Biologia Sintética e de Sistemas
Código
10827
Unidade Orgânica
Faculdade de Ciências e Tecnologia
Departamento
Departamento de Química
Créditos
6.0
Professor responsável
Isabel Maria Godinho de Sá Nogueira, Rui Manuel Freitas Oliveira
Horas semanais
7
Total de horas
85
Língua de ensino
Português
Objectivos
The general goal of the Systems Biology curricular unit is to provide advanced training, competencies and skills in systems level analysis of complex biological phenomena following a holistic modeling paradigm. Students are trained in a number of topics that are central to Systems Biology
• Translation of biological mechanisms into mathematical systems.
• Implementation of simulation models in computers according to the standards currently adopted in Systems Biology.
• Bottom-up (holistic) analysis. Integration of mechanisms to infer biological function from mechanisms.
• Top-down (holistic) analysis: systems analysis to identify mechanisms from high throughput
molecular biology data.
Through attending this curricular unit, students are expected to acquire critical practical skills to solve systems biology problems, namely:
- The ability to organize disparate biological information into a coherent self-consistent whole using mathematical models.
- The ability to identify important components/interactions within a complex biological system from the analysis of molecular biology data.
- The ability to disprove hypotheses and to define improved hypotheses in the process of model development.
- The ability to identify and understand the essential features of a biological system.
- The ability to simulate, predict, and optimize procedures, experiments and technologies.
This curricular unit also aims at framing these subjects within relevant biotechnological applications. Thus another important goal of this curricular unit is to provide specific training in the application of systems biology fundaments to the engineering of cell factories and processes, namely:
- Metabolic (genetic or medium) engineering,
- Synthetic biology, and
- Bioprocess engineering.
Systems biology is a thorough science with its own quest for scientific principles. Apart from the main scientific competencies, the Systems Biology curricular unit aims at promoting self-learning and entrepreneurship inducing competencies to make novel discoveries, to develop new methods, and to establish new paradigms.
The ultimate goal of this curricular unit is to provide students with the required tools to assume critical leadership roles in both academia and industry in topics related to the emerging discipline of Systems Biology.
Pré-requisitos
Students attending a life sciences master (Molecular biology, Biochemistry, Bioinformatics,
Biotechnology) and Bioengineering master (Chemical, Biochemical, Biomedical and Biological engineering) will find this curricular unit indispensable. It provides a thorough formation in quantitative analysis of complex biological phenomena using mathematical modeling and computational analysis. Students attending the Systems Biology curricular unit should have a strong background in
- Mathematics, namely linear algebra, statistics and differential calculus;
- Numeric methods and computation;
- Systems theory, particularly dynamic systems theory and dynamic systems properties;
- Biochemistry and molecular cell biology.
The first two topics are basic sciences normally present in the curriculum of a bachelor in Sciences and Engineering. Dynamic systems theory is typically present in the curriculum of an engineering bachelor. Biochemistry and molecular cell biology is horizontal to any life sciences formation.
Conteúdo
Módulo I - Biologia de Sistemas
1. Introdução à biologia de sistemas e sintética
2. Modelação baseada em restrições
2.1 Análise metabólica de fluxos
2.2.Análise de balanceamento de fluxos
2.3. Redes de regulação genética
3. Modelação estatística
3.1 Modelos não paramétricos
3.2. Métodos de classificação
3.3 Métodos de regressão linear e não-linear
4. Desenho de partes biológicas ‘standard’
5. Desenho de circuitos biológicos sintéticos
Módulo II - Biologia Sintética ( 15 Abril a 30 de Maio )
1- Introdução à Biologia Sintética (ISN)
2- Partes genéticas para programar bactérias (ISN)
3- Circuitos regulatórios genéticos (ISN)
- engenharia do comportamento colectivo
4- Moléculas Sintéticas
- Proteínas (CR)
- Ácidos Nucleicos (PB)
5- Biologia Sintética e Engenharia Metabólica de Leveduras (PG)
6- RNA em Biologia Sintética (ISN)
7- Desafios da Biologia Sintética (ISN)
Bibliografia
Foundations of Systems Biology, Kitano, H.(ed.), The MIT Press, 2001-10-15, ISBN 0262112663
Alon, Uri. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: Chapman & Hall, 2007. ISBN: 9781584886426.
