PPGBM - Genetics and Molecular Biology Graduate Program

Master’s degree / Doctorate

1. Mandatory Disciplines

Biostatistics (3 Credit Units, 45 Credit Hours)

Syllabus: Program development: populations, sampling, descriptive and inference statistical functions, multivariable analysis, survival analysis, analysis of variance, bootstrap, correlation, probability distribution, hypothesis testing for one sample, two independent samples and two paired samples, estimation of parameters, meta analysis, normality, logistical and linear regression, data transformation, sample size, biomedicine evidence-based aspects.

Molecular Genetics (3 Credit Units, 45 Credit Hours)

Syllabus: It is intended that the student learn about nucleic acid topology; the growing process of the DNA molecule by the replication of nucleic acids; the transcription into prokaryotes and eukaryotes; the reading of genetic information contained in the genes through the genetic code; the apparatus used by the cell in the synthesis mechanism of proteins; and the genomic constitution of prokaryotes and eukaryotes.

Participation in Seminars (1 Credit Unit, 15 Credit Hours)

Syllabus: Participation in seminars presented by researchers and Master’s degree students in the different lines of research regarding the Graduate Course and outside of it.

2. Mandatory Disciplines by area

Concentration area: Animal Genetics

Evolution (3 Credit Units, 45 Credit hours)

Syllabus: The focus of this subject is the evolutionary history of natural populations, essentially in the analysis of how a genetic structure and the variation affect the ecological and evolutionary processes that may lead to the speciation or extinction. In this context, after evaluation aspects like the maintenance of biodiversity and the genetic consequences of the habitat fragmentation, the course culminates in the approach of the processes of genetic erosion, like the depression by inbreeding and outbreeding, and the extinction of small populations.

Concentration Area: Human and Medical Genetics

Population genetics I (2 Credit Units, 30 Credit Hours)

Syllabus: Prediction of genotype frequency in panmictic populations. Hardy-Weinberg principle. Maintenance of equilibrium. Extension of the Hardy-Weinberg principles to multiple alleles and polyploids. Adjustment test of equilibrium. Deleterious mutation and estimate of mutation rates. Balanced and transient polymorphisms. Demography and Natural selection. Inbreeding and Populational Structure.

Concentration Area: Molecular and Microbial Genetics

Genetic Engineering (3 Credit units, 45 Credit Hours)

Syllabus: The human genome and other mechanisms; importance of the study of the genomes. Mapping genomes through genetic and physical techniques. Sequencing of genomes. Understanding the genomic sequence. Genome anatomy.

Concentration Area: Vegetal Genetics

Vegetal Biotechnology (2 Credit Units, 30 Credit Hours)

3. Elective Disciplines for all areas

Medical applications of molecular genetics (3 Credit Units, 45 Credit Hours)

Syllabus: Modern methods to detect defective genes; Tracking of genetic mutations using SSCP and DGGE techniques; Identification of genic mutations through the direct DNA sequencing; Diagnosis of genetic diseases using PCR, RFLPs, VNTRs, STRs techniques; Sequencing.

Molecular Basis of Human Genetic Diseases (3 Credit Units, 45 Credit Hours)

Syllabus: Structure, organization and regulation of human genes; variation PUBLICATION ACTIVITY Ia, polymorphisms and mutation; the molecular basis of mutations; molecular and biochemical basis of genetic diseases; mutations affecting beta globine; mutations in other genetic diseases; alpha thalassemia, familial hypercholesterolemia, Duchenne muscular dystrophy, hemophilia A, cystic fibrosis, fragile X syndrome, adrenogenital syndrome, phenylketonuria.

Metabolic Biochemistry and Genetics of Inborn Errors of Metabolism (3 Credit Units, 45 Credit hours)

Syllabus: The Inborn Errors of Metabolism (EIM – Portuguese acronym) are genetically determined diseases, generally caused by a specific enzymatic flaw that leads to the blockade of a given metabolic pathway. This blockade has as consequence the accumulation of the substrate, the depletion of the product of the reaction or the bypass of the substrate to an alternate metabolic pathway. The curriculum of this discipline seeks to provide the graduate students more detailed knowledge about current topics regarding the genetic, biochemical, physiological, and molecular mechanisms involved in the pathogenesis of the EIMos. Theoretical content: Clinical, biochemical, nutritional, genetic, epidemiologic and molecular aspects of the Inborn Errors of Metabolism: a) metabolic disturbances of small molecules; b) metabolic disturbances of complex molecules; laboratory investigation of the Inborn Errors of Metabolism: biochemical analysis and molecular analysis; Epidemiologic studies: - Frequencies of human genetics diseases: Founder effect with genetic drift or selection. - A comparison of disease and gene frequencies of inborn errors of metabolism among different ethnics group in the west midlands. Prenatal diagnosis: advancements and perspectives; Prevention strategies in Inborn Errors of Metabolism; Treatment strategies for EIM; Genotype-Phenotype relation for hereditary metabolic diseases. Gene therapy and enzyme replacement therapy: new strategies for the treatment of metabolic hereditary diseases.

