INPhINIT Fellowship @ ITQB NOVA
Start your application now!
The role of the ER membrane complex (EMC) in the biogenesis of transmembrane proteins (Pedro Manuel Dias Neto Domingos)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Human Biology, Microbiology, Molecular Biology, Genetics, Cell Biology, Genomics and Proteomics, Biochemistry, Basic Neuroscience
GROUP LEADER
Dr.Pedro Manuel Dias Neto Domingos
RESEARCH PROJECT/RESEARCH GROUP
Website of the Laboratory of Cell Signalling in Drosophila
https://www.itqb.unl.pt/research/biology/cell-signaling-in-drosophila
POSITION DESCRIPTION
-Research Project / Research Group Description:
The Laboratory of Cell Signalling in Drosophila, headed by Pedro Domingos, has been interested in the mechanisms regulating proteostasis in the Endoplasmic Reticulum (ER), including the physiological role of the ER stress signalling pathways during development and in disease models [1,2]. Recently, we were awarded by La Caixa Foundation a collaborative grant to study the organismal role of the ER Membrane Complex, using both Drosophila (in Pedro Domingos’ group) and mammallian models (in the Laboratory of Membrane Traffic, headed by Colin Adrain, the project leader of La Caixa Foundation grant HR17-00595 “Organismal role of the ER membrane complex: a conserved machinery for membrane protein biogenesis”).
The biogenesis of membrane proteins in the ER often involves the import machinery comprised by the signal recognition particle (SRP) and the Sec61 import channel. SRP recognizes hydrophobic regions present in N-terminal signal peptides or transmembrane domains (TMDs) within client polypeptides emerging from the ribosome, coordinating their Sec61-dependent co-translational insertion into the ER membrane [3].
Another family of membrane proteins - the tail anchored (TA) proteins - contain a TMD at their extreme C-terminus, which is shielded within the ribosome during translation. These proteins undergo post-translational membrane insertion, mediated by a complex called the TRC (TMD recognition complex) in mammals, also called the GET (guided entry of TA) pathway in yeast [3].
Recently, it was shown that a third protein complex called the EMC (ER membrane complex) [4] is required for the import into the ER of a subset of multi-TMD and TA proteins that contain TMDs with low hydrophobicity [5] [6] [7].
-Job position description:
The PhD student position will be developed in the context of the La Caixa Foundation grant HR17-00595. Exploiting the observation that EMC TA client proteins exhibit reduced TMD hydrophobicity [5], we did a pilot experiment to predict EMC clients in the Drosophila genome. Our analysis identified ~300 TA proteins from which we isolated a group of proteins of reduced TMD hydrophobicity, which we screened for candidate EMC clients. This analysis revealed 2 potential novel EMC TA clients: Fan, which controls sperm individualization [8], and Xport-A [9]. Intriguingly, Xport-A is required for the biogenesis of both Rhodopsin-1 (Rh1) and TRP [9], proteins whose biogenesis is affected in EMC mutants [10], raising the possibility that EMC may affect the biogenesis of Rh-1 and TRP indirectly, by controlling the biogenesis of Xport-A. The PhD candidate will test this hypothesis in a set of rescue experiments, where constructs of Xport-A with an increasingly more hydrophobic TMD, will be expressed to attempt to rescue Xport-A and Rh-1 biogenesis. The PhD candidate will expand our screen for EMC clients in Drosophila, in the context of the consortium that was recently funded by La Caixa Foundation.
OTHER RELEVANT WEBSITES
Website of the Laboratory of Membrane traffic, headed by Colin Adrain, a collaborator in this project. www.igc.gulbenkian.pt/cadrain
REFERENCES
1. Ryoo, H.D., et al., Unfolded protein response in a Drosophila model for retinal degeneration. Embo J, 2007. 26(1): p. 242-52.
2. Coelho, DS, et al., Xbp1-independent Ire1 signaling is required for photoreceptor differentiation and rhabdomere morphogenesis in Drosophila. Cell Reports, 2013. 5(3):791-801.
3. Shao, S. and R.S. Hegde, Membrane protein insertion at the endoplasmic reticulum. Annu Rev Cell Dev Biol, 2011. 27: p. 25-56.
4. Christianson, J.C., et al., Defining human ERAD networks through an integrative mapping strategy. Nat Cell Biol, 2011. 14(1): p. 93-105.
5. Guna, A., et al., The ER membrane protein complex is a transmembrane domain insertase. Science, 2018. 359(6374): p. 470-473.
6. Shurtleff, M.J., et al., The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins. Elife, 2018.
7. Chitwood, P.J., et al., EMC Is Required to Initiate Accurate Membrane Protein Topogenesis. Cell, 2018. 175(6): p. 1507-1519 e16.
8. Ma, Z., Z. Liu, and X. Huang, OSBP- and FAN-mediated sterol requirement for spermatogenesis in Drosophila. Development, 2010. 137(22): p. 3775-84.
9. Rosenbaum, et al., XPORT-dependent transport of TRP and rhodopsin. Neuron, 2011. 72(4): p. 602-15.
10.Satoh, T., et al., dPob/EMC is essential for biosynthesis of rhodopsin and other multi-pass membrane proteins in Drosophila photoreceptors. Elife, 2015.
Tailoring enzymes to serve as technological tools in the biorefinery field (Lígia O Martins)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Biotechnology, Bioinformatics, Pharmaceuticals, Food Technology
GROUP LEADER
Prof.Lígia O Martins
RESEARCH PROJECT/RESEARCH GROUP
Host Research Group website
https://www.itqb.unl.pt/research/biological-chemistry/microbial-enzyme-technology
POSITION DESCRIPTION
-Research Project / Research Group Description:
The “new” Industrial Biotechnology is intimately linked to the biorefinery concept where renewable raw feedstocks are converted into bio-chemicals, bio-materials, bio-energy and bio-fuels using enzymes and microorganisms. It addresses current global challenges including, (i) reduction of CO2 emissions, (ii) replacement of fossil feedstock supply, (iii) creation of highly qualified workforce and attractive employment opportunities and (iv) implementation of a bio- and knowledge-based society to replace the petrol-based society that we have relied upon in the past. The host research activities are targeted in the discovery of new enzymes, their characterization and engineering and in the design and set-up of bioprocesses for the valorization of xeno or natural plant-based aromatic compounds. Enzymes are considered key tools in the development of sustainable technologies. They offer specific and cleaner reactions with lower energy requirements as compared with traditional chemical processes. Considering that the majority of microorganism’s native enzymes are not efficient or robust enough for the industrial uses, the generation of tailor-made enzymes represents a proficient way to design highly efficient biocatalysts. Here we propose the application of iterative laboratory and computational evolution methodologies to enhance the fitness of bacterial enzymes targeted at the construction of a phenolic platform of chemicals by conversion of lignin bio-wastes. This is a potential attractive environmental-friendly breakthrough application for the successful valorisation of lignocellulose feedstocks and implementation of economically feasible biorefineries for the XXI century.
-Job position description:
In this proposal, research will focus in a model bacterial ligninolytic enzyme, the McoA laccase from hyperthermophilic bacteria Aquifex aeolicus. A multidisciplinary approach based in iterative laboratory-computational evolution methodologies will be pursued towards enhanced efficiency of McoA for chemically diverse guaiacyl- and syringyl lignin-derived compounds. Directed evolution mimicking natural evolution is a powerful protein engineering tool to tailor biocatalysts through iterative rounds of mutagenesis and screening. The in-depth biochemical and biophysical characterization of enzyme hits and evolutionary intermediates, using enzyme kinetics, stability assays and X-ray crystallography, will allow identifying structural and functional determinants of substrate specificity, to track evolutionary trajectories and recognize the dynamics and constraints of enzyme evolution. This knowledge will start new rational or semi-rational design cycles targeted at enlarging the tool-box of biocatalysts for valorization of components of lignocellulose. This project directly addresses current limitations in ligninocellulose bio-transformation by generating technological solutions inspired by fundamental research. It will certainly contribute for changing the production processes of the European chemical industry to sustainable and cost-effective processes. The research is funded by FCT´s (Portugal) and European Union´s Horizon H2020 (RISE-BLigzymes and BBIJU SMARTBOX) projects and offers an exceptionally enlarged international network of collaborations with strong links to industrial biotechnology and state-of-the-art equipment.
Pathogen-driven phase separation during infection (Tiago Neto Cordeiro)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Human Biology, Microbiology, Molecular Biology, Genetics, Cell Biology, Genomics and Proteomics, Biochemistry, Basic Neuroscience
GROUP LEADER
Dr.Tiago Neto Cordeiro
RESEARCH PROJECT/RESEARCH GROUP
The site describes the research projects ongoing in the Dynamic Structural Biology of ITQB NOVA, headed by Tiago N Cordeiro. The site lists the present members of the group and also includes links to recent publications.
www.itqb.unl.pt/research/biological-chemistry/dynamic-structural-biology
POSITION DESCRIPTION
-Research Project / Research Group Description:
Emerging infections are a worldwide burden to the human public health, agricultural and food sector. They reflect the remarkable capability of pathogens to subvert host processes and immunity. Pathogens produce a vast repertoire of effector proteins to interface and gain control over essential host proteins, and in turn, reshape host signalling in favour of infection. Bacterial effectors can be fully disordered or proteins containing disordered regions. A trait also found in viruses effectors. Given the ubiquitous presence of intrinsically disorder proteins (IDPs) in eukaryotic signalling and regulation, disordered effectors emerge as an efficient way to precisely modulate critical host processes. My lab aims to illuminate how these sophisticated machines work inside host-cells from an integrative structural biophysics perspective. We focus on pathogen-host interactions mediated by disordered scaffolds, such as type III secretion system (T3SS) effectors produced by life-threatening human pathogens. Within this framework, the future candidate will investigate the role of phase-separation as in virulence by characterizing liquid-like phase-separated states forms of pathogen-host protein complexes. He/she will combine various biophysical methods relevant to state-of-the-art integrated structural biology, with a particular emphasis on NMR spectroscopy and Small-angle scattering, exploiting directly from preliminary results and proven-track of expertise of the lab. Elucidating the dynamic-structural principles underlying the function of disordered effectors, that mimic host-like IDPs to drive phase-separation, will provide essential insights into the mechanisms of host subversion by life-threatening pathogens, and potentially establish a basis for anti-infection strategies.
