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This course explores the application of high-throughput DNA sequencing technologies and associated bioinformatic tools to investigate microbial diversity, with a focus on their roles in biotechnology and biomedicine. Genomics, metabarcoding, and metagenomics approaches will be covered in detail. The course integrates lectures, practical laboratory sessions, and seminars by invited researchers actively working in the field. Students will gain expertise in applying these methodologies to address scientific inquiries, fostering their ability to independently manage and analyze genome-wide datasets. A hallmark of this course is its emphasis on hands-on learning. Students will have the opportunity to develop and implement bioinformatic workflows, actively testing and refining their newly acquired skills.
Next-Generation Sequencing in Environmental Monitoring
Coordination: Filipe Costa & Pedro Soares
This course provides a broad perspective on the use of DNA-based technologies and tools for biodiversity research and monitoring, with a focus on (e)DNA (meta)barcoding approaches. The concepts, terminology, applications and specificities of (e)DNA (meta)barcoding, metagenomics, metatranscriptomics, will be addressed. Diverse case-studies will be presented by invited researchers, followed by Q&A and discussion. In addition, the students will carry out a hands-on bioinformatics analyses of a sub-set of published data to simulate a small NGS-based monitoring study. This will provide opportunity for detailed a) identifying the most fit applications and particularities of the various types of molecular tools; b) recognizing uncertainty and limitations of each molecular tool; c) train interpretation of NGS-derived monitoring data and perceive the critical aspects of the experimental design, procedure implementation and bioinformatic analyses that must be take into consideration.
This course examines the different types of interaction between plants and microorganisms. Specifically, the morphological, biochemical and molecular characterization of plant-microorganism interactions will be studied, as well as the recognition of the role of microorganisms in the sustainability and productivity of plants of interest and in the functioning of ecosystems. A general overview of the ecological and agronomic importance of plant-microbe interactions is discussed, including mycorrhizal interactions, interactions with nitrogen-fixing bacteria, interactions between rhizobia and legumes, plant-pathogen interactions, as well as epiphytes and endophytes. The course includes lectures, laboratory work and seminars, with the generous participation of invited researchers and PhD students working in the field.
This comprehensive course delves into cutting-edge research strategies in Plant Molecular Biology. It covers the intricate regulation of eukaryotic gene expression at three primary levels: chromatin structure, small RNAs, and transcription factors. Students will explore the molecular mechanisms driving plant developmental processes and learn advanced methods for studying transcription factors, such as Protein-DNA and Protein-Protein interactions. The curriculum includes an in-depth analysis of reverse and forward genetics, utilizing mutagenic agents, insertion mutants, and genome editing techniques. Additionally, the course integrates bioinformatics for functional gene and protein discovery. Learning outcomes include the ability to explain the significance of gene expression regulation in plant development and responses to biotic and abiotic stresses, comprehend the role and tools of functional genomics, evaluate the techniques for studying transcription factors, and develop robust laboratory skills for investigating molecular mechanisms in plants.
Molecular Responses of Plants in a Changing Environment
Coordination: Hernâni Gerós
The course explores the theoretical aspects related to the physiological and molecular mechanisms of plant response to environmental stress. Key laboratory experiments will be conducted, such as studying the expression and function of genes involved in the response of plants to environmental cues. This approach will provide students with an integrated understanding of the interactions between plants and the environment, while also helping them acquire laboratory and science communication skills. Topics include: (i) environmental stress factors that limit plant development and productivity, such as water, salt, heat, and metal stresses; (ii) plant response mechanisms to stress at the morphological, cellular, and molecular levels; (iii) experimental strategies to assess plant responses to environmental stress; (iv) stress response hormones in plants; (v) transformation and improvement strategies; (vi) transport of solutions in the interaction of plants with the environment.
Plant Adaptations to Climate Changes
Coordination: Hernâni Gerós
This is a Blended Intensive Program (BIP), co-organised by the members of the Arqus Cluster on Sustainable Development and Climate Change. The course addresses the challenges that climate change and pollution pose on plant production (agriculture) through a multifaceted approach. Theoretical sessions are conducted both online and in-person, in synchronous and asynchronous formats, exploring diverse facets of plant physiology, development, and productivity in response to abiotic and biotic stresses induced by climate change and pollution. Hands-on experimental activities enable participants to apply theoretical concepts. Furthermore, seminars by national and international specialists enrich participants’ understanding of cutting-edge research and emerging trends. In-person components also include technical visits to explore issues of a more applied nature.
