycosylation in neurodegeneration, namely, in Amyotrophic Lateral Sclerosis, for the identification of potential biomarkers; glycoproteins and glycans of exosomes in cancer, namely glioma and ovarian cancer, with implications in biomarker identification and drug delivery.

Which expertise can you get from us? Protein glycosylation, glycosyltransferases, glycans, glycomics, neurodegeneration, amyotrophic lateral sclerosis, neuron, cancer

Main fields for collaboration Biotechnology and Protein glycosylation

JĂşlia Costa, PhD | jcosta@itqb.unl.pt

Expertise by lab

GPlantS

Margarida Oliveira What do we do? Our aim is to understand how plants perceive the environment to regulate development and adapt to adverse conditions, and use this knowledge for crop improvement. We have: -Identified/characterised the function of stress-responsive rice genes, establishing new links between abiotic cues and developmental patterns; -Defined conditions to uncover SUMOylation role in Arabidopsis drought-response proteome; -Got the first evidence of CBF genesâ&#x20AC;&#x2122; role along seasonal cold acclimation and ecodormancy break in a fruit tree; -Established in Jatropha curcas a reliable protocol for drought stress assays and obtained the drought-response transcriptome (RNAseq); -Established a link between stress-induced transcription changes, and modifications of histones and DNA methylation; -Been identifying PTM modifications in key enzymes of photosynthesis.

Which expertise can you get from us? Environment perception, plant stress response, regulation of development, increased yield, drought, salinity, temperature, rice, maize, Jatropha curcas, and woody species

Main fields for collaboration Plant biotech companies

Margarida Oliveira, PhD | mmolive@itqb.unl.pt

Expertise by lab

Homogeneous Catalysis Beatriz Royo

What do we do? Our research activities are based on strong expertise in synthetic organometallic chemistry. Organometallic compounds find application in many areas of knowledge; we are mainly interested in the following topics: catalysis, energy chemistry and medicinal chemistry. Catalysis: we work on the synthesis of efficient catalysts for the functionalization of organic molecules (in reduction and oxidation processes). As an example, organometallic catalysts for hydrogen transfer and dehydration for conversion of bio-renewables. Energy: we work on the synthesis of catalysts for water oxidation (splitting water to produce oxygen and hydrogen). Medicinal Chemistry: we are exploring the utility of metal complexes containing N-heterocyclic ligands as bioactive molecules (starting area in my group).

Which expertise can you get from us? Synthetic Chemistry; Homogeneous Catalysis; Organometallic Chemistry

Main fields for collaboration Bulk chemistry and petrochemistry; refinery catalytic processes for crude oil conversion into chemical feedstock; Production of chemicals e.g. polymers and transformation of raw materials in fine chemicals with high added relevant to industries such as: textiles, food, paper, construction, electronics, medicine, national health care; Environment protection, e.g. Sulphur removal from liquid fuels; Renewable energies: conversion of biomass in chemical products; artificial photosynthesis: catalysis of water splitting to oxygen and hydrogen.

Beatriz Royo, PhD | broyo@itqb.unl.pt 41

Expertise by lab

Industry and Medicine Applied Crystallography Pedro Matias

What do we do? RuvBL1 and its homolog RuvBL2 are evolutionarily highly conserved AAA+ ATPases (ATPases Associated with diverse cellular Activities) essential for many cellular activities and are implicated in some types of cancer. We solved the first crystal structure of the human RuvBL complex and our structural and biochemical results suggest that in vivo activities of these potential drug targets are regulated by cofactors inducing conformational changes via domain II. Hydrogen is a potential environmentfriendly fuel, and biological H2 production via hydrogenases will use clean technologies and renewable sources. We have determined the 3D structure of [NiFeSe] hydrogenase from D. vulgaris Hildenborough in several redox states and are now investigating the structural basis for its O2-sensitivity, aimed at designing O2-tolerant enzyme variants that can be used in bioelectrical devices.