-Job position description:
The project aims to determine the structure, dynamics, and molecular interactions of large assemblies mediated by disordered proteins. In particular, we will focus on liquid-liquid separated forms of virulent effectors bound to host components associated with blocking host immune response during infection. Using a combination of NMR spectroscopy approaches and computational tools supplemented by biophysical and imaging methods, we will determine the high-resolution structures of these pathogen-host assemblies. This integrated experimental platform is well suited to observe the detailed structure and interactions of these assemblies, whose disordered and transient nature makes them challenging to study by classic structural techniques. We will take particular interest in studying pathogen-driven phase-transition condensations on distinct membrane-mimics with tailored lipid-composition. We intend to extract site-specific information on binding preferences and lipid-induced changes in structure and dynamics with high precision.
The candidate will be exposed to a broad range of research questions that require a genuine interest in basic biochemistry to advanced structural biology methods and computational biophysics. The project is a primary focus of the Dynamic Structural Biology Lab, with its wet-lab facilities for molecular biology, protein handling, and expression, as well as access to state-of-the-art technological platforms. The group has shared access to 500 and 800 MHz Bruker instruments equipped with cryoprobes maintained by CERMAX, the highest-field NMR facility in Portugal. The ITQB-NOVA has a complete infrastructure dedicated to structural biology, including an X-ray diffractometer and computational facilities. Also, the ITQB-NOVA is part of several Beam Allocation Groups (BAG) to access the best SAXS and X-ray beamlines in Europe, including ESRF and Diamond. The resources available pose no limit to her/his ambition and imagination.
Novel Antiviral Agents for HIV resistant strains (Ana Rita Guerreiro de Brito Petronilho)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Physical Sciences, Mathematics and Engineering Panel
GROUP OF DISCIPLINES
Chemistry and Chemical Engineering
GROUP LEADER
Dr.Ana Rita Guerreiro de Brito Petronilho
RESEARCH PROJECT/RESEARCH GROUP
Description of the research interests and team of the Research group headed by Dr. Petronilho.
https://www.itqb.unl.pt/research/chemistry/bioorganometallic-chemistry
POSITION DESCRIPTION
-Research Project / Research Group Description:
The Bioorganometallic Chemistry group at ITQB-NOVA focuses its research on the development of novel compounds active as antiviral, antifungal or anticancer drugs based on the combination between transition metals and biorelevant ligands.
We recently devoted efforts to develop efficient drugs for HIV-1 treatment, based on modification of AZT(zidovudine). AZT was one of the very first drugs found to be active against HIV its currently used in combinatorial therapies. Currently, there are over 30 drugs utilized for the treatment of HIV that have reduced morbidity dramatically over the past decades. Nonetheless, current therapies face the rapid emergence of resistant strains, the side effects resulting from extended use of the drugs and poor bioavailability. However, the emergence of HIV-1 resistant strains is predominantly due to mutations occurring in AZT molecular target, i.e. in the HIV-1 reverse transcriptase.
Our work on the functionalization of AZT, mostly with triazoles, shows that these new molecules have a great potential for terminating on-going viral replication, but, most importantly, are promising candidates in preventing the occurrence of infection and thus display higher potential as pre-exposure prophylactic drugs. These preliminary results indicate that AZT derivatives can be further developed, to not only to treat infected cells but, most importantly, prevent infection in healthy individuals.
We will work specifically with resistant HIV-1 strains, collected from patients from Portugal and Angola. Portugal presents an unusually severe HIV/AIDS profile, with the second highest incidence rate in the European Union13. In Angola it was estimated that 280,000 people were living with HIV/AIDS (a prevalence of 2.2%). The outcomes of this research project will enable to develop drugs that prevent infection, and will indisputably contribute to improve health of the populations where infection is problematic.
-Job position description:
The main objective of this PhD project is the development of highly efficient anti-retrovirals for the treatment of HIV resistant strains. Our approach is based on the modification of AZT with highly polar substituents to maximize solubility, while introducing transition metal complexes to maximize anti-viral-activity. We will target not only treatment, but also prevention of HIV1 infection, and will work specifically with HIV resistant strains isolated from patients from Portugal and Angola. To achieve these objectives we designed five main work packages:
- WP1: Combining sterics and solubility: Synthesis of functionalized AZT derivates bearing higly polar triazole linkers.
- WP2: Novel anti-viral drugs with dual functionality: Synthesis of silver complexes derived from triazoles based on AZT derivatives.
- WP3: Evaluation AZT derivatives derivatives for anti-retroviral activity against resistant HIV strains
- WP4: Evaluation AZT triazole derivatives for anti-retroviral activity against HIV-1 ongoing replication in follicular “sanctuaries”
- WP5: Evaluation AZT triazole derivatives for anti-retroviral activity, ex vivo
Discovering compounds that can penetrate the lymphoid tissues will significantly impact current HIV treatment, as one of the main challenges to effectively cure patients is the ongoing viral replication that occurs in lymphoid organs to which current treatments are not able to penetrate. This project will advance considerably our current knowledge of drug development for the treatment and prevention of HIV resistant strains. At the end of the project, we will be able to establish protocols for AZT derivatization, and understand their modus operandi. This research project will benefit society, academia and research industry, by introducing a simple modification on a widely utilized antiviral drug, using cost effective methodologies and employing processes that are easily transferable to scaled production.
New organocatalysts for light activated asymmetric catalysis. (Maria Rita Mendes Bordalo Ventura Centeno Lima)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Physical Sciences, Mathematics and Engineering Panel
GROUP OF DISCIPLINES
Chemistry and Chemical Engineering
GROUP LEADER
Dr.Maria Rita Mendes Bordalo Ventura Centeno Lima
RESEARCH PROJECT/RESEARCH GROUP
Bioorganic Chemistry is the interface of organic chemistry and biology. Our research uses the principles and techniques of organic chemistry in attempting to solve problems of relevance to biology. We can design synthetic derivatives of natural products, that improve on nature.
https://www.itqb.unl.pt/research/chemistry/bioorganic-chemistry
POSITION DESCRIPTION
-Research Project / Research Group Description:
Organocatalysis is an important area of modern catalysis complementing traditional metal catalysis and enzyme catalysis. Synthetic chemists have started to look at organocatalysis as a valuable tool for the asymmetric total synthesis of natural products and biological active compounds. However, there are still classes of products difficult to obtain by enantioselective catalysis. One example is the reactions that require photochemical activation. These light driven reactions are a powerful tool for organic chemistry, they include important chemical transformations that are not available by conventional thermal activation. Additionally, visible light is abundant, inexpensive and appropriate for sustainable and green chemical processes. However, photochemical reactions involve excited states with very short lives which are challenging to stereochemically control to afford products with high enantio- and/or diastereoselectivity. In this project, new organocatalysts derived from readily available chiral acids will be prepared and tested in several photochemical asymmetric reactions.
The Bioorganic Chemistry Group main research aim is to synthesise biologically active molecules, to modify their structure in order to enhance or modulate their biological properties and to contribute to the understanding of the biological phenomena in which they play a crucial role. This knowledge is important for the design and synthesis of new molecules that can interfere with the molecular mechanisms responsible for pathogenic behaviours, with potential innovative therapeutic application. The Lab is located at ITQB NOVA, an institute of the Universidade Nova de Lisboa that develops high-quality research, teaching, science communication and outreach activities in chemistry and the life sciences. The ITQB has the research facilities, equipment, and scientific support services required to conduct activities at the interface between Chemistry and Biology.
-Job position description:
Light driven enantioselective organocatalysis is a recent subfield of catalysis, offering a great potential for rapid development and important applications in synthetic organic chemistry.
In this project, new organocatalysts derived from pyrrolidine and chiral acids will be synthesised. The catalysts proposed possess a pyrrolidine ring, which is present in the most successful organocatalysts (for example proline and its derivatives), where the activation mode involves the formation of an enamine. Additionally, they will have other functional groups (amide, alcohol, carboxylic acid) that can participate in the transition state by forming hydrogen bonds, which have been very important for example in the [2+2] photocycloadditions high stereoselectivities. The stereochemistry of the chiral acid moiety is expected to exert a strong influence in the stereoselective outcome of the reactions to be studied.
The new organocatalysts obtained will be applied in several light driven stereoselective reactions, such as the alpha-alkylation of several aldehydes with several alkyl bromides in the presence of light, in photochemical [2+2] cycloadditions of enones and photocatalytic oxyamination of aldehydes.