Agroecology combines fundamental and applied research to sustainably increase food production. The overarching aim of the course is to understand the dynamics and interactions of agroecosystem components to improve their performance in an ecologically-sound manner. The course will provide knowledge and skills to understand, evaluate and discuss agroecosystem biodiversity and function as affected by different agricultural management practices, in the context of current societal challenges and global change. Lectures will cover agroecosystem services in crop protection, soil quality, yield stability and One Health, and review Agroecology principles in comparison with various agricultural management paradigms. This will provide tools to enhance student creativity in assessing areas of Agroecology that need further research. Critical thinking and team skills will be improved in practical group assignments to assess and discuss topics on yield sustainability and agroecosystem resilience.
Ecosystem Services, Nature and Governance: Concepts, Tools and Applications
Coordination: Cláudia Pascoal & Cláudia Carvalho-Santos
Ecosystem services, as the contributions of nature to people, are increasingly highlighted in research, political and business agendas. This course covers the scientific, economic, and socio-political dimensions of ecosystem services, through a mix of theory and hands-on sessions, and interactions with different specialists. The course is designed for post-graduate students, post-doctoral researchers, and professionals. Participants will be able to: i) explore different tools and methods to evaluate and monitor ecosystem services; ii) perform a valuation of the benefits and contributions from biodiversity to people; iii) recognize the opportunities and risks of ecosystem services at the business-politics-society interface.
River Restoration: from Theory to Practice
Coordination: Cláudia Pascoal
River restoration involves managing rivers to reinstate natural processes, thereby restoring biodiversity and providing benefits to both people and wildlife. This course counts on the participation of different experts that cover river restoration methodologies, mainly natural engineering techniques, and the application of ecosystem services in river restoration and water management. Topics include i) approaches to mitigate the impacts of river regulation to improve connectivity, ii) links between hydro-morphology and biodiversity (e.g., ecological requirements for fish), iii) river restoration in urban areas, iv) GIS in restoration (e.g., designing green infrastructure networks), v) environmental solutions to waste valorisation, vi) mapping and valuation of ecosystem services, vii) evaluation and monitoring of river restoration projects, and viii) field work and case-studies. Target audience: post-graduate students, post-doctoral researchers and professionals.
Linking Biodiversity to Ecosystem Services under Global Change
Coordination: Cláudia Pascoal, Giorgio Pace, Cláudia Carvalho-Santos & Fernanda Cássio
Ecosystem services, as the contributions of nature to people, are increasingly highlighted in research, political and business agendas. This course covers the scientific, economic, and socio-political dimensions of ecosystem services, through a mix of theory and hands-on sessions, and interactions with different specialists. The course is designed for post-graduate students, post-doctoral researchers, and professionals. Participants will be able to: i) explore different tools and methods to evaluate and monitor ecosystem services; ii) perform a valuation of the benefits and contributions from biodiversity to people; iii) recognize the opportunities and risks of ecosystem services at the business-politics-society interface.
Invasive species are currently one of the leading threats to biodiversity, being responsible for important ecological, economic and health impacts. Public and scientific recognition of the problems associated with invasive species has grown exponentially in the last two decades. Given the high ecological and economic impacts generated by biological invasions and the academic recognition of this topic, it is mandatory to prepare graduate students from different backgrounds in this scientific area. This advanced course has the overarching goal of providing an overview of the study of Invasion Ecology. We will cover topics about transportation and dispersal of species, species distribution modelling applied to invasive species, ecological and economic effects mediated by invasive species, and discuss some possible management measures to mitigate those impacts.
Ecotoxicology & Environmental Risk Assessment
Coordination: Fernanda Cássio & Cláudia Pascoal
This course adopts a multidisciplinary approach to describe the interactions between contaminants, biodiversity and ecosystems, as well as to estimate the probability of ecosystems being affected by such contaminants. It includes a mix of theoretical and practical sessions, along with interactions with various experts. The course covers the following topics: i) model organisms and bioassays, ii) biomarkers of stress, iii) toxicology of emerging contaminants, iv) mixture toxicity, v) environmental biomonitoring, vi) statistics in ecotoxicology, vii) environmental risk assessment, and viii) regulation and legislation. Target audience: post-graduate students, post-doctoral researchers and professionals.