Which expertise can you get from us? Structural biology of hydrogenases and cancer-related AAA+ proteins

Main fields for collaboration Biomedicine, Pharmaceutical, Energy

Pedro Matias, PhD | matias@itqb.unl.pt

Expertise by lab

Inorganic Biochemistry and NMR Ricardo Louro

What do we do? We study the molecular bases for novel bioenergetics processes capable of linking bacterial metabolism with bioelectrochemical devices for production of electricity, added value compounds, and biorremediation. All these processes are strictly dependent on the efficient contact between the microorganisms and electrodes and on a novel organisation of the bioenergetic electron transfer chains that enables the contact with the cell exterior. The experimental strategy is based on a combination of molecular biology, NMR spectrocopy, rapid kinetics followed by stopped-flow and spectroelectrochemistry.

Which expertise can you get from us? Bioenergetics, NMR, biochemistry, reaction kinetics, molecular biology of metalloproteins

Main fields for collaboration Water and soil remediation, wastewater treatment, clean energy, bioelectrosynthesis, exobiology, origin of bioenergetics

Ricardo Louro, PhD | louro@itqb.unl.pt

Expertise by lab

Mass Spectrometry Ana Coelho

What do we do? We implement and develop Mass Spectrometry methodologies and its applications to the study of biological systems, in particular with biomedical applications, namely tissue and organ regeneration. We develop protein characterisation methods, in what concerns post-translational modifications and de novo sequencing of proteins, a relevant issue for the proteome characterisation of non-sequenced species.

Which expertise can you get from us? Mass spectrometry, functional proteomics, protein structural characterization, tissue/ organ regeneration, host-pathogen interactions

Main fields for collaboration Pharmaceutical Industry, Food Industry, Environment, Forensic science related institutions

Ana Coelho, PhD | varela@itqb.unl.pt

Expertise by lab

Membrane Protein Crystallography Margarida Archer What do we do? We determine the three-dimensional structure of biological macromolecules. Our goal is the structural and functional characterisation of proteins. We are particularly interested in complexes and membrane-bound proteins, such as membrane transporters, sensor kinases (from pathogenic bacteria), enzymes involved in phospholipid biosynthesis, and proteins with biomedical relevance. We also collaborate with various groups (at national at international level) so that our crystallographic analysis for the proteins of interest, combined with biochemical and biophysical experiments, may shed lights into their biological functions.

Which expertise can you get from us? Structural Biology, X-ray Crystallography, Structure and Function of Proteins, Protein Production and Biochemical/Biophysical Characterisation, Membrane Proteins, Biomedical relevant Proteins, Membrane Transporters, Sensor Kinases, Phospholipids Biosynthesis

Main fields for collaboration Pharmaceutical Industry (Drug Design)

Margarida Archer, PhD | archer@itqb.unl.pt

Expertise by lab

Microbial & Enzyme Technology LĂgia Martins

What do we do? We want to contribute for the eco-efficient use of natural resources, the set-up of new bioremediation processes, and the production of bio-based products, through the use of microorganisms and enzymes. Our research activities are in the area of Molecular Biotechnology in the interface of protein science and protein technology. We are interested in 1) identifying oxidoreductase enzymes with potential for biotechnological applications, 2) exploring their structurefunction relationships, 3) improving enzyme properties by mutagenesis and directed evolution approaches followed by robotic high-throughput screening and 4) optimising bioprocesses related with xeno and natural aromatic compounds degradation with implications in the biorefinery and bioremediation fields.

Which expertise can you get from us? Biocatalysis, structure-function bioremediation.

studies,

enzyme

engineering,

biorefinery,

Main fields for collaboration Food Industry, Textiles, Petroleum (Bioremediation), Pharmaceutical Industry (Enzyme engineering)

LĂgia Martins, PhD | lmartins@itqb.unl.pt

Expertise by lab

Microbial Development Adriano Henriques What do we do? Our main field of work is on the Developmental Biology of Bacillus subtilis and related organisms. In particular, we study the cell cycle (cell division, chromosome segregation; cytoskeleton function) and the cell differentiation (spore morphogenesis; coupling between gene expression and morphogenesis; mechanisms of protein subcellular localization; assembly of macromolecular structures; assembly and properties of the spore surface layers; sporulation in relation to the pathogenesis of C. difficile). These spores/sporeforming bacteria might have many applications. Namely, display of enzymes and antigens; applications in biotechnology and biomedicine; spore formers as probiotics for uses in humans, animals or plants.

