Advanced Courses and Seminars I

 

COURSE: Cell Biology / Biologia Celular

 

 

Coordinator(s): Claudio Sunkel
Faculty and invited speakers: Claudio Sunkel, Carlos Conde, Elsa Logarinho and Eurico Morais-de-Sá

Short summary: The cell is the basic unit of life and so understanding cell biology is essential to learn how organisms develop, grow and maintain homeostasis. The cell biology course is focused in cell-cycle control, regulation of chromosome segregation, generation of cell polarity, and also covers how aberrant cellular function contributes for aging. Lectures provide basic knowledge and emerging research in the field.

Outline of the course: 4 lectures

.......................................................................................................

 

COURSE: Ethics, Science and Society/ Ética, Ciência e Sociedade

 

 

Coordinator(s): Anna Olsson
Faculty and invited speakers: Anna Olsson, Júlio Borlido Santos

Short summary: The Ethics, Science and Society module gives students an introduction to ethics and research integrity as well as science with and for society. Focus is on issues of general relevance (e g research integrity, authorship issues, public dialogue) and on an interactive way of teaching.

Outline of the course: 2 lectures

.......................................................................................................

 

COURSE: Functional Genetics/Genética Funcional

 

 

Coordinator(s): Alexandra Moreira & Didier Cabanes
Faculty and invited speakers: Maria João Prata, Carolina Lemos, Isabel Silveira, Alexandra Moreira, Jorge Vieira, Cristina Vieira, Daniel Osório, Sandra Sousa, Didier Cabanes

Short summary: Functional genetics is devoted at unravelling the function of DNA at the level of genes, RNA transcripts and protein products so as to understand the relationship between genome and functional properties, or phenotype, of a given organism. A major focus of functional genetics is the development of treatments for many diseases, namely human genetic diseases. Experts in the area will present state-of-the-art research on functional genetics during the physiological events that occur in different types of cells and in different systems. Scientific challenges in the field and how they are experimentally addressed will be discussed with the students.

Outline of the course: Lectures, journal clubs, research seminars

.......................................................................................................

 

COURSE: Infection and Immunity/ Infeção e Imunidade

 

 

Coordinator(s): Nuno Alves & Margarida Saraiva
Faculty and invited speakers: Nuno Alves, Alexandre Carmo, Nuno Santarém, Margarida Saraiva, Joana Tavares, Manuel Vilanova

Short summary:This course covers the principles underlying the function of the immune system in health and disease. In particular, it will detail the molecular basis of immunity and tolerance induction, and discuss how the understanding of pathogen-host interactions can be therapeutically explored to improve the immune response during infection.

Outline of the course: Lectures

.......................................................................................................

 

COURSE: Molecular mechanisms/Mecanismos moleculares

 

Coordinator(s): João Morais Cabral & Sandra Macedo-Ribeiro
Faculty and invited speakers:

Short summary:This course aims at providing an understanding about molecular mechanism through the analysis of well characterized model systems and exploration of concepts underlying molecular recognition and selectivity, strength of interaction, molecular reaction and molecular regulation.

Outline of the course: Lectures and practical work

.......................................................................................................

 

COURSE: Neurobiology/Neurobiologia

 

 

Coordinator(s): Mónica Sousa
Faculty and invited speakers: Mónica Sousa, João Relvas, Pedro Brites, Teresa Summavielle, Boris Safronov

Short summary:This course will address different aspects of neuronal and glial cell biology, from axon growth to myelination, cytoskeleton organization and dynamics, mechanisms of addiction and organization of neuronal networks.

Outline of the course: Lectures, group discussions, journal clubs

 

.......................................................................................................

 

Advanced Courses and Seminars II

 

Analysis and Interpretation of Next-Generation Sequencing data

 

 

 

Coordinator(s): Patrícia Oliveira/ Pedro Ferreira/ Carla Oliveira
Faculty and invited speakers: Patrícia Oliveira/ Pedro Ferreira/ Abel Sousa/ Marta Ferreira/ Rita Monteiro

Short summary: Large-scale Sequencing projects have created a wealth of data for scientist that is worth to explore. However, the challenge is its analysis and even accessing these data to extract useful information connect to the system being studied. This course focuses on employing Open-source bioinformatics software, tools and resources – including web-based programs, databases and common-line programs– to access and analyse the extraordinary volume of data available, to answer relevant biological questions. It includes practical exercises for students.