Mukhatar Ullah, Olaf Wolkenhauer, Stochastic Approaches for Systems Biology, Springer Verlag New York 1 (July 15, 2011), ISBN-10: 1461404770
Systems Biology : Properties of Reconstructed Networks, by Bernard Palsson, January 2006, published by Cambridge Univ. Press, ISBN: 0521859034
Herbert M. Sauro (2011) Enzyme Kinetics for Systems Biology, Ambrosius Publishing, USA, ISBN: 0-9824-7730-9 (e-book); ISBN:0-9824-7731-7
Método de ensino
Subjects are covered in theoretical lectures (2 × 14 = 28 hours) where topics are exposed in a powerpoint. Illustrative examples of modeling methods will be presented and supported by in class MATLAB simulations. Problem-solving sessions take place in computer classrooms (4 × 14 = 56 hours hours).
MATLAB is the computational language adopted in this curricular unit. Students typically implement models, simulate and optimize solutions of problems representative of the subjects taught in the theoretical lectures. Given the highly interdisciplinary nature of Systems Biology, a cooperative-learning strategy will be adopted for instruction of systems biology (Anuj Kumar, 2005). Students normally have some background in a given research method or two; however, very rarely they have a background in all topics encompassed within a typical systems biology problem. For this reason, working collectively in groups is a major component of the teaching method. Work groups are built, based on their backgrounds and skills in a way to ensure a broad knowledge base with students within each group complementing each other''''''''s background. In order to achieve this, students will be interviewed individually and fill a form with a set of question on their background and skills, based on which the teacher decides upon the composition of each group of 4 elements.
This curricular unit aims at promoting autonomy, self-learning and entrepreneurship inducing competencies. In order to promote these competencies, the problem solving sessions and homework activities are based on published scientific papers. Scientific papers readings and their critical review is a systematic methodology implemented in this curricular unit. This has the advantage to train students to research the scientific literature, to understand the science involved, to become familiar with the nomenclature, to recognize flaws in published scientific works, and ultimately to distinguish between relevant and not so relevant results or scientific quality. This will turn invaluable for their future professional activity in this particularly dynamic discipline, but also in other areas of activity.
Furthermore, students are encouraged to take risks and choose their own paths and to assess critically their achievements. For this reason, the problems roadmap and the holist modeling project are categorized in broad areas, but the specifics of these activities are decided by the students themselves. This basically means that they will need to research the scientific literature and decide upon the particular problems they want to solve within the categorized areas. Leadership is also a topic that is trained in this curricular unit. The problems roadmap is composed by 4 problems each of them solved by the same group of 4 elements. However, each problem will be assigned a leader, who will take the lead and assume the management of the team to solve that particular problem. So each student will have the opportunity to lead the resolution of at least one problem, and then to present it to the classroom.
Also the training of communication skills is a major concern in this curricular unit. Students will present a 5 powerpoints in total. After completion of each roadmap problem they, present a 5 minutes powerpoint. After completion of the holistic modeling project they present a 20 minutes powerpoint.
Método de avaliação
NOTA FINAL (BSS) = 0,5 * (Módulo Biologia de Sistemas) + 0,5 * (Módulo Biologia Sintética)
Nota mínima para aprovação = 9,5 valores
Módulo Biologia de Sistemas (0-20)
Componentes da avaliação:
T1 (0-20 valores) - Trabalho MATLAB e relatório (grupo)
T2 (0-20 valores) - Trabalho MATLAB e relatório (grupo)
SEM (0-20 valores) - Seminário (individual)
NOTA FINAL (Modulo Biologia de Sistemas) = 0,35 * T1 + 0,35 *T2 + 0,3*SEM
Nota mínima para aprovação = 9,5
Módulo de Biologia Sintética (15 Abril a 30 Maio) (0-20 valores)
Componente teórica:
A - Teste teórico - 3 Junho - vale 60% nota final. Nota mínima para aproveitamento é 9,5 valores
Componente prática:
B - Mini teste prático - 6 de Maio – vale 20% da nota final
C - Trabalho de grupo - entrega 28 de Maio – vale 20% da nota final
Nota mínima para aproveitamento componente prática é 9,5 valores. Presença nas aulas práticas é obrigatória.