Which expertise can you get from us? Microbial genetics, microbial physiology, sporulation, bacterial cytoskeleton, probiotics, spore surface display, Clostridium difficile, Bacillus subtilis, Bacillus cereus, cell division, chromosome segregation

Main fields for collaboration Pharmaceutical Industry and Biotech (Probiotics, Mechanisms of action of drugs; Spore forming pathogens)

Adriano Henriques, PhD | aoh@itqb.unl.pt

Expertise by lab

Molecular Genetics of Microbial Resistance Lígia Saraiva

What do we do? For bacterial pathogens with clinical relevance, we aim at elucidating the molecular mechanisms of processes and proteins underpinning microbial survival and to uncover new antibiotic drug targets. In particular, we study: • the resistance of pathogens to effectors of the innate immune system and to antibiotics; • he biosynthesis of heme, a process that contributes to bacterial resistance; • the action of new potential antibiotics based on carbon monoxide releasing molecules. We analyse pathogens that cause a wide array of infection diseases in the community and hospitals, and that show concerning degree of multi-antibiotic resistance, namely Helicobacter pylori, Escherichia coli and Staphylococcus aureus. These studies are done at the genetic, biochemical and animal cell level.

Which expertise can you get from us? Genomics, transcriptomics, protein production; Manipulation of pathogen and animal cells; Drug toxicity assays; Tetrapyrrole chemistry

Main fields for collaboration Pharmaceutical Industry and Biotech

Lígia Saraiva, PhD | lst@itqb.unl.pt

Expertise by lab

Molecular Microbiology of Human Pathogens Raquel Sá Leão

What do we do? To improve our understanding of human health and disease, we need to gain a deeper knowledge on the intra- and interspecies bacterial interactions, and host-bacteria interactions that occur in the human body influencing which species and strains persist in it. We are focusing on the nasopharyngeal ecosystem, a rich niche frequently inhabited by potentially pathogenic bacteria such as Streptococcus pneumoniae (or pneumococcus). Colonisation by these bacteria, which is typically asymptomatic, is particularly frequent among young children. Although disease per se is incidental in the lifestyle of these bacteria, the burden of disease caused by them is substantial worldwide. In recent years, multivalent pneumococcal conjugate vaccines, targeting a limited subset of the circulating pneumococcal capsular types have been introduced in several countries. We are studying how these vaccines, together with antibiotic use, impact on the pneumococcal population and on the nasopharyngeal ecosystem as a whole.

Which expertise can you get from us? Pathogens, vaccines, antibiotics, evolution, molecular epidemiology

Main fields for collaboration Pharmaceutical Industry (infection: antibiotics, vaccines)

Raquel Sá Leão, PhD | rsaleao@itqb.unl.pt

Expertise by lab

Molecular Simulation Ant贸nio Baptista What do we do? We perform Molecular Modelling/Simulation studies of (bio)molecular systems, focusing on both the development of new methods and their application. We develop methods to study electrostatic effects, including constant-pH MD (which we have pioneered), linear response approximation, and Monte Carlo of electron-proton coupling. Other developments include methods for energy landscape analysis and Markov models. Our methodology has been applied to a wide range of systems, including soluble and membrane redox proteins (e.g., cytochrome c oxidase), misfolding proteins (e.g., prion), proteins in non-aqueous solvents (e.g., cutinase), neuropeptides (e.g., kyotorphin), and synthetic molecules (e.g., peptide dendrimers).

Which expertise can you get from us? Molecular modelling/simulation, computational chemistry, protein electrostatics, constant-pH molecular dynamics

Main fields for collaboration Pharmaceutical industry, materials development

Ant贸nio Baptista, PhD | baptista@itqb.unl.pt

Expertise by lab

Molecular Thermodynamics Luis Paulo Rebelo What do we do? Recent years have witnessed the growing importance of ionic liquids â&#x20AC;&#x201C; excellent solvents, which are liquid salts at or close to room temperature, and have been frequently studied as part of the important field of green chemistry. Their study has impacted a wide range of distinct areas, from chemistry to physics, from the environmental to the life sciences. Generally non-flammable and non-volatile, these liquids are easily manipulated in order to engineer distinct chemical functionalities, while offering extraordinary solvent quality and easy recovery. It is these characteristics which have driven the recent development of these salts as alternative clean media for chemical and enzymatic reactions, novel composites, separation and extraction processes, fuel cells, nuclear fuel reprocessing, additives for lubricants, and, more recently, biotechnology and pharmaceutical applications.