Outline of the course: The course will span 4 days with a total of 20 hours with practical sessions and 4 modules.

 

.......................................................................................................

 

COURSE: Topics in Quantitative Analysis of Biological Data

 

 

Coordinator(s): Paulo Aguiar / António Pereira
Faculty: Paulo Aguiar / António Pereira

Short summary: Translating experimental data into meaningful information often requires the use of mathematical tools. In practice, this procedure usually involves data reduction into a few meaningful quantities (metrics) and, more generally, analysis of the data against one or a number of mathematical model templates. This course provides a short introduction to some key concepts and practical applications of quantitative and semi-quantitative analysis, including: mathematical models in biology, noise filtering, linear and non-linear regression, periodic features extraction (Fourier analysis), error propagation, dimensional analysis and order-of-magnitude estimations.

Outline of the course: Lectures and class-room exercises.

.......................................................................................................

 

COURSE: Proteómica baseada em espectrometria de massa / Mass Spectrometry-based Proteomics

 

 

Coordinator(s): Hugo Osório/Sara B. Pereira
Faculty and invited speakers: Hugo Osório/Sara B. Pereira/Celso Reis

Short summary: Recent developments in the field of proteomics have revolutionized the way that proteins and their function are studied. This course provides an overview of the most relevant Mass Spectrometry-based Proteomics (MS-proteomics) techniques, from experimental design, to sample preparation and data analysis. After the course, the students will be able to identify the critical steps and successfully design MS-based proteomics experiments.

Outline of the course: The course includes lectures on MS-based proteomic techniques, tutorials on experimental design, sample preparation and data analysis. Practical sessions will focus in the identification and quantification of proteins and characterization of protein post-translational modifications based on real data (18h).

.......................................................................................................

 

COURSE: Escrita Científica / Scientific Writing

Coordinator(s): Anna Olsson
Faculty and invited speakers: Anna Olsson, Júlio Borlido Santos, Helder Maiato, Alan Weed

Short summary: This course addresses the different steps and aspects in the process from research results to published paper.

Outline of the course: Lectures, exercises, group discussions.

.......................................................................................................

 

COURSE: Microscopia ótica / Light Microscopy

Coordinator(s): Paula Sampaio
Faculty and invited speakers: Paula Sampaio

Short summary: The course is design to provide the basis of light microscopy including sample preparation, optical contrast techniques, fluorescence microscopy and digital imaging. It focuses also in advanced light microscopy techniques and applications, such as optical sectioning methods, live cell imaging, molecular analysis, super-resolution microscopy and correlative light-electron microscopy.

Outline of the course: 12h lectures + 3h tutorials + 20 h labs/practical classes.

.......................................................................................................

 

COURSE: Histologia e Microscopia eletrónica / Histology and Electron Microscopy

Coordinator(s): José Pissarra/ Rui Fernandes
Faculty and invited speakers: José Pissarra, Fernanda Fidalgo, Rui Fernandes, Ana Rita Malheiro, Rossana Correia, Nuno Mendes

Short summary: The module is centered on Transmission Electronic Microscopy (TEM) namely conventional ultrastructure; immunoelectromicroscopy; elemental analysis – EDX; STEM. Training in tissue preparation, and Optical Microscopy namely in tissue preparation and equipment usage for cryomicroscopy. Fixation, embedding, sectioning and staining for LM applications. Principles of Immunohistochemistry.

Outline of the course: lectures, tutorials and labs/practical classes (20h).

.......................................................................................................

 

COURSE: Bioinformática / Bioinformatics

Coordinator(s): Jorge Vieira/Cristina Vieira
Faculty and invited speakers: Jorge Vieira, Cristina Vieira, Hugo Lópes Fernandez

Short summary: Genome and transcriptome sequence data is accumulating at an explosive pace. For instance, more than one thousand animal genomes are now available, and there are hundreds or even thousands of gene sequences available for the most studied viral species. Such information can be used to address many biological problems. Therefore the students will learn how to get the data into the appropriate format for running the needed phylogenetic, positive selection, polymorphism, recombination and other analyses.