Stress Ecology and Ecotoxicology
Coordination: Fernanda Cássio
This course addresses the stress response pathways of biota and ecosystems to biotic and abiotic stressors. It includes a mix of theoretical and practical sessions, along with interactions with various experts. The course covers the following topics: i) linking ecology to ecotoxicology, ii) biotic interaction under chemical stress, iii) emerging (e.g., nanoparticles, microplastics, pharmaceuticals) and classical contaminants (e.g., metals), iv) mechanisms of defence against stressors, v) environmental omics, v) on- and off-site effects of wildfires, vi) mixture toxicity under a warming environment, and vii) data treatment. Target audience: post-graduate students and post-doctoral researchers.
This course has a strong field component, profiting from the field logistics available at the CBMA (access to a 7.5 m rib boat; an 18 m/80 t oceanic vessel; ROVs-Remote Operated Vehicles capable of diving at 200 m; dredges; plankton and Manta nets; field station in Viana do Castelo…). It aims to i) deepen students’ knowledge of marine biology and coastal ecosystems, with particular emphasis on subtidal (including mesophotic habitats), coastal (intertidal and dune systems) and estuarine environments; ii) study the services provided by coastal natural systems and the consequences for humans of their destruction or degradation; iii) introduce sampling methodologies in the marine environment, including the use of dredgers, plankton nets and the operation of ROVs. Field sessions will be a strong point in the course, complemented by case study-based theoretical sessions in the target environments of the course.
Fungal infections significantly impact public health, food security, and the environment. The World Health Organization (WHO) recognizes fungi as critical pathogens, highlighting the need for targeted research and information dissemination. Environmental changes, including climate change and habitat destruction, drive the emergence and spread of fungal infections, affecting their distribution, virulence, and host range. This course addresses these issues by: (i) presenting the physiological mechanisms behind fungal pathogenicity; (ii) identifying methods for fungal species identification; (iii) understanding antifungal resistance and virulence mechanisms; and (iv) exploring Next-Generation Sequencing and genomic analysis. Additionally, the course emphasizes (v) training in skills such as oral and written expression, teamwork, communication, and critical thinking, integrating the study of fungal diseases with environmental factors through real-case studies.
Structural Biology of Membrane Transporters
Coordination: Margarida Casal & Isabel João Silva
The control of solute transport across biological membranes is crucial for maintaining cellular homeostasis and long-term stability. Therefore, understanding the molecular mechanisms underlying this process is a significant focus of both fundamental and applied research. Cells utilize integral membrane proteins (IMPs) to facilitate the movement of lipid-insoluble molecules, which account for approximately one-third of an average organism’s gene coding capacity. Due to their essential roles in various cellular functions, IMPs are estimated to constitute 80-90% of targets relevant to the chemical and pharmaceutical industries. This course is designed for postgraduate students and researchers dedicated to studying solute transport across biological materials. It will offer seminars and lectures covering diverse aspects of transport-related research, along with laboratory classes and computer-assisted sessions. Participants will learn about various methodologies used to study and engineer transport systems, including their evolution, functional characterization, and structural analysis.
Biopolymers Based on Renewable Resources: from Synthesis to Applications
Coordination: Margarida Casal, Pedro Martins & Raul Machado
One of the main challenges in global sustainability is mitigating the extensive use of petroleum-based polymers by using biopolymers of natural origin. This demanding transition requires further exploration of these polymers in terms of their physical-chemical properties and the development of new processing techniques to leverage their increasing use in several applications. This course comprehensively explores the latest advancements in biopolymers, focusing on their design, processing, and diverse applications. It combines theoretical knowledge with laboratory hands-on experiences, providing participants with opportunities to engage with renowned specialists in the field. Participants will also acquire the knowledge necessary to conduct assessments of biopolymer properties, focusing on innovative processing, such as additive manufacturing (3D printing), and physical-chemical characterisation techniques. Additionally, the course addresses the environmental impact of biopolymers and explores strategies for their sustainable development and application.