Which expertise can you get from us? Ionic Liquids, molecular thermodynamics of liquids and liquid solutions, Isotope effects, polymer solutions, metastable liquids

Main fields for collaboration Chemistry; Pharmaceutical Industry

LuĂs Paulo Rebelo, PhD | lrebelo@itqb.unl.pt

Expertise by lab

Nutraceuticals and Delivery Lab Catarina Duarte

What do we do? We optimise clean processes, such as supercritical fluid extraction, pressurized liquid extraction and adsorption methods, for the isolation of natural extracts with health promoting effects. We also perform an exhaustive chemical and biological characterisation of bioactive products; and assess biological properties of active components (e.g. anti-oxidant, anti-inflammatory and anti-proliferative activities) studying the impact on different biomarkers at cellular level. Moreover, we establish the relationship between composition-function and recognition of synergetic effects between the different molecular entities present in food and natural ingredients, and we develop final formulations of functional ingredients through the precipitation, micronization and/ or encapsulation of bioactive compounds into biocompatible carriers, using green processes.

Which expertise can you get from us? Natural products; extraction; precipitation/encapsulation; formulation; bioactivity characterisation

Main fields for collaboration Agro-food Industry; Pharmaceutical Industry; Phytopharmaceuticals and functional cosmetics products

Catarina Duarte, PhD | cduarte@itqb.unl.pt

Expertise by lab

Organometallic Chemistry Carlos Rom達o

What do we do? We have long experience in the field of synthetic transition metal organometallic chemistry and catalytic applications of transition metal oxo complexes particularly in areas like oxidation and reduction. We develop CO Releasing Molecules (CORM) based on transition metal carbonyl complexes for anti-inflammatory, cytoprotective, bactericide and other applications supported by the therapeutic potential of carbon monoxide.

Which expertise can you get from us? Inorganic and organometallic synthesis, homogeneous catalysis, metal-based drugs

Main fields for collaboration Chemical and Pharmaceutical Industry

Carlos Rom達o, PhD | ccr@itqb.unl.pt

Expertise by lab

Pharmacokinetics and Biopharmaceutical Analysis Ana Luísa Simplício What do we do? We study the pharmacokinetic properties of prospective drugs and designs strategies for improving their bioavailability. In this context, we develop practical solutions (prodrugs, novel drug delivery systems and new in vitro models) to answer clinical and research needs. Furthermore, the group pursues the fundamental questions raised during this development, using mass spectrometry and other analytical tools. For example, we have developed a cellular in vitro model to study the role of human carboxylesterase 2 (hCES2) in the bioavailability of drugs. We are now evaluating how post translational modifications affect the activity, selectivity and stability of this enzyme. More recently, we have been developing disease modifying Alzheimer drugs capable of penetrating the Blood Brain Barrier through receptor mediated transcytosis.

Which expertise can you get from us? Pharmacokinetics, medicinal chemistry, drug delivery, carboxylesterases, prodrugs

Main fields for collaboration Pharmaceutical Industry

Ana Luísa Simplício, PhD | anas@ibet.pt

Expertise by lab

Pilot Plant

António Cunha What do we do? iBET’s Pilot Plant is equipped for biotechnological process development, optimisation and scale-up, including upstream and downstream processing. Its modular character also enables the autonomous and independent utilization of each unit operating step, being a 400 L fermenter is available for bacterial based processes and a 50 L bioreactor for cell based processes). It has capability for processes based on different biological agents including bacteria, yeast, and fungi as well as animal cell technology including virus production and is mainly dedicated to biopharmaceutical, veterinary, agroindustry and cosmetic industries relevant processes. The premises include dedicated areas for cell based processes and bacterial based processes. A pilot scale freeze dryer (4 m2 shelf area) is also available. Its fermentation, extraction and purification rooms are configured for biological containment (fully compliant with OECD and EU rules and directives) to allow production and processing using genetically modified organisms. All bioreactors are connected through a CAN field-BUS network to a centralized control system (UBICON) used for process supervision