For the rational screening of catalysts, solvents and other variables (catalyst loading, solution concentration, temperature), we will employ a strategy known as the Design of Experiments (DoE). The Design of Experiments is a set of statistical/mathematical tools employed to investigate in a rational way the chemical space. By varying all factors simultaneously over the set of experiments it allows to identify the most important variables to be controlled, to study their interactions, to make models and predictions leading in a rational way to the real optimum conditions. DoE is a well established technique for reaction optimisation in industry, which is raising interest in academia, but it can still be considered a new tool for asymmetric organocatalysed reactions optimisation.
Manganese Complexes as New Drugs Against Antimicrobial Resistance (Beatriz Royo)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Physical Sciences, Mathematics and Engineering Panel
GROUP OF DISCIPLINES
Chemistry and Chemical Engineering
GROUP LEADER
Prof.Beatriz Royo
RESEARCH PROJECT/RESEARCH GROUP
Research group description featuring research interests and team.
www.itqb.unl.pt/research/chemistry/organometallic-catalysis
POSITION DESCRIPTION
-Research Project / Research Group Description:
We are a synthetic organometallic chemistry group. Our research activities focus on the development of bio-relevant metal complexes with specific properties for their use in catalytic and biological applications. In particular, we work on the development of new organometallic complexes of 3d metals (Mn, Fe, Co, Ni) containing N-heterocyclic carbene ligands (NHCs). We are fascinated by the diversity of effects that these type of ligands can impart to their metal complexes. Important features of NHCs are their tremendous synthetic flexibility, which allows
to tailoring them to specific functions, and their strong sigma-donor electron donor properties. The present project aims to develop a new family of manganese NHC complexes with high thermodynamic and water stability for their application as antimicrobial drugs. Modulation of the NHC ligand scaffolds will allow us to control the desired properties of the metal complexes.
Our strategy is to combine the manganese NHC complexes with well-established drugs in order to increase the activity of antibiotic-based drugs through synergestic or additive activity, decrease the required doses, and increase the spectrum of activity, thwarting drug resistance.
-Job position description:
Antimicrobial resistance has been identified by the World Health organization as one of the greatest current threats to global health. Some studies have predicted that drug-resistance infections will kill 10 million people a year by 2050. Therefore, there is an urgent need for the development of new drugs with novel mechanisms of action capable to control multidrugresistance pathogens. New classes of compounds, such as metal complexes, can be used to supplement traditional antibiotics, which have become ineffective due to antimicrobial resistance. It has been demonstrated that the antibacterial activity of some antibiotics, that are
no longer effective, is significantly enhanced when using in combination with metal complexes.
To date, the majority of these studies are limited to combine antibiotics with metal coordination complexes containing N-based ligands as supporting ligands. A very important aspect in the design of antimicrobial metal complexes is their stability under physiological conditions, which allows a better delivery and transport to the specific targets. For that reason, strong ligand-metal bonds are needed, and in this respect N-heterocyclic carbene (NHC) ligands can play a crucial role. It is expected that the great stability, ease modulation of the electronic properties and excellent s-donating capacity displayed by NHC ligands, will allow metal-NHC derivatives to
reach high stability in biological media.
This project aims to develop new manganese NHC complexes as potent antimicrobial agents. Coordination of well-established drugs to manganese NHC complexes will be explored. We aim to investigate how metal binding will modulate the biological activity of the drug and explore if synergistic effects can be achieved in this way. The antibacterial activity of the new drugs will be tested in a variety of bacterial strains, including Gram-positive Staphylococcus aureus, and
Gram-negative Escherichia coli, and Helicobacter.
INITIATION - Sulfide Sensing and Homeostasis in Bacterial Pathogens (Jose Artur Alves de Brito)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Human Biology, Microbiology, Molecular Biology, Genetics, Cell Biology, Genomics and Proteomics, Biochemistry, Basic Neuroscience
GROUP LEADER
Dr.Jose Artur Alves de Brito
RESEARCH PROJECT/RESEARCH GROUP
Elucidation of structure as a mean of understanding function is the basic principle of structural biology. The main goal of the hosting Laboratory is the three-dimensional structure determination of proteins by X-ray Crystallography and more recently by single-particle cryo-electron microscopy. We collaborate with various groups at national and international level, so that our structural analysis of proteins, combined with other complementary methods, such as biochemical and biophysical experiments, may provide insides into their biological function and reaction mechanism. Our objective is a better understanding of protein structure-function relationship. In this website you will find all the information regarding the hosting laboratory, the Head of Lab and the Project Supervisor.
https://www.itqb.unl.pt/research/biological-chemistry/membrane-protein-crystallography
POSITION DESCRIPTION
-Research Project / Research Group Description:
Sulfur is a very abundant and versatile element on Earth. A major constituent of vitamins, hormones and the amino acids methionine and cysteine, sulfur exists in oxidation states ranging from -2 (in H2S) to +6 (in SO42-). In human physiology, it plays a major role in specific metabolic processes. Despite being a toxic gas, hydrogen sulfide (H2S) is important as a gasotransmitter, like nitric oxide (NO) and carbon monoxide (CO,) acting as a signaling molecule and regulating multiple physiological processes. Moreover, recent studies implicate H2S oxidation in bacterial antibiotic resistance and sulfide homeostasis.
Staphylococcus (S.) aureus is an extremely versatile Gram positive pathogen capable of minor to life thretening infections, such as bacteremia or endocarditis, with high morbidity and mortality rates. In 2010, it was estimated that it caused more deaths than AIDS in the USA. S. aureus is also known for its increasing resistance to virtually all classes of antibiotics. Methicillin-resistant S. aureus (MRSA) strain, recently emerged in the community, are the most important causes of antibiotic-resistant nosocomial infections worldwide.
Recent data reveals that the cst operon in S. aureus encodes a nearly complete mitochondrial-like sulfide oxidation system (S2- to thiosulfate, S2O32-), with its core determinants duplicated in MRSA strains. We seek to understand the cellular metabolic adaptation to sulfide misregulation in S. aureus. Studying H2S synthesis, regulation and distribution will enhance our understanding of critical pathways in pathologies related to H2S metabolism. Moreover, dysfunctional human H2S metabolism has been increasingly associated with pathologies, from cardiovascular (atherosclerosis) to neurodegenerative diseases, diabetes and cancer. A deeper knowledge of the structure and function of H2S-metabolizing enzymes will support the discovery and development of modulatory compounds as prospective therapies for a wide range of diseases.
-Job position description:
This project results from a bilateral Portugal-United States collaboration between the Archer Lab at ITQB NOVA (Portugal) and the Giedroc Lab at the Indiana University (USA). This is an exciting synergetic opportunity to combine the knowledge, expertise and resources of both teams to develop a strong collaborative network on sulfide metabolism. The long-term goal is to obtain a better understanding these enzymes, while elaborating a strategy to develop future international research projects.
The expertise of the teams is fully complementary, ranging from X-ray crystallography, spectroscopy and other experimental and computational biophysical tools, to biochemistry and microbiology. These competencies allow interdisciplinary research: the American team harbors the necessary knowledge to express, purify and characterize the target enzymes and the Portuguese team has a long and fruitful output in the field of Structural Biology.
The candidate will be involved in a “from gene to structure” approach and will be trained in molecular biology, biochemical and biophysical tools, X-ray crystallography and, possibly, cryo-electron microscopy. ITQB NOVA recently won an EU Twinning project for a consortium of countries/labs to share knowledge and create cryo-EM expertise in Portugal. We note that Cryo-EM expertise already exists at Indiana University; thus, the candidate will have an opportunity to work abroad (USA and Twinning project partners), as part of a young, dynamic and multidisciplinary team.
This work is expected to pave the way for a deeper knowledge on sulfide homeostasis enzymes. Taken together, the outcome of this project will ensure advances in fundamental and applied science.
