Functional Omics

Code:

BIOL4068

Acronym:

BIOL4068

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2022/2023 - 2S (of 02-03-2023 to 09-06-2023)

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Master in Applications in Biotechnology and Synthetic Biology

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:ABBS	19	The study plan from 2019/20	1	-	6	42	162

Teaching language

Portuguese and english

Objectives

This UC meets the latest tools in the study of biotechnology and synthetic biology. It gives the student a transversal and integrative view of how to study different degrees of organization of the cell /organism. At the end of this course the student will:
• Understand the fundamentals of the main methods used in each omic (genomic/ transcritomic /metabolomics and cytomic) and the respective methodologies and instrumental bases of analysis.
• Know methodologies associated to the acquisition of multiparametric data and bioinformatics based tools associated with the different levels of omics, and how to work with software commonly used in its analysis.
• Recognize the potential of integrating these data / omics datasets into biological inference strategies
• Understand, for each level, potential applications in biology, biotechnology and synthetic biology
• Develop independent thinking in experimental design using omics tools especially in these areas

Learning outcomes and competences

Teaching methodologies include formal interactive classes, fostering the expository components with interpellation and dialogue with students. It includes, whenever necessary, lectures involving students in a more active process, and the study of "case studies"/articles, using tools such as books, articles and internet, is aimed at orienting the students in a structured way for the understanding of subjects and/or use bioinformatics analysis programs that allow them to develop transversal and integrated laboratory and computer skills in the omics area. E-learning approaches will be used.
The aforementioned teaching methodologies will be adjusted to allow students to integrate the objectives of the curricular unit.

Working method

Presencial

Program

Genomic: Genome analysis / sequencing; Cloning of DNA. Sequencing, structural and functional analysis of genes. RNAseq. RNA Sequence search and analysis; Expression of Genes in cDNA Libraries; RT-qPCR.
Proteomic: Importance of non-covalent interactions in biological systems. Properties/molecular structure of amino acids and proteins. Conformational freedom. Relationship Structure / Function. 3D structure forecast. In-silico algorithms for protein structure prediction. Visualization / manipulation of models - VMD program. Protein structure databases PDB and PDB Sum.
Metabolomic: Preparation of samples. General concepts of chromatography (eg HPLC, GC) and NMR analysis; Applications; Data analysis with bioinformatic tools.
Cytomic: image/flow cytometry. Flow cytometers, FACS and IFCs. Principle and applications. Specific fluorochemicals (molecules, immunology, cellular functions). Sample processing; Multiparametric analysis. Prokaryotic and eukaryotic models.

Mandatory literature

Jonathan Pevsner; Bioinformatics and functional genomics. ISBN: 978-0-470-08585-1
Haleem J Issaq and Timothy D. Veenstra; Proteomic and Metabolomic Approaches to Biomarker Discovery, Elsevier, Academic Press , 2013. ISBN: ISBN 978-0-12-394446-7
Bernd Mayer; Bioinformatics for Omics Data: Methods and Protocols (Methods in Molecular Biology), Springer, 2011. ISBN: ISBN 978-1-61779-027-0
Debmalya Barh and Vasudeo Zambare; OMICS: Applications in Biomedical, Agricultural, and Environmental Sciences, CRC Press Taylors & Francis Group. , 2013. ISBN: ISBN 9781466562813
Muhammad Sarwar Khan and Iqrar Ahmad Khan; Applied Molecular Biotechnology: The Next Generation of Genetic Engineering , CRC Press Taylors & Francis Group, 2016. ISBN: ISBN-13: 978-1498714815
M.Tomita,T. Nishioka; Metabolomics: The Frontier of Systems Biology. , Elsevier , 2010. ISBN: ISBN 978-4-431-28055-2
Macey, M. G. (Ed) ; Flow cytometry. , Springer . ISBN: 978-1-58829-691-7

Comments from the literature

Several ISI papers (including from the teachers)

Teaching methods and learning activities

The programmatic contents include topics of current scientific knowledge (tools, concepts and applications) in the various levels of functional omics in biological models and biotechnological applications. The vision of the program is integrated into a pyramid of functional/organizational complexity giving an integrative perspective to the student from the gene to the cell/organism. The program also aims to merge areas of chemistry and biology, and bioinformatics, allowing the student to understand different methodologies/approaches of the subjects, and apply them alone or together to a biotechnological problem. Teachers' knowledge/expertise in the area is integrated, reflecting their experience and their pedagogical and scientific knowledge relevant to teach this UC. The syllabus allows students to acquire a solid knowledge and skills combined in an integrative vision of the omics potentialities, to respond to concrete problems of biotechnology, health, environment, biology, etc.

Evaluation Type

Evaluation with final exam

Assessment Components

designation	Weight (%)
Teste	100,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Frequência das aulas	42,00
Total:	42,00

Eligibility for exams

Frequency of the UC classes.

Calculation formula of final grade

Final Exam (0 to 20 values).

Observations

Contact Professor: Agostinho Antunes