Applied Genetics

Code:

RM26

Acronym:

GA

Keywords
Classification	Keyword
OFICIAL	Marine Biology and Ecology

Instance: 2024/2025 - 2S (of 17-02-2025 to 18-07-2025)

Active?	Yes
Responsible unit:	Microscopy
Course/CS Responsible:	Master Degree in Marine Sciences - Marine Resources

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
MCMRM	2	Oficial Plan 2018	1	-	5	50	135

Teaching language

Portuguese and english
Obs.: Slides em inglês

Objectives

This elective course will delve into the exciting world of population genomics and its application to understanding adaptive evolution in marine organisms. We'll explore how the power of genomics allows us to link genetic variation with phenotypic traits that enable marine life to thrive in diverse and ever-changing environments.
Elsa Froufe, PhD (ORCID: https://orcid.org/0000-0003-0262-0791), a distinguished scientist with expertise in aquatic ecology and evolution, will co-teach this course. Dr.ª Froufe has a prolific record of publications, focusing in recent years on the investigation of climate change impacts on aquatic biodiversity. This presents a unique opportunity for students to learn directly from a leading authority in the field of marine molecular biology.
The course equips students with a comprehensive understanding of molecular biology techniques and their applications in marine conservation. Students will develop both the practical skills needed to conduct laboratory experiments and the critical thinking abilities required to interpret results and contribute to scientific research. The course also fosters a sense of environmental responsibility and a commitment to preserving marine ecosystems.

Learning outcomes and competences

The skills, knowledge, and attitudes developed throughout the course can be applied in various fields such as research, environmental management, and education.

Knowledge:

• Understanding of the various types of molecular markers used in genetic diversity studies and species identification.


• Comprehension of the challenges faced in conserving marine species and populations, including the successes and failures of different conservation strategies.


• Knowledge of the most commonly used molecular techniques in marine genetic diversity studies, including NGS, metabarcoding, eDNA, RNAseq, and low-coverage genome.


• Ability to analyze and interpret molecular data using bioinformatics tools.

Skills:

• Proficiency in performing, analyzing, and interpreting results from various molecular techniques.


• Ability to identify and resolve problems that arise during experiments showing capacity to work effectively in a team, collaborating with other students and researchers


• Ability to critically assess scientific literature and experimental results


• Skill in communicating results clearly and concisely, both orally and in writing

Attitudes:

• Interest in learning more about molecular biology and marine conservation


• Awareness of the importance of conducting experiments in a responsible and ethical manner.


• Appreciation for the significance of conserving marine biodiversity

Working method

Presencial

Program

Theoretical concepts and development of laboratory activities in the following areas:
- manual and automated DNA extraction from marine organisms: fresh, canned, and processed;
- electrophoresis and PCR of molecular markers for the study of genetic diversity and species identification;
- introduction to the analysis and interpretation of results to assess amplification success and potential genetic variation in marine species;
- applied molecular methods and studies of genetic diversity in marine organisms;
- exploring cutting-edge technologies (NGS) that play a role in marine conservation, including metabarcoding, eDNA, RNAseq, and low-coverage genome sequencing.

Case Studies:
1 - examples of successes in the conservation of a single species;