OTHER RELEVANT WEBSITES
The Macromolecular Crystallography Unit at ITQB is a top research group that aims the study and characterization of biological molecules, such as proteins and nucleic acids, to a resolution higher enough to help elucidating the detailed mechanisms by which these macromolecules carry out their functions in living cells and organisms. The Unit is presently composed of five laboratories each one specialized in a different field of research: Structural Genomics, Industrial and Medical Applied Crystallography, Structural Biology, Membrane Protein Crystallography, and Structural Virology. In this website you will find all the relevant information regarding the Unit’s organization, composition, facilities and equipments, European projects involvement and synchrotron access. http://mx.itqb.unl.pt/
Professor David P. Giedroc’s research interests fall under a common umbrella termed “biophysical chemistry of infectious disease”. Prof. Giedroc seeks a molecular-level understanding of macromolecular structure, dynamics and regulation, and uses the tools of biophysical chemistry, bioinorganic chemistry, proteomic profiling and NMR structure determination. In this website you will find the relevant literature on the target proteins and some of the methodologies to be employed throughout the project.http://www.indiana.edu/~dpglab/
Under the “IMpaCT” project, we have established collaborations with three research Centres in Europe, with proven track record and expertise in the different aspects and applications of cryo-EM: the National Centre for Biotechnology of the Spanish National Research Council (CSIC-CNB, Spain), the Institute of Biotechnology at the University of Helsinki (Finland) and the Weizmann Institute of Science in Rehovot (Israel). The main goal of the project is knowledge transfer in cryo-EM methodologies from the partners to ITQB NOVA researchers, allowing them to acquire expertise in sample preparation, image acquisition to high resolution and data processing both for Single Particle Analysis and Cryo-Tomography. In this website you will find all the relevant information regarding “IMpaCT” itself, namely the partners where teaching and training will be carried out, planned workshops and other activities within the scope of the project.https://www.itqb.unl.pt/impact
Exploring thermophilic organisms for enhanced biocatalytic reduction of carbon dioxide (Inês Antunes Cardoso Pereira)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Biotechnology, Bioinformatics, Pharmaceuticals, Food Technology
GROUP LEADER
Prof.Inês Antunes Cardoso Pereira
RESEARCH PROJECT/RESEARCH GROUP
Group website; more details at
http://www.itqb.unl.pt/research/biological-chemistry/bacterial-energy-metabolism
POSITION DESCRIPTION
-Research Project / Research Group Description:
Developing sustainable processes to reduce the levels of CO2 is one of the most urgent and challenging issues of our society. Reduction of CO2 for the production of added-value biofuels, such as formate, is a valuable process for CO2 capture and a way to produce an attactive H2 storage material1. Notably, formate is a non-toxic liquid with high energy density, which can be easily transported and stored. Thus, it is very important to find suitable catalysts for the production of formate from CO2. Formate dehydrogenases (Fdh) catalyse the reversible reduction of CO2 to formate, and are an excellent alternative to fix CO2 relative to chemical catalysts and carboxylases2. The most active Fdh are the metal-containing enzymes present in anaerobes, which have the advantage that they can be applied in electro- and photocatalysis. This project will focus on the study of novel Fdhs from thermophilic anaerobes, which should have increased stability and high catalytic activity, and also on developing photocatalytic and electrocatalytic systems for CO2 reduction. The work will involve multidisciplinary training and expertise in bioinformatics, molecular biology, protein expression, protein engineering, protein structure, biocatalysis, photocatalysis and nanobiotecnology.
1.Shi et al 2015 Chem Soc Rev 44, 5981
2.Cotton et al. 2018 Curr Op Biotechnol 49, 49
3.Bassegoda et al 2014 JACS 44, 15473
The Bacterial Energy Metabolism group studie anaerobic organisms and in how they, and their enzymes, can be explored for biotechnological applications. These organisms live in the absence of oxygen, and thus in low redox potential habitats, which endows them and their enzymes with very interesting catalytic properties. The group has a very strong expertise in working at the interface between biochemistry, microbiology and biotechnology, and extensive knowhow in microbial physiology, enzyme catalysis, protein structure and biocatalytic applications of proteins and microorganisms.
-Job position description:
The PhD student will be integrated in an active and stimulating lab with researchers at different stages of career (BSc, Masters, PhD and Post-Doc) working on different topics and providing ample opportunities for training and career development. The first task will comprise the genomic mining of thermophilic anaerobic organisms to identify Fdhs with the desired properties, based on predicted cellular location, quaternary structure and cofactor composition. This task will provide training in bioinformatics and protein analysis. The 2nd task will involve the expression of the chosen enzymes (two to three) using appropriate expression vectors for the selected hosts (either Escherichia coli, Desulfovibrio vulgaris Hildenborough or Shewanella oneidensis), and later on the expression of variants for these enzymes. This task will provide training in molecular biology tools and in protein expression. The 3rd task will consist of purification and characterization of the isolated proteins namely in terms of biochemical, biophysical and kinetic properties, temperature and oxygen tolerance and inhibition behavior. This task will provide training in several biochemical and biophysical techniques (electrophoresis, mass spectrometry, GC, UV-Vis and EPR spectrometry). The 4th task will involve the crystallization and structure determination of the expressed proteins, as the basis for the design of improved variants. This will provide training in crystallization and protein structure determination and analysis. The 5th task will involve development of electrocatalytic and photocatalytic systems for CO2 reduction. For this the enzymes will be immobilized on different types of electrodes (incl. nanostructured ones) for electrochemical experiments or on photoactive nanoparticle systems for photocatalytic experiments. Several possible systems will be tested and optimized. This task will provide training in electrochemistry (cyclic voltammetry and chronoamperometry) and photocatalysis.
Exploring anammox bacteria towards a more sustainable environment (Filipe dos Santos Folgosa)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Biotechnology, Bioinformatics, Pharmaceuticals, Food Technology
GROUP LEADER
Dr.Filipe dos Santos Folgosa
f.folgosa@itqb.unl.pt
RESEARCH PROJECT/RESEARCH GROUP
“Metalloenzymes and Molecular Bioenergetics”’s laboratory description featuring research interests and team
https://www.itqb.unl.pt/labs/metalloenzymes-and-molecular-bioenergetics/
POSITION DESCRIPTION
-Research Project / Research Group Description:
The growing environmental awareness has imposed new global challenges in order to find more efficient solutions to wastes’ management, inevitably increasing its associated costs. Wastewater (WW) management is one of the current issues, presenting several technological limitations that impairs its utilization in an efficient and global manner. The use of microorganisms as a supplement in WW’s treatment facilities to improve efficiency at lower costs may be a solution.
Anammox bacteria have shown good performance in WW treatment as they are able to bypass the denitrification step of the nitrogen cycle, do not require expensive carbon sources, have a very high affinity for their substrates, and are able to survive to temperatures up to 85ºC. However, the duration of WW treatment cycles as well as the resistance to oxygen exposure are limitations to the use of anammox bacteria.
This proposal aims to shed light in mechanisms involved in the response to oxygen in anammox bacteria and, in a long-term, use their capacities to improve and to obtain more resistant and effective strains. To tackle this objective, we aim to understand 1) the role of two proteins, identified as part of the response to oxygen, 2) to identify other proteins involved in this mechanism and 3) how they influence the efficiency of these organisms in WW treatment.
The success of this proposal will also help in building tools to improve the methodologies used in WW treatment and to mitigate one of the most alarming environmental problems in the World, which is the major point of the Goal 6 of the 2030 Agenda for Sustainable Development, namely with the topics 6.3, 6.4 and 6.5.
The work proposed will be performed in the “Metalloenzymes and Molecular Bioenergetics” laboratory, which has a solid experience and is internationally recognized in this research field. This will give the prospective student the access to all the equipment and know-how necessary for the execution of the project.
-Job position description:
The successful candidate selected for the INPhINIT Fellowships Programme will engage in the “Molecular Biosciences” PhD programme coordinated by ITQB NOVA. Our laboratory is part of the MOSTMICRO-ITQB Research Unit, also coordinated by ITQB-NOVA, a renowned academic and research centre in Portugal. ITQB NOVA carries out research and postgraduate training in life sciences, chemistry and associated technologies, aimed at improving human health and the environment. The unique conditions at ITQB NOVA provide an excellent environment for young students to develop a research career.
The successful candidate will have the opportunity to learn several techniques such as cloning, expression and protein purification, biochemical and spectroscopic, structural and functional characterization of proteins. Finally, at the last stage, the candidate will also learn to produce complemented bacterial strains that will be used in laboratory scale WW treatment studies.
By being part of this project, the successful candidate will also have the chance to engage in international stays in other renowned research centers. A thorough formation in different skills (such as scientific writing, oral communication) will also be offered by the host institution.
It is expected that the accomplishment of the goals established for this proposal will translate into high quality publications and/or patent submissions. In a later stage, it is also expected that the work performed will translate into the creation of a new alternative to the current WW treatment processes. Also, due to the nature of this research work, it is also expected that it becomes attractive to science dissemination activities not only in international scientific meetings but also to the society in general using a diverse set of activities and approaches, for example in ITQB NOVA Open Day.
OTHER RELEVANT WEBSITES
“Molecular Biosciences” PhD programme https://www.itqb.unl.pt/education/phd-molecular-bioscience/phd-molecular-bioscience
Assembly and functional architecture of the Clostridioides difficile spore surface layers ( Adriano O. Henriques)
CENTRE
ITQB - Microbiologia Molecular, Estrutural e Celular
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Human Biology, Microbiology, Molecular Biology, Genetics, Cell Biology, Genomics and Proteomics, Biochemistry, Basic Neuroscience
GROUP LEADER
Prof.Adriano O. Henriques
RESEARCH PROJECT/RESEARCH GROUP
the site describes the research projects ongoing in the Microbial Development group of ITQB NOVA, headed by HENRIQUES. The site lists the present members of the group and also includes links to recent publications as well as resources.
http://www.itqb.unl.pt/research/biology/microbial-development
POSITION DESCRIPTION
-Research Project / Research Group Description:
Clostridioides difficile, a strict anaerobic bacterium with the ability to form highly resistant spores, and the main cause of a range of nosocomial intestinal diseases linked to antibiotic therapy in adults, is classified as an urgent health threat. This pathogen also imposes an enormous economic burden onto the health care systems worlwide because of very high rates of disease recurrence. Disease recurence has been linked to the ability of this pathogen to form spores, which persist in the host or the close environment. Infection usually begins wiht the ingestion of spores which will germinate in response to bile salts to establish an actively growing cell population in the colon. Other than being the main infectious vehicle, spores are also important for the infectious cycle because interactions of their surface layers with the intestinal mucosa allow spore binding and germinate properly. Importantly, immunization with at least one abundant component of the spore surface layers confers protection against infection as shown in an animal model. In spite of the importantce of spores for the disease-causing ability of C. difficile, basic knoweledge on the function, assembly, interactions and structures of the proteins that form the spore coat and exosporium, has been lacking. We propose to fill this gap by using genetics, cell biology, biochemistry and structural biology to examine the role, localization, interactions and structure of key componenents of the C. difficile spore surface layers. The work addresses an important question in bacterial pathogenesis and antibiotic resistance.