Which expertise can you get from us? Fermentation, bioreaction, protein production, VLP production, process development

Main fields for collaboration Biopharmaceutical Industry (human and veterinary), Agroindustry, cosmetic industry

António Cunha, PhD | cunha@ibet.pt

Expertise by lab

Plant Cell Biology Rita Abranches

What do we do? Our main current focus is on the use of plant cell cultures for production of recombinant proteins with applications in various industries, including the food and health sectors. We have developed plant expression platforms for the cost effective production of proteins from any source: human, animal, plant, microbial. These proteins are safe and low cost when compared to other production systems such as bacterial or animal cells. We are also working on the improvement of plant systems to obtain higher yields of recombinant product, namely the development of genetically engineered cell lines with lower protease activity, and also by adding chemical enhancers to the cell culture medium which improve protein synthesis.

Which expertise can you get from us? Molecular Farming, Plant Cell Cultures, Cost-effective production of recombinant proteins, Host engineering, Epigenetic modulation

Main fields for collaboration Pharmaceutical Industry; Food and feed Industry; Biotechnology; Cosmetics Industry

Rita Abranches, PhD | ritaa@itqb.unl.pt

Expertise by lab

Plant Cell Biotechnology Pedro Fevereiro

What do we do? We use/develop molecular tools to shorten the time to identify desired genotypes in selection or breeding programs and to alter a specific genotype to cope with biotic or abiotic stresses. To select a new trait, or to identify a modification, we characterise the physiological and molecular responses of the varieties under study. We also analyse how the allelic variants of genes influencing a specific characteristic are spread in populations. We utilize genomic - DNA arrays, qRT-PCR, Genotyping (SNPs and SSRs) and Southern and northern blots - and proteomic - 2D electrophoresis and Mass spectrometry - tools to identify genes and alleles involved in plant adaptation to specific conditions and to understand the regulations of their expression either at the transcriptional or at the post-transcriptional level. We use in vitro culture and DNA recombinant technologies to modify the expression of genes or to introduce new genes in specific crops.

Which expertise can you get from us? Plant Sciences; Plant Molecular Biology; Plant Biotechnology; Plant Cell, Tissue and Organ Culture

Main fields for collaboration Seed companies; Breeding companies

Pedro Fevereiro, PhD | psalema@itqb.unl.pt

Expertise by lab

Plant Gene Regulation Nelson Saibo

What do we do? Our research focuses on the transcriptional network regulating plant responses to environmental and developmental stimuli. We are particularly interested on the molecular mechanisms underlying photosynthesis response to different environmental and developmental cues. An integrated approach has been used, from the identification of new players in the transcriptional network regulated by stress to the study of post-translational protein modifications and regulation of chromatin structure and epigenetic modifications. This knowledge is expected to support the development of breeding strategies contributing to sustainable crop production under adverse environmental conditions.

Which expertise can you get from us? Molecular biology, Plant molecular physiology, Signal transduction pathways, Transcriptional regulation, Epigenetics, Abiotic stress, C4 metabolism, Photosynthesis

Main fields for collaboration Plant Sciences

Nelson Saibo, PhD | saibo@itqb.unl.pt

Expertise by lab

Plant Metabolomics Carla Ant贸nio

What do we do? Our research interests are related to the regulation of plant responses to changing environments which greatly affect plant productivity. Plants under abiotic stress are screened in order to detect and identify the cellular agents associated with plant tolerance and survival. We study plant reactions to these stresses through the changes in metabolite profiles using Metabolomics approaches such as LC-MS/MS and GC-TOF-MS. Metabolite profiling using GC-TOF-MS is a rapidly expanding technology in plant biology and continues to grow with fields of application, including diagnostic and descriptive analysis of metabolic responses to various genetic and/or environmental perturbations. No single analytical platform can cover the whole metabolome, thus combined LC- and GC-MS approaches are often used for better metabolite coverage.