Cytogenetics and Chromosomic Evolution (3 Credit Units, 45 Credit Hours)

Syllabus: Polymorphisms. Intra and interspecific chromosome variation. Chromosomic mechanism of speciation. Evolution of the sex chromosomes. Evolution of human chromosomes. The karyotype in systematics. Cytotaxonomy.

General Cytogenetics (2 Credit Units, 30 Credit Hours)

Syllabus: The mitotic cycle and metaphasic chromosomes. Molecular organization of chromatin. Heterochromatin. Chromosome banding: methods and applications. Molecular cytogenetics. Meiosis and crossing-over. Sex-determination system. Numeric chromosome variation: euploidy, aneuploidy. Structural chromosome variation. Karyotypic evolution.

Teaching Internship (2 Credit Units, 30 Credit Hours)

Syllabus: Participation in didactic training internships in theoretical and practical lessons from disciplines of undergraduate courses in the field of Biological Sciences.

Human Evolution (3 Credit Units, 45 Credit hours)

Molecular Evolution (3 Credit Units, 45 Credit Hours)

Syllabus: Evolutionary changes in nucleotide sequences. Rates and patterns of nucleotide replacement. Evolution through gene duplication and exon shuffling. Evolution through transposition. Genome organization and evolution.

Population Genetics II (3 Credit Units, 45 Credit Hours)

Syllabus: DNA polymorphisms; Minisatellites and Microsatellites; mtDNA and Y-DNA; Alu insertions and SNPs; Analysis methods; Distribution of paired differences in mtDNA; Evolutionary significance of gene diversity; Interpopulation gene differentiation and genetic distance; Identification of demographic events: migration and variation of the effective size. Comparative analysis; mtDNA, Y-DNA e autosomal loci; Autosomal loci with different mutation rates.

Cancer Genetics (3 Credit Units, 45 Credit Hours)

Syllabus: Cancer genetics principles. Genetic markers: study methods of cancer. Solid tumors. Nervous system tumors. Leukemias. Familial cancer: hereditary cancer and chromosome instability syndromes. Cellular cycle.

Aging genetics (3 Credit Units, 45 Credit hours)

Syllabus: Genetics is multiform, related to the human genetic variation of clinical importance. Within this broad field, aging genetics is a science that analyses the senescence theories and their biological aspects. The analysis of programmed and non-programmed aging. The study methodologies and the progeroid syndromes. Environmental agents and damage to the DNA.

Introduction to Bioinformatics (3 Credit Units, 45 Credit hours)

Syllabus: Discuss the theoretical concepts and the algorithms used DNA, RNA and protein sequences analysis and evaluate the possibilities and limitations of the methods. Allow students to know and familiarize with the use of the various search and sequence analysis software in available databases. Justification: nowadays, bioinformatics is an important tool for biochemistry and molecular biology. In some areas, like genomics and proteomics, bioinformatics is essential for the analysis of the data obtained in experiments. There are various specific online software, some openly available in the network, others available with specific licensing (Wisconsin package) in a Department’s computer. The course makes the access to these tools easier for students who use molecular biology techniques in their work. Content: measurements of the replacement frequency of a residue by another in a set of divergent sequences of a protein family: "Accepted Point Mutation (PAM) matrix". PAM and BLOSUM matrixes for sequence comparison. Comparison techniques of homologous sequences: paired and multiple comparison; Gap, Bestfit, Compare, Pileup. Search techniques in databases: Blast, FastA, Stringsearch, Fetch, Motifs, Framesearch, Wordsearch. Evolutionary analysis: reconnaissance of the phylogenetic tree, calculation of the divergence. Sequence analysis: reconnaissance of coding regions, terminators, standard guidelines. Sequence mapping: DNA restriction map; peptides cleavage; Fingerprint, map of the RNA digestion through T1 ribonuclease. Translation of nucleotide sequences in peptides and reverse translation. Search of homologous sequence: Threader. Databases. Software of mounting and clustering of sequences.