-Job position description:
We will start with genetics and cell biology by constructing a fusion between the coat/exosporium proteins to examine the dynamics of their synthesis and assembly; we will also construct mutants in key morphogenetic determinants or regulatory proteins to examine the dependency for localization of the various coat/exosporium proteins. We will use biochemical and biophysical assays to examine the interactions established by the coat/exosporium proteins during their assembly. These assays will be complemented by studies in vivo in animal models of colonization, disease and recurrence. Finally, we will use structural biology to determine the structures of individual components and complexes Our NMR platform is composed of two 500 MHz and an 800 MHz spectrometers with cryo-probes. Access to higher magnetic fields (e.g., 950 MHz) is possible through European Large facilities. The ITQB-NOVA has a complete infrastructure dedicated to structural biology including an X-ray diffractometer and computational facilities. Also, the ITQB-NOVA is part of several Beam Allocation Groups (BAG) to access the best SAXS and X-ray beamlines in Europe, including ESRF and Diamond. In-house collaborations are anticipated with the Dynamic Structural biology lab. We thus seek a candidate that is thrilled by the prospect of studying Biology from a multidisciplinary angle, able to identify and ask relevant and ambitious questions.
The candidate should have a curricular basis in Biology or Microbiology, but we consider backgrounds in other fields of the Natural Sciences, as the work will benefit greatly from novel ideas/concepts and approaches. The candidate is expected to be highly motivated and interactive with other members of an international multicultural team. The official lab language is English. Finally, the candidate should have an interest in Science Communication and Outreach, as this is also an important aspect of life at ITQB NOVA.
Understanding RuBP regeneration to improve crop productivity (Nelson Saibo)
CENTRE
GREEN-IT - Biorecursos para a Sustentabilidade
https://www.itqb.unl.pt/green-it
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Medicine, Public Health, Sports Science, Nutrition, Clinical Neuroscience and Psychology, Healthcare Management
GROUP LEADER
Dr.Nelson Saibo
RESEARCH PROJECT/RESEARCH GROUP
Research Group website: Plant Gene Regulation
https://www.itqb.unl.pt/research/plant-sciences/plant-gene-regulation/plant-gene-regulation
POSITION DESCRIPTION
-Research Project / Research Group Description:
Global climate changes and a fast growing world population require higher crop production even under adverse environmental conditions. To achieve this goal, we need plants with increased photosynthetic efficiency and improved tolerance to abiotic stress. Since these traits of high agronomic impact are both highly regulated at transcriptional level, our research team is focused on their transcriptional regulation. An improved knowledge on the regulation of photosynthesis efficiency will help to achieve higher crop yields, under favourable and adverse environmental conditions.
Photosynthesis sets maximum crop yield but is neither optimized for current atmospheric conditions nor agricultural practices. For example, carbon assimilation in the Calvin cycle can be limited by Ribulose 1,5-Biphosphate (RuBP) regeneration. This limitation is predicted to become more severe with atmospheric CO2 rising levels, and so requires a deeper understanding of how RuBP regeneration is regulated so that a more efficient photosynthetic process can be designed. The main goal of this project is to better understand how RuBP regeneration is regulated in rice and to transform rice to improve its photosynthesis efficiency. Rice is the staple food for more than half of the world population, therefore, improving rice production will have a great impact on feeding the world population.
The results expected from this PhD project will contribute to better understand the molecular mechanisms underlying photosynthesis regulation and will allow the identification of key players critical to address crop yield improvement. Besides rice yield improvement, the knowhow generated within this project can also be translated into other important food crops, such as wheat, maize, and barley. Therefore, the objectives of this project make it highly aligned with goal two of the United Nations´ Sustainable Development Goals (Zero Hunger).
-Job position description:
This PhD project has two main objectives: a) to identify and characterize the main players regulating one of the limiting photosynthesis steps (RuBP regeneration) and b) to use this knowledge together with what is already known from tobacco (Simkin et al., 2015) and Arabidopsis (Simkin et al., 2017) to modulate RuBP regeneration in rice, thus improving photosynthesis efficiency and consequently plant yield. In order to achieve these objectives, the project is divided in 4 tasks:
T1- Identification of TFs regulating RuBP regeneration associated genes
a) Construct a light-induced rice cDNA expression library enriched in photosynthesis-related genes.
b) Identification of TFs binding to promoters of genes (up to 3) involved in RuBP regeneration (Yeast one-Hybrid and in silico approach).
T2- Analysis of the protein (TF) – DNA interactions
a) Each putative TF-DNA interaction will be further validated by both direct re-transformation of the bait strain with the TF identified and Electrophoretic Mobility Shift Assays.
b) Transactivation assays will be performed to assess the activity of the TFs.
T3- Identification/characterization of TF - TF interactions
a) Direct Yeast two Hybrid (Y2H) and Bi-molecular Fluorescence Complementation assays will be carried out to identify putative interactions between the TFs identified for each gene, as well as to retrieve information about homo- or heterodimers.
b) A Y2H screening might be set to identify new TF interactors.
T4- Rice transformation and analysis of the transgenic plants
a) Rice plants will be transformed to OX and KO (CRISPR/cas9) a selection of TFs identified.
b) Transformation of rice plants with a combination of genes involved in RuBP regeneration in order to improve photosynthesis efficiency. This has already been successful in Arabidopsis and tobacco.
c) Transgenic rice plants will be analysed at molecular (RNA-seq, ChIP-seq), biochemical and physiological (photosynthetic parameters and agronomic traits) levels.
Regulation of photosynthesis by sugars: understanding the mechanisms to improve crop yields (Elena Baena-Gonzalez)
CENTRE
GREEN-IT - Biorecursos para a Sustentabilidade
https://www.itqb.unl.pt/green-it
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Plant, Animal and Environmental Biology, Physiology, Ecology and Conservation
GROUP LEADER
Dr.Elena Baena-Gonzalez
RESEARCH PROJECT/RESEARCH GROUP
Research Group website: Plant Stress Signaling
http://www.igc.gulbenkian.pt/ebaena
POSITION DESCRIPTION
-Research Project / Research Group Description:
This project combines the expertise and research interests of two labs within the GREEN-IT Unit. The Baena-González lab is interested on how the plant carbon status influences plant growth and development and on the regulation of this process by the SNF1-related Protein Kinase1 (SnRK1), a highly conserved kinase that regulates energy homeostasis in all eukaryotes. The Saibo lab is interested on how photosynthesis is regulated and how this knowledge can be used to improve crop productivity. Combining the research interests of both labs, the main goal of this project is to investigate how SnRK1 regulates photosynthetic performance and how this knowledge can be translated into higher crop productivity. The project is therefore highly aligned with goal 2 of UN Sustainable Development Goals (Zero Hunger).
Plant biomass and crop yield are highly determined by the efficiency by which photosynthesis produces sugars. Despite its fundamental importance, little is known about how plants sense and adapt to the daily light–dark cycle, or how they adapt to unpredictable environmental stresses that compromise photosynthesis and deplete energy supplies. In addition to their role as an energy source, several sugars play key regulatory functions in many vital processes in plants, including photosynthesis. Moreover, SnRK1, whose activity is modulated by sugars, seems to be highly involved in the regulation of photosynthesis at the transcriptional and post-translational levels (1-3). To better understand how plants sense sugar levels and transduce this signal to modulate photosynthesis, this project aims at unveiling the molecular mechanisms underlying regulation of photosynthesis by SnRK1. This project will initially be performed in Arabidopsis, but the results will be translated into rice, a highly important cereal crop.
1-Baena-Gonzalez et al., Nature 2007, 448:938
2-Baena-Gonzalez and Sheen, Trends Plant Sci. 2008, 13(9): 474–482.
3-Nukarinen et al., Sci. Reports 2017, 6:31697
-Job position description:
Photosynthesis is highly regulated at transcriptional and post-translational levels in genes/proteins associated with electron transport chain or the Calvin-Benson cycle. To dissect the mechanisms by which SnRK1 regulates photosynthesis in Arabidopsis and rice, this project will be divided in 4 tasks:
Task 1
a) Analysis of transcriptomic datasets available for the Arabidopsis snrk1 knockdown mutant and of those generated by the student (e.g. response to light and/or dark) to identify differentially expressed photosynthesis-associated genes.
b) Establishment of a reporter system to investigate the factors that regulate the selected genes: generation of reporter plasmids (promoter of the genes of interest fused to luciferase), use of these in transient assays with co-expression of SnRK1 to validate SnRK1 function.
Task 2
a) In silico analysis of the selected genes (up to 3) to identify cis-elements in their promoters and the respective binding transcription factors. A yeast-one-hybrid (Y1H) approach may also be used to identify new TFs.
b) Interactions of the TFs with the promoters will be validated by EMSA, direct Y1H, and transactivation assays.
Task 3
a) Transient reporter assays with the constructs generated in Task 1 will be used to assess whether the identified TFs regulate the selected genes in vivo and whether SnRK1 controls the activity of these TFs.
b) The physical interaction between SnRK1 and the TFs as well as the potential phosphorylation of the TFs will be investigated in detail (e.g. by co-immunoprecipitation, by in vitro kinase assays and mass spectrometry)
c) Potential homolog TFs in rice will be identified and their function as regulators of the corresponding photosynthetic genes in rice will be validated in a transient protoplast system.