Which expertise can you get from us? Plant Functional Genomics, Plant Metabolomics, Abiotic Stress, GC-TOF-MS Metabolite Profiling, LC-MS/MS Metabolite Target Analysis, Primary Metabolism, Metabolic Pathways

Main fields for collaboration Plant responses to abiotic stress

Carla Ant贸nio, PhD | antonio@itqb.unl.pt

Expertise by lab

Plant Molecular Ecophysiology Manuela Chaves What do we do? We study the interaction between plants and the environment, namely the mechanisms underlying the response of photosynthetic metabolism, water relations, growth, yield and fruit biochemistry of plants subjected to water deficits. Most of our studies are concentrated on grapevines but we also have research on legumes (chickpea, Lupinus spp) and Quercus spp. In grapevine, we showed that large fluxes of water are not essential for optimal plant performance. Moderate water deficits, induced by irrigation below evapotranspiration (deficit irrigation), might be used to control sink-source relationships while sustaining berry quality. Grapevine varieties were shown to differ in stomatal control, leaf cooling capacity and finally drought/heat resistance. On berry metabolism, we study differentially expressed transcripts of enzymes encoding for anthocyanin, proanthocyanidins and stilbenes in both skin and seeds in grape vines grown under different irrigation regimes.

Which expertise can you get from us? Crop physiology, metabolism under stress, grapevines

Main fields for collaboration Vineyards

Manuela Chaves, PhD | mchaves@itqb.unl.pt

Expertise by lab

Plant Quantitative Genetics Carlota Vaz Patto What do we do? Ou studies are focused on understanding the genetic control of quantitative traits such as quality (nutritional, organoleptic and processing), resistance to biotic (fungal diseases) and abiotic (drought) stresses on national plant germplasm. We exploit the potential of national underused plant germplasm (maize and legumes such as common bean and grasspea) as sources of interesting agronomic traits, contributing indirectly to enhance their cultivation. We also develop molecular tools to assist quality and resistance plant breeding programs. We activelly engage end-users (farmers & industry) on the plant breeding process through the establishment of participatory research approaches to provide society with adequate information about on going research and to answer its conserns.

Which expertise can you get from us? Quantitative Genetics, Plant Breeding, Statistical genomics, genetic mapping and QTL analysis, Comparative mapping, Zea mays, Lathyrus sp., Phaseolus vulgaris, stress resistance and quality traits

Main fields for collaboration Plant Breeding and Food and Feed Quality

Carlota Vaz Patto, PhD | cpatto@itqb.unl.pt

Expertise by lab

Protein Modelling Clรกudio Soares

What do we do? We work on molecular modelling of proteins using physical methods. Our members have experience in a quite large number of areas, from basic research in methods, to applications with biotechnological and biomedical interest. A lot of work is centred on redox proteins, but we are also doing modelling work in other areas. Besides our own research objectives, we have extensive collaborations with many experimental groups and, together, we aim at understanding Life at the molecular and atomic levels, from its smallest components to large supramolecular assemblies.

Which expertise can you get from us? Main areas: Molecular modelling of biomolecules / Structural bioinformatics, Structural Biology, Biophysics, Bioenergetics Specialised areas: Redox proteins and processes, Electron and Proton transfer, Protein structure prediction, Enzyme catalysis, Proteins with biomedical interest, Software development for molecular modelling

Main fields for collaboration Pharmaceutical Industry, Cosmetics, Agro-Food, Materials, Bioenergy

Clรกudio Soares, PhD | claudio@itqb.unl.pt

Proteomics Unit Pedro Matias

What do we do? We carry out the production, purification, crystallization and structural characterisation by X-ray crystallography of selected target proteins. We can also perform limited proteolysis for protein construct design, and Differential Fluorimetry Assays (Thermofluor) for protein stability studies prior to crystallization assays. This work is done in a well equipped IBET Research Contract Services Laboratory, and also in collaboration with the Macromolecular Crystallography Unit at ITQB. X-ray diffraction data collection can be done in-house or using Industry beamtime at European synchrotron radiation facilities.