Challenges and Therapeutic Opportunities of Bionanoparticles
Coordination: Andreia Gomes, Paula Sampaio & Ana Preto
The fast pace at which nanotechnology-based products have been introduced in our daily life has led to concerns regarding safety and eventual risks of exposure to nanoparticles, whilst opening possibilities in the development of increasingly sophisticated nanodevices for precision therapy. This course will focus on the presentation and discussion of important concepts for understanding the potential risks of exposure to nanoparticles, in particular in the human immune system. Simultaneously, the cutting edge progresses in nanotechnology-based strategies to control and modulate immune responses to treat and potentially cure diseases (such as cancer and chronic infections) will also be discussed. Practical classes will allow the participants to produce specific types of nanoparticles and evaluate their cytotoxicity and interaction with immune cells.
This course aims to inform attendees of the relevance and relationship of oxidative stress to a series of plant and animal physiologic processes and pathologies. At the same time, it explores the antioxidant activities of many plant secondary metabolites, and their physiological relevance for the plant, as well as their potential pharmacological application in animal pathologies, particularly for human health. Besides theoretical classes, practical lab-work is implemented, which include various biochemical and cellular bioactivity testing assays, including: (i) induction of oxidative stress and measurement of antioxidant responses in plant cells and animal cells models (phytochemicals, free radical assessment, lipid peroxidation); (ii) antioxidant and antigenotoxic properties of plant compounds (yeast comet test, flow cytometry and antioxidant activity measurement); (iii) evaluation of several enzyme activities (e.g. anti-acetylcholinesterase, anti-COX, and nitric oxide scavenging of natural compounds).
In the last decades, there has been a growing interest in studying regulated cell death (RCD), as changes in these processes, either their decrease or increase, are associated with different pathologies, such as cancer or degenerative diseases. Apoptosis has been the most well study and characterized form of RCD but it has become evident that different regulated necrosis processes have also a significant impact in different physiological and pathological scenarios. Autophagy, although essentially a survival process, has also been associated with RCD in response to conditions of high stress. In addition, studying cell death mechanisms in microorganisms, besides contributing for the advancement of knowledge, can also open potential avenues for biotechnological advancements and therapeutic interventions. Due to the intense research on RCD and its importance both from a fundamental and applied perspective, the course aims to give an advanced knowledge of the state of the art of this field.
This course is organized for postgraduates and focuses on the mechanisms of protein and traffic degradation in different organisms, and on their modes of signalling and regulation. A panel of renowned international experts are involved in teaching. The course includes seminars and lectures on various aspects of this area of research, as well as practical sessions on several advanced Molecular Biology techniques, such as ex-editing of genomes (CrisprCas9), biochemical tools (SILAC) and bioinformatics analysis (supramolecular networks). The following themes will be specifically addressed: endocytosis and exocytosis mechanisms, retrograde traffic, Rab regulation in membrane traffic, the ESCRT, SUMO and MBV pathways. The practical classes will focus on (i) the use of protein markers to study protein traffic, (ii) ubiquitination in vivo and in vitro (yeast cells and tumor lines), (iii) bioinformatics approaches to study intracellular traffic. Two sessions will be held on “Grant writing” and “How to plan and write a scientific paper”.
The definition of Metabolic Engineering used in this course encompass all steps between the initial concept of a process to the finished design, in an attempt to cover and integrate the disparate areas that necessarily make up the field of Metabolic Engineering. Practical classes will showcase the assembly of a metabolic pathway in the yeast Saccharomyces cerevisiae using modern 2nd generation cloning methods. Computer classes will cover the planning of cloning constructs using the pydna tool in the Jupyter notebook environment. The mathematical treatment of metabolism will be done using Optflux 3 and/or COBRApy. At the end of this course the student should be able (i) to define the central concepts of Metabolic Control Analysis such as control coefficients, elasticities and the summation theorem, (ii) to construct a stoichiometric matrix given a simple model of metabolism, (iii) calculate intracellular fluxes given a stoichiometric matrix and a flux vector, (iv) translate simple cut & paste cloning and homologous recombination strategies into pydna.