Task 4
a) Mutants of SnRK1 and selected TFs will be generated in rice (CRISPR/cas9 technology) and analysed at molecular, transcriptomic, phosphoproteomic, and physiological (photosynthesis, growth, and yield) levels.
OTHER RELEVANT WEBSITES
Research Group website of co-supervisor: Plant gene Regulation
https://www.itqb.unl.pt/research/plant-sciences/plant-gene-regulation/plant-gene-regulation
Host Institution website (IGC)
Host Institution website of co-supervisor (ITQB NOVA)
Physiological and molecular mechanisms behind cereal crop adaptation to climate change (Rubén Vicente Pérez)
CENTRE
GREEN-IT - Biorecursos para a Sustentabilidade
https://www.itqb.unl.pt/green-it
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Plant, Animal and Environmental Biology, Physiology, Ecology and Conservation
GROUP LEADER
Dr.Rubén Vicente Pérez
RESEARCH PROJECT/RESEARCH GROUP
ORCID ID of Dr Rubén Vicente which is now moving from the Max Planck Insitute of Molecular Plant Physiology: Potsdam, Brandenburg, DE; to the GREEN-IT Research Unit at ITQB NOVA
https://orcid.org/0000-0001-5469-2645
POSITION DESCRIPTION
-Research Project / Research Group Description:
Ensuring food security is facing new challenges due to the increase of the world population and the impacts of climate change on agriculture. Cereals are economically and culturally important crops in the Mediterranean basin, such as bread and durum wheat, barley, maize and rice, among others. The response of these crops to future climate scenario (e.g. high temperatures, water/salt stress, nutrient deficiencies) involves changes in physiological, biochemical and molecular mechanisms and can severely affect food production and human diet.
The study of these responses will help (i) to predict the impacts of climate change on plant growth and productivity, (ii) to understand the physiological and molecular mechanisms underlying the plant adaptation to such growth conditions, and (iii) to identify biomarkers associated with tolerance and/or high productivity under future climate scenario.
Plant responses to abiotic stresses define a complex and sophisticated regulatory network. To address this issue, in our group we work with a multi-level approach to investigate at whole plant level such responses by combining agronomic, physiological and molecular analyses and by covering different organs of the plants. Our main objective is to study the source-sink coordination in cereal crops and model plants, identifying the time and the place when and where the nutrients (mainly carbon and nitrogen) are being assimilated and used for the grain filling. Carbon and nitrogen metabolism are very relevant processes in the plant that greatly affect plant growth, grain yield and quality and are susceptible to changing environmental conditions. The final goal of this research is to provide useful information for future breeding programmes to improve crop yield while enhancing nutrient use efficiency on a sustainable basis contributing to the “Zero Hunger” objective of the Sustainable Development Goal 2.
-Job position description:
This job opportunity is available at the Plant Sciences Division in the Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA). This is an exciting PhD position for highly motivated students that want to learn and acquire new skills in a broad range of methodologies, experimental setups and growth conditions and be actively involved in the research projects of the group. The PhD project will include: (i) experimental design of field trials and/or experiments in greenhouses and growth chambers, (ii) plant cultivation under abiotic stresses that will be more recurrent with climate change, (iii) plant growth and health monitoring through the use of different non-invasive phenotyping techniques, (iv) collection of plant material for further analyses, and (v) estimation of the different environmental conditions on crop productivity. To understand better all these parameters and the underlying molecular mechanisms related to stress response, different laboratory measurements will be carried out to depict the metabolic status of the plants at transcript, metabolite and protein level. The position also include the possibility to collaborate with other research groups in foreign institutions inside Europe, with whom we have a strong collaboration (e.g. Institute of Natural Resources and Agrobiology of Salamanca, IRNASA-CSIC; University of Barcelona; Max Planck Institute of Molecular Plant Physiology, MPIMP). At the end of this project, the student will have a very complete background to continue developing her/his professional activity in academy or industry in the field of plant physiology, agriculture, biochemistry, ecophysiology or any other related field. This project integrates fundamental science and innovation in the form of translational approaches, covering a broad range of the value chain in food production.
OTHER RELEVANT WEBSITES
Host Institution website (ITQB NOVA)
FAO Report on the State of Food Security and Nutrition in the World
http://www.fao.org/state-of-food-security-nutrition/en/
FAO's strategy on climate change
http://www.fao.org/climate-change/our-work/what-we-do/climate-change-strategy/en/
Food security and food production systems. In: Climate Change 2014: Impacts, Adaptation, and Vulnerability
https://www.ipcc.ch/site/assets/uploads/2018/02/WGIIAR5-Chap7_FINAL.pdf
Building a regulatory network for cork development under different water regimes, from field to genes (Maria Margarida Oliveira)
CENTRE
GREEN-IT - Biorecursos para a Sustentabilidade
https://www.itqb.unl.pt/green-it
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Medicine, Public Health, Sports Science, Nutrition, Clinical Neuroscience and Psychology, Healthcare Management
GROUP LEADER
Prof.Maria Margarida Oliveira
RESEARCH PROJECT/RESEARCH GROUP
Description of the Plant Functional Genomics Lab general goals and team members involved in the project (Dr. Pedro M. Barros - https://www.researchgate.net/profile/Pedro_Barros)
https://www.itqb.unl.pt/labs/gplants/welcome
POSITION DESCRIPTION
-Research Project / Research Group Description:
Climate changes are increasing the intensity and frequency of extreme drought events and heat waves. This affects Mediterranean ecosystems, challenging forest productivity and resilience and increasing tree mortality. To support a bio-based economy and better explore available natural resources, we need more sustainable practices. Cork oak (Quercus suber L.) is a unique and emblematic tree from the Mediterranean region, with high economical, ecological and social significance mostly due to its renewable resource, cork. The sustainability of cork production is mostly affected by (1) the time needed for 1st harvest and (2) groundwater management. Through a collaboration of the Plant Functional Genomics Lab (PFG-GPlantS, ITQB NOVA) with the Forest Research Centre (CEF, UL), we are merging molecular biology and ecophysiology skills, to uncover cork development regulation in field conditions.
We study how environmental factors regulate gene expression and plant development, using molecular biology and biotechnology tools. We have been deeply involved in generating basic knowledge for Q. suber, participating in transcriptome assembly and whole genome sequencing. We are further studying the role of drought, heat and combined stresses in cork cambium development and suberin biosynthesis and composition. We aim to identify key regulatory pathways and, mostly, genes that could be used as markers to screen and select genotypes better fitted to a given environment (to apply the “right tree on the right place” principle). Also, one of our main goals is to understand how the interactions between carbon, water and nutrients affect the functioning of forest ecosystems, namely in a global change context. To this end we use an integrated approach of plant and soil ecology, and ecophysiology and biochemistry tools. We are particularly focused on the cork oak ecophysiological functioning and in deepening our understanding on the tree resilience to drought and tree mortality mechanisms.
-Job position description:
Some of our previous studies have shown a direct effect of drought and heat stress on the activity of the cork cambium and biosynthesis of suberin, the main biopolymer present in cork. From our transcriptomic and genomic studies, we have gathered important data now available for this project. Moreover, we established and have also available a study-site (monitored for almost 10 years) containing 50y-old cork oak trees, with and without the invasive shrub species Cistus ladanifer (that competes for soil water). A rain water exclusion strategy was also applied to both conditions in this site, to include a variable for extreme drought.
The PhD student will implement a comprehensive analysis of the cork oak response to different water regimes, coupling ecophysiology with multi-omics approaches to identify the main drivers of cork development regulation in natural ecosystems. The student will participate in the: (1) collection of multiple physiological parameters (i.e. sap flux density, ecosystem transpiration, leaf gas exchange) along the first 2 years; and (2) transcriptomic and metabolomics analysis of cork samples collected at the end of each growth period (late summer). Major transcriptomic changes occurring in developing cork between the treatments, and differences in suberin monomeric composition will be assessed and a regulatory network will be constructed integrating all data gathered. This systems biology approach will bring new insights into the regulatory mechanisms of cork formation under stress conditions, and highlight (genetic/chemical) markers to further screen genotypic variability in order to find the trees better fitted to a given environment. This data will also be relevant to maintain or optimize cork production and resilience of cork oak stands (‘Montado’ ecosystem), while optimizing water usage.
The PhD student will work closely with a multidisciplinary team with experience in ecophysiology, molecular biology, biochemistry and bioinformatics.
OTHER RELEVANT WEBSITES
Host Institution website (ITQB NOVA) https://www.itqb.unl.pt/
Description of the Centro de Estudos Florestais (Instituto Superior de Agronomia) and main research areas (Dr. Maria Conceição Brálio de Brito Caldeira - https://www.researchgate.net/profile/Maria_Caldeira) http://www.isa.ulisboa.pt/en/cef/about
Unravelling the role of astrocyte-induced neural microenvironment remodelling in traumatic brain injury pathobiology (Catarina Brito)
CENTRE
iNOVA4Health - Programa de Medicina Translacional (iBET, CEDOC/FCM, IPOLFG e ITQB)
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Medicine, Public Health, Sports Science, Nutrition, Clinical Neuroscience and Psychology, Healthcare Management
GROUP LEADER
Dr.Catarina Brito
RESEARCH PROJECT/RESEARCH GROUP
http://www.itqb.unl.pt/research/technology/advanced-cell-models
POSITION DESCRIPTION
-Research Project / Research Group Description:
Our research is mostly translational, targeting cellular microenvironment in disease for the identification of novel disease biomarkers and therapeutic targets. We develop innovative disease cell models, applying advanced cell culture approaches to human stem cells and other patient-derived cells. To identify molecular players of extracellular and intercellular communication, involved in pathobiology and/or therapeutic response, we integrate cell biology, biochemical, imaging and omics approaches. Our projects address carcinomas and neurological diseases.