They will use software applications developed by us such SEDA (SEquence DAtaset builder; http://www.sing-group.org/seda), ADOPS (https://sing.ei.uvigo.es/ADOPS), BDBM (www.sing-group.org/BDBM/ ), as well as standard bioinformatics tolls.

Outline of the course: Lectures, practical classes (20h)

.......................................................................................................

 

COURSE: PCR quantitativo em tempo real / qPCR and gene expression analysis

Coordinator(s): Marta Vaz Mendes/ Catarina Pacheco
Faculty and invited speakers: Marta Vaz Mendes; Catarina Pacheco

Short summary: Quantitative real-time PCR (qPCR) remains as the gold standard for targeted gene expression analysis. This course provides an overview of the qPCR methodology covering different aspects of a qPCR experiment from assay design to data analysis following the MIQE guidelines. The course provides the skills to identify the critical steps of a qPCR experiment that impact the quality and robustness of the experiment.

Outline of the course: The course includes lectures on the qPCR theoretical background, tutorial on the selection and validation of reference genes and a practical session on gene expression analysis based on real data (12h).

.......................................................................................................

 

COURSE: Expressão, Purificação e Caracterização de Proteínas / Protein expression, Purification and Characterization

 

Coordinator(s): Frederico Silva
Faculty and invited speakers: Frederico Silva, Fátima Fonseca, Margarida Bastos, Rita Rocha, Tony Rodrigues, Jorge Rosada

Short summary: Proteins do most of the work in the cells and intercellular matrices of tissues, being required for all life processes including the catalysis of reactions, the regulation of pathways and the structural properties and movement of molecules, organelles and cells. This course will cover comprehensively the productions and purification of recombinant proteins and a wide range of protein characterization approaches. Technologies used in this context include: Chromatography, Ultracentrifugation, Spectrofluorimetry, Circular Dichroism, Surface Plasmon Ressonance, Isothermal Titration Calorimetry.

Outline of the course: The course will span a week (5 days) with practical sessions (Aprox. 16 hours) and 7 lectures (7 hours)

.......................................................................................................

 

COURSE: Cristalografia / Macromolecular Crystallography

Coordinator(s): Pedro J. B. Pereira, Sandra de Macedo Ribeiro
Faculty and invited speakers: Pedro J. B. Pereira, Sandra de Macedo Ribeiro


Short summary: This course will introduce the students to the field of Structural Biology and guide them through thinking about biological problems in 3D. It will include training on methods used to visualise and interpret macromolecular structures and an overview of the experimental flowchart used to determine 3D structures by X-ray crystallography. An overview on protein crystallization, data collection and processing, structure refinement and model building will be provided using the equipment and facilities available at i3S.

Outline of the course: The course will consist of tutorials focusing on macromolecular crystallography data collection, analysis and 3D structure interpretation (16h).

.......................................................................................................

 

COURSE: Citometria de Fluxo / Multicolor Flow Cytometry

 

Coordinator(s): Catarina Meireles/ Nuno Alves
Faculty and invited speakers: Catarina Meireles/ Nuno Alves

Short summary: Flow Cytometry is a laser-based technology that permits analyzes of expression of cell surface and intracellular molecules, characterizing and defining different cell types in a heterogeneous cell population. It is mainly used to measure fluorescence intensity produced by fluorescent-labeled antibodies detecting proteins, or ligands that bind to specific cell-associated molecules. This is a powerful tool which allows a simultaneous multiparametric analysis of the physical and chemical characteristics of up to thousand particles per second. Thus, a number of applications, including the multicolor analysis of cell phenotype, gene expression, membrane potential, Ca2+ and Mg2+ influx and cell cycle can be performed. Additionally, you can purify subpopulations of interest in high-speed and high-purity (up to 99.0%) by multi-laser cell-sorting.

Outline of the course: 15h

 

DAY 1 Morning Flow cytometry basis
  Afternoon Design experiment
DAY 2 Morning  Hands on cytomers (Practical)
  Afternoon  Data Analysis (FlowJo Software)

 

.......................................................................................................

 


Home | Site Map | Contacts | Credits |