Methods of Phylogenic Analysis (3 Credit Units, 45 Credit Hours)

Syllabus: Systemic schools. Distance methods (UPGMA, NJ, ME). Parsimony methods (DNPARS SOG, PAUP). Maximum likelihood estimation. Statistic methods: bootstrap, clustering. Notions about the Operational System UNIX: list and copy of files, use of the visual editor – vi – file compilation process, etc. Use of the main packages of phylogenic analysis (PHYLIP, MEGA, SOG, ME).

Proteomics (3 Credit Units, 45 Credit Hours)

Syllabus: The discipline provides an introduction to the main methods of analysis of the set of proteins of a particular or parasitic cellular type (proteomics), focusing applications aimed at the study of proteins of parasites and antigens involved in the immune response of hosts, in which strategies of proteinic isolation and sequencing are discussed; method of analysis of proteomes; Technologies for analysis of differential proteinic expression and post-translational modifications of proteins; methodology of protein-protein interaction analysis and heterologous expression systems; study of proteomes of organelles and bioinformatic tools used in the application of proteome studies.

Advanced Topics 01 – Protein modeling and mechanisms (2 Credit Units, 30 Credit hours)

Syllabus: Introduce the basis of the protein modeling through homology technique by presenting an up-to-date view of future perspectives for the use of this technique in the development of molecular models; Demonstrate the importance of the catalytic enzymatic study in the making of new medicine. At the end of the course, It is expected that students have knowledge to build three-dimensional models of proteins and analyze the possible catalytic mechanism through a given enzyme.

Advanced Topics 02 – Microbial Ecology (2 Credit Units, 30 Credit Hours)

Syllabus: Conference cycles and courses presented by specialists approaching theoretical issues and methodologies regarding Genetics and Molecular Biology.

Advanced topics 02 – Epigenetics and Evolution of plants (2 Credit units, 30 Credit hours)

Syllabus: The last ten years have revealed the fundamental role of the RNAs (ncRNA, miRNA and siRNA) in the control of gene expression. The discipline aims at stablishing the basic principles of RNAs regulation’s way of action, in both the control of stability and translation of the mRNA, and the regulation of the chromatin structure (epigenetic and epigenome). A major emphasis is given to vegetal gene species.

Advanced topics 02 – Introduction to the New Generation Sequencing (2 Credit Units, 30 Credit hours)

Syllabus: Polymorphisms in the human genome. Presentation of the project “1000 genomes” and related database. Polymorphism database (NCBI, EBI). Formats of files obtained from new generation sequencers (NGS). File manipulation. Informatic tools to detect polymorphism. Visualization of polymorphisms in “Genome Browser”. Annotation techniques.

Advanced topics 03 – Genomes (3 Credit Units, 45 Credit Hours)

Syllabus: Introduce the basis of mogenomics technique showing an updated view of future perspectives of the use of this technique in the construction of knowledge regarding the observation of new molecular species; demonstrate the importance of genomic study. It is expected that at the end of the course, students have knowledge to understand the genetic variability existing amongst the different species.

Advanced Topics in Molecular Biology: Expression/Silencing of Eukaryotes (3 Credit Units, 45 Credit Hours)

Syllabus: Gene expression control: Pre-transcriptional mechanisms – main mechanism involved in the transcription control, regulating sequences (promoters, enhancers, silencers), regulating proteins, general factors of transcription and specific of sequence, epigenetics. Post-transcriptional mechanisms – at the messenger RNA level – maturation, polyadenylation, splicing, exportation and stability of RNAm. At the level of translation – post-translational processing, glycosylation, phosphorylation, and acetylation; integral and membrane-associated protein intracellular traffic, protein degradation mechanisms. Silencing of genes: interference RNA (RNAi), regulation and function mechanisms, proteinic complexes of RNA degradation, micro RNAs specific tissue.

Advanced Topics in Cytogenetics (2 Credit Units, 30 Credit Hours)

Syllabus: Recent advancements of Cytogenetics; Single-Sequence and Repetitive-Sequence probes; hybridization in polytenes; FISH and assossiated banding; Genomic Painting and Chromosome Painting; FISH analysis in meiosis; Interphase Cytogenetics; PRINS; Hybridization and micromanipulation; PCR in situ.