This project targets traumatic brain injury (TBI), for which therapeutic options are scarce and no pharmaceutical options are available. Following TBI, astrocyte activation plays a major role in tissue damage by modulating inflammation and inducing extracellular matrix (ECM) remodelling. The latter is associated with abnormal neuronal activity and synaptic reorganization.
As such, the main objective of the project is address how the changes in neural microenvironment induced by astrocyte activation upon TBI impact neuronal functionality. We will employ human induced pluripotent stem cell-derived 3D cell models developed in the Lab. Mechanical and/or chemical insults will be applied to induce TBI-like astrocyte activation. We will characterize the astrocyte population and the changes in secreted extracellular matrix (ECM) and soluble molecules. These will be correlated with pathological synaptic activity, to identify potential therapeutic targets.
The project is coordinated by C. Brito & D. Simão (iBET), in collaboration with N. Raimundo (Gottingen University), E. Gualda (ICFO, Barcelona), T. Galli (Center of Psychiatry and Neuroscience, Paris) and the pharmaceutical company Tecnimede (PT).
-Job position description:
To address how the changes in neural microenvironment induced by astrocyte activation upon TBI impact neuronal functionality. We will employ human iPSC-
derived 3D neural cell models developed previously by our team. We have already demonstrated that in these models, the endogenous neural microenvironment and its remodelling along differentiation are recapitulated. Herein, we will apply mechanical and/or chemical insults to induce TBI-like astrocyte activation. The activated astrocyte populations will be characterized by single cell gene expression profiling; e changes in secreted extracellular matrix (ECM) and soluble molecules induced by the injury will be characterized employing a multi-omics comprehensive approach (proteomics and transcriptomics). The profiles of cellular samples from sequential post-injury time-points, as well as upon exposure to neuroprotective drugs targeting inflammation and remodelling of neural microenvironment, will be compared. The ECM changes identified will be correlated with neuronal function, namely with the development/amelioration of pathological synaptic activity. Multivariate analysis of the obtained datasets will be performed in order to identify the most promising targets of therapeutic value. This therapeutic potential will be further validated by gene-editing tools for the knock-down of the identified genes of interest and targeted pharmacological approaches, assessing its impact on functional recovery of neuronal activity.
The project outputs will be new mechanistic insights in secondary injury effects on neuronal activity and therefore uncover novel potential molecular targets to improve the therapeutic options and outcome of TBI. Moreover, it will provide the community innovative acute brain injury in vitro modelling approaches, suitable to study the sequence of events underlying the impact of insults not only at cellular level but also on the modulation of neural microenvironment.
Targeting human hydrogen sulfide metabolism against ovarian and breast cancer (João Filipe Bogalho Vicente)
CENTRE
iNOVA4Health - Programa de Medicina Translacional (iBET, CEDOC/FCM, IPOLFG e ITQB)
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Medicine, Public Health, Sports Science, Nutrition, Clinical Neuroscience and Psychology, Healthcare Management
GROUP LEADER
Dr.João Filipe Bogalho Vicente
RESEARCH PROJECT/RESEARCH GROUP
Webpage of the Structural Genomics Group, where the Vicente Team is integrated
https://www.itqb.unl.pt/research/biological-chemistry/structural-genomics
POSITION DESCRIPTION
-Research Project / Research Group Description:
The Vicente Team, at ITQB-NOVA/iNOVA4Health, studies the molecular mechanisms linking human hydrogen sulfide (H2S) metabolism with disease, employing a structural biochemistry approach complemented with work on human disease models within a n international collaborative network.
Growing evidence clearly associates several cancer types with dysregulation of H2S metabolism. Overexpression of H2S-synthesizing enzymes and increased H2S production was documented in cancer cells and shown to promote cancer progression by stimulating cellular bioenergetics, angiogenesis and sustaining resistance against chemotherapeutics. Cancer cells also require an efficient H2S detoxification system for their survival and proliferation, to deal with this potentially cytotoxic molecule. Indeed, enzymes of the mitochondrial sulfide oxidation pathway are also reportedly overexpressed in colorectal cancer patient samples.
This project will focus on the correlation between H2S metabolism enzymes and the development of ovarian and breast cancer, where increased expression of H2S-expressing enzymes has been associated with a stimulated cell bioenergetics and enhanced chemoresistance.
Combining gene silencing and cell biology studies on relevant breast and ovarian cancer specimens and cell lines, with molecular biophysics and structural biology studies on the recombinant human H2S metabolism enzymes, the relevant players linking H2S metabolism with ovarian and breast cancer will be identified. The validated enzyme targets will be engaged into compound screening, including hit validation in cell models, aiming to develop new therapeutics against cancer.
This project will be developed with Dr. Alessandro Giuffrè (CNR-IBPM, Rome, Italy) and Dr. Jacinta Serpa (IPOL-FG and CEDOC-NOVA/NMS) as co-Supervisors, granting the necessary complementary expertise to accomplish the proposed goals and providing access to patient samples for validation of the project’s targets.
-Job position description:
The PhD candidate will develop a multi-disciplinary and translational research plan within an exciting international network to identify and validate hydrogen sulfide metabolism enzymes as targets (Task 1) for the development of new anti-cancer pharmacological interventions (Task 2).
In Task 1, the PhD candidate will interrogate tissue specimens form breast and ovarian cancer patients compared to paired normal tissues (obtained in collaboration with the Pathology Service, JCabeçadas, who coordinates the IPOLFG Bio-Bank), for the expression levels of human H2S metabolism enzymes (western blots, WB, and immunofluorescence microscopy, with commercially available antibodies). Once the key enzymes have been identified, target validation will involve gene silencing by shRNA or with CRISPR/CAS9 technology, and confirmed by WB and specific enzymatic activity assays. The functional impact will be evaluated by comparative analysis of parental and gene-silenced cell lines in terms of cancer phenotypes (e.g. proliferation/migration, viability, apoptosis, among others) and susceptibility to currently used chemotherapeutic agents.
In Task 2, the PhD candidate will produce the recombinant protein targets (validated in Task 1), employing vectors already obtained and routinely used by the host Team for bacterial expression and purification. Pharmacological targeting of the selected H2S metabolism enzymes will involve compound screening employing biophysical methodologies. Lead compounds will be further tested in the appropriate cell models (Task 1) for their ability to affect cancer phenotypes and susceptibility to common chemotherapeutics.
We are looking for an enthusiastic and open-minded PhD candidate who will develop a challenging and impactful project. The candidate will engage into the MolBioS PhD Programme at ITQB-NOVA, providing both scientific training and acquisition of soft skills (science communication, entrepreneurship, ethics).
Melanoma-on-a-chip (Abel Martin González Oliva)
CENTRE
iNOVA4Health - Programa de Medicina Translacional (iBET, CEDOC/FCM, IPOLFG e ITQB)
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Medicine, Public Health, Sports Science, Nutrition, Clinical Neuroscience and Psychology, Healthcare Management
GROUP LEADER
Dr.Abel Martin González Oliva
RESEARCH PROJECT/RESEARCH GROUP
www.itqb.unl.pt/labs/biomolecular-diagnostic
POSITION DESCRIPTION
-Research Project / Research Group Description:
Despite remarkable efforts, metastatic melanoma remains incurable, presenting with significant mortality and an increasing public health burden. Improved skin model that better mimics the three-dimensional architecture of melanoma is urgently needed to facilitate the development of effective therapies. In recent years, advances in biomaterials and microfluidics technology made it possible for the culture of artificial skin to move a step ahead giving rise to the development of skin-on-chip platforms. The main goal of the project will be to use an innovative skin-on-a-chip to grow and maintain a model of melanoma. The model will be used to study the underlaying mechanisms mediating tumor invasion and to assess the effects of novel anti-cancer drugs.
The project will take advantage of the previous experience of the group in developing an optimized fully-humanized 3D skin inside a chip. In the developed protocol, a co-culture of primary cells (keratinocytes, melanocytes and fibroblasts) is established, resulting in fully-humanized dermis and differentiated epidermis structure, resembling the in vivo human skin. The device allows an apical and basal perfusion of media, reagents and collection of expressed compounds in the supernatant. The skin-on-a-chip also includes a transepithelial electrical resistance measurement approach (embedded electrodes) to monitor the tissue development during incubation.
The Biomolecular diagnostic (BMD) laboratory has extensive experience in the development of microfabricated chips for cell handling and in the development of 3D reconstructed human skin. The preliminary work developed in our group in this area paved the way to explore the chip prototype of the 3D fully-humanized skin for specific diseases assays, taking advantages of the collaborative work with Dr. Marta Pojo (co-superviser of this work - martapojo@gmail.com), head of the melanoma group of the Portuguese Oncology Institute (IPO).
-Job position description:
The main goal of the project is the development of a co-cultured melanoma skin inside of an innovative chip, towards the development of a personalized model to test specific therapies.
To achieve this goal, the first step will be the protocol optimization to produce a melanoma skin model onto a polymeric scaffold by developing a co-culture of fibroblasts, keratinocytes and melanocytes with different melanoma cell lines. Peripheral blood mononuclear cells will also be introduced in the model to study the interactions between tumor and immune cells as well as to investigate the molecular crosstalk of cancer cells with the immune system and to evaluate novel molecular targets towards new strategies for melanoma treatment.
The next step will be the development of the melanoma skin model inside the chip, using the previously designed protocol. The available chip can be reversibly sealed and presents a module-based architecture, allowing new configurations using techniques related to digital fabrication (3d printing, laser cutting and precision milling). Also, the platform includes a dynamic double perfusion system for controlled supply of nutrients and collection of metabolites for physiological evaluation of the tissue and a complete control of the experimental parameters. Perfusion of media, air-liquid interface or the topical application of drug treatments will be performed in the apical section of the chip. The basal section will be used also for media feeding and for collection of supernatant samples. Characterization of the melanoma model will be by immunohistochemistry and compared to other available models and literature.
Finally, the skin-on-a-chip platform will be used for personalized medicine. In collaboration with the melanoma group of the IPO, a personalized organ model of a patient with melanoma will be explored. This personalized melanoma-on-a-chip will allow the evaluation of alternative treatments and the test of standard or new drugs.
Foodomics approaches to unveil the health benefits of virgin olive oiL towards colorectal cancer (Ana Teresa de Carvalho Negrão Serra )
CENTRE
iNOVA4Health - Programa de Medicina Translacional (iBET, CEDOC/FCM, IPOLFG e ITQB)
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Biotechnology, Bioinformatics, Pharmaceuticals, Food Technology
GROUP LEADER
Dr.Ana Teresa de Carvalho Negrão Serra
RESEARCH PROJECT/RESEARCH GROUP
The Food Functionality and Bioactives Laboratory has strong competences on Analytical Chemistry applied to the study of foods concerning their features in different approaches as quality, safety and sensory characteristics. Research has been also focused on the beneficial health effects of food bioactives, such as, phenolic compounds, whenever they come from food products or are extracted from food wastes. Liquid and gas chromatography associated with mass spectrometry, are used by the group in the characterization of samples. In vitro (cell-free and cell-based) assays, in vivo studies using animal models of diseases and human intervention trials are performed, in house or in collaboration with other research groups, in order to evaluate the health benefits of foods consumption and bioavailability of food bioactives
https://www.ibet.pt/laboratory/food-functionality-and-bioactives-lab/
POSITION DESCRIPTION
-Research Project / Research Group Description:
The main research focus of our lab is to study the health benefits of food bioactives and translate to the clinical application. In the field of colorectal cancer, our key research lines include: i) Development of phytochemical – enriched extracts; ii) Evaluation of the effect of natural extracts and food bioactives in colorectal cancer cells; iii) Development of 3D cell models of colorectal cancer; iv) Development of scalable culture strategies for the expansion of patient-derived cancer cells; and v) Design of human intervention trials to evaluate the impact of food bioactive compounds in improving the efficacy of therapy and reducing its side effects.
From epidemiological and case control studies it is reported that virgin olive oil (VOO), the main source of dietary fat in the Mediterranean diet, is associated with the reduction of the incidence and prevalence of colorectal cancer (CRC). Although it has already been recognized that hydroxytyrosol, the most important phenolic and antioxidant compound of VOO (native compound and also a metabolite derived from other phenolics such as oleuropein), has key roles in inhibiting proliferation of several tumor cell lines, little is known about its underlying molecular mechanisms as well as the effect of VOO-derived colonic metabolites on CRC. The aim of this project is to elucidate the protective effect of VOO on CRC. In particular, a foodomic strategy involving transcriptomics and metabolomics, will be applied to generate novel insights on the molecular mechanisms operating in 3D cell models of human CRC after treatment with VOO compounds, mainly phenolics and colonic metabolites. More importantly, this knowledge will support the rational design and implementation of the first human intervention study aiming at evaluating the effect of VOO diet supplementation on cancer prevention and therapy.
-Job position description:
The objectives of this project are:
1. Develop physiologically relevant 3D cell models of CRC using immortalized cell lines and patient derived cell lines;
2. Evaluate the effect of VOO compounds in targeting colorectal cancer stem cells;
3. Identify of novel metabolic processes and potential signalling pathways modulated by VOO compounds;
4. Evaluate the effect of a nutritional intervention with VOO/VOO compounds on disease and patient outcomes in CRC patients.
This project is divided in 4 tasks:
T1.DEVELOPMENT OF 3D CELL MODELS OF CRC
Recently, our lab developed a 3D cell model with cancer stem cell-like traits by culturing HT29 cells as aggregates in stirred culture systems. The knowledge gained with this model will be applied for the development of cell spheroids derived from other human CRC immortalized cell lines encompassing different tumorigenesis pathways and also primary cultures derived from CRC surgical specimen.
T2.EVALUATION OF THE EFFECT OF VOO COMPOUNDS ON CELL MODELS
The compounds selected for this project will include mainly phenolics and their metabolites that are expected to reach the colon after a diet supplementation with VOO. The effect of VOO compounds in inhibiting cancer cell growth and in modulating cancer stem cell population on the 3D cell models developed in T1 will be carried out as described in our previous works.
T3.FOODOMICS
To discover the main mechanisms of action of VOO compounds in CRC cells, a foodomics approach involving transcriptomics and metabolomics will be applied using high-throughput technologies.
T4.HUMAN INTERVENTION STUDY
A pilot study will be conducted in CRC patients to evaluate the effects of VOO/VOO compounds in improving the efficacy of therapy and reducing its side effects (collaboration w/IPOLFG).
This work will be co-Supervised by Prof. Maria do Rosário Bronze, from Faculty of Pharmacy University of Lisbon.
Advancing Manufacture of cell-based therapy products through metabolic understanding: application in ischemic Heart diseases (MyHeart) (Maria Margarida de Carvalho Negrão Serra)
CENTRE
iNOVA4Health - Programa de Medicina Translacional (iBET, CEDOC/FCM, IPOLFG e ITQB)
AREA OF KNOWLEDGE
Life Sciences Panel
GROUP OF DISCIPLINES
Biotechnology, Bioinformatics, Pharmaceuticals, Food Technology
GROUP LEADER
Dr.Maria Margarida de Carvalho Negrão Serra
RESEARCH PROJECT/RESEARCH GROUP
https://www.ibet.pt/innovation/biopharma/rd-areas/cell-therapy/
POSITION DESCRIPTION
-Research Project / Research Group Description:
Our research is driven by the vision to bridge engineering and stem biology, with the goal of accelerating next generation therapies from bench to bedside. The key research line that highlights our competences has been focused on streamlining robust manufacturing of cell therapy products with improved functionality. We have experience in expansion, differentiation/maturation and cryopreservation of human stem cells including adult, embryonic and induced pluripotent stem cells (hiPSC) as well as their derived extracellular vesicles (EV), including exosomes.
Our work aims to develop bioinspired and integrated strategies to improve the generation and functionality of key cell therapy products. The key research line has been focused on the development of novel cell culturing strategies that recreate environmental conditions excelling stem cell proliferation as well as their differentiation/maturation into functional cell therapy products, through metabolic and process understanding. In particular we have been designing processes based on expertise in 3D cell culture, bioreactor technology, co-culturing approaches and microencapsulation strategy. Noteworthy, we also applied robust multi-parametric techniques including advanced “-omics” technologies (proteomics, transcriptomics, metabolomics and fluxomics) as complementary analytical tools to support bioprocess understanding and optimization as well as to unveil the mechanism of action of cell therapy products.
We have also been developing hiPSC-derived in vitro cardiac tissue models for application in pre-clinical pharmacological screening based on a robust and scalable protocol for generation of hiPSC-derived cardiomyocytes (hiPSC-CM). Modulation of key environmental factors namely, metabolic substrate, co-culture with other hiPSC-cardiac derivatives, biomaterials and components of the ECM, were also evaluated to improve hiPSC-CM maturation features and functionality.
-Job position description:
MyHeart project aims to generate technological tools and scientific knowledge to empower the translation of hPSC-based therapies for the treatment of MI, through quantitative dissection and manipulation of cellular metabolic programs, using a holistic and systems-level approach. In particular, the project aims to improve our ability to modulate cardiomyocyte commitment and functionality as well as EV biology and potency by dissecting the role of metabolism during hPSC differentiation.
We will optimize in vitro protocols aiming at increasing the production of clinically relevant numbers of hPSC-CM and EV with improved functionality. In particular, we will elucidate the metabolic pathways that regulate the proliferative capacity of cardiac progenitors to further stimulate their expansion and improve final hPSC-CM yields. Since current protocols generate hPSC-CMs that retain a fetal rather than adult state that can lead to arrhythmia, we will also investigate the role of metabolism in functional CM maturation and subtype specification (ventricular, nodal, atrial). Simultaneously, we will evaluate the impact of metabolic wiring on EV release, biology and functionality at different stages of CM commitment.
We will compressively characterize the 3 most clinically relevant hPSC-cardiac populations and derived EV, generated by the optimized bioprocess. Multi-parametric techniques including omics technologies and cell-based assays will be used to assess critical quality attributes of these products. Their preclinical efficacy will be also evaluated by our partners of ongoing European projects holding strong expertise in AMI animal models.
The research plan is divided into 3 work packages (WP):
WP1. Modulation of metabolome during hPSC-CM differentiation and maturation
WP2. Bioprocess intensification for production of hPSC derived cardiac cells and EV
WP3. Functionality and efficacy of hPSC derived cardiac cells and EV