Which expertise can you get from us? Protein construct design, Protein stabilization, Structure-guided drug design

Main fields for collaboration Biotechnology, Pharmaceutical Industry

Pedro Matias, PhD | matias@ibet.pt

Expertise by lab

Raman Spectroscopy of Metalloproteins Smilja Todorovic What do we do? We are specialised in advanced Raman spectroscopy (RS), including: Resonance Raman, Surfaceenhanced Raman scattering (SERRS) and spectroelectrochemistry. In particular, we are interested in: i) Mechanistic properties of metalloproteins, which perform diverse functions in cells, from energy conversion and detoxification, to catalysis and signalling; ii) Interfacial electron transfer processes in enzymes with biotechnological applications. We also work on development of strategies for protein immobilization on biocompatible sold surfaces, crucial for the functioning of enzyme-based biosensors and biocatalysts. In addition, we use RS to obtain molecular details on novel materials, such as diamond like carbon and carbon nanotubes, hierarchical Ag/Au nanostructures and ionic liquids.

Which expertise can you get from us? Resonance Raman Spectroscopy, SERRS, Metalloproteins, Electron transfer, Spectroelectrochemistry, Protein Immobilization

Main fields for collaboration Pharmaceutical Industry, Biotech

Smilja Todorovic, PhD | smilja@itqb.unl.pt

Expertise by lab

Structural Biology Carlos Fraz達o

What do we do? We aim the understanding of biochemical processes at atomic level. We use mainly crystallographic X-rays diffraction analysis, which allows the 3D structure determination of biological macromolecules. Their structure analysis and interpretation originate clues on how biomolecules may interact, which has enabled the rationalisation of applications in many and diverse fields of Life Sciences. We promote collaborations with other research groups to study key biological macromolecules, including enzymes and their complexes with substrates and analogues, or between proteins and nucleic-acids.

Which expertise can you get from us? Three dimensional (3D) visualization of key biological molecules; 3D protein structures; 3D enzyme-inhibitor structures; 3D protein-nucleic acid structures

Main fields for collaboration Pharmaceutical Industry

Carlos Fraz達o, PhD | frazao@itqb.unl.pt

Expertise by lab

Structural Genomics Maria ArmĂŠnia Carrondo What do we do? The main goals of our group are the study of eukaryotic proteins that are involved in the innate immune response and in viral latency. A hallmark of herpesvirus infection is the establishment of lifelong latency in the host. The latent phase of infection is associated with the different malignancies caused by virus. Our research is also dedicated to the study of proteins from prokaryotes. In particular, we are interested in the mechanism of cleavage of glycosidic bonds of glycoside hydrolases and in the mechanism of dioxygen reduction to water by multi-copper oxidases. We also study metalloproteins from the radiation resistant bacterium Deinococcus radiodurans which are involved in oxidative stress and belong to different families.

Which expertise can you get from us? Structural biology; protein production; biophysical characterization; protein interactions; crystallisation; X-ray crystallography; bioSAXS, structural analysis.

Main fields for collaboration Pharmaceutical Industry

Maria ArmĂŠnia Carrondo, PhD | carrondo@itqb.unl.pt

Expertise by lab

Sustainable Separation Technologies Isabel Marrucho What do we do? The central aim of our research is to understand solvents and solvency processes and to find how these can influence solutes properties. We traditionally use experimental techniques to search for effects and insights on liquid structure, neighbourhoods and specific interactions. Currently, we are very much interested on the thermodynamics of Ionic Liquids, on their thermophysical characterisation and application to different areas of knowledge. For example, we have been studying CO2 separation using ionic liquid and poly(ionic liquids) membranes, active developing pharmaceutical ingredients through the use of the ionic liquid synthetic strategies, separations of complex mixtures using liquid-liquid or liquidvapor equilibria, preparing new sustainable biomaterials with improved properties.

Which expertise can you get from us? Ionic liquids, thermodynamics, separation, green chemistry

Main fields for collaboration Pharmaceutical Industry, Gas Separations

Isabel Marrucho, PhD | imarrucho@itqb.unl.pt

Horizon 2020 is the perfect opportunity for us to work together. contact us

sciencefunding@itqb.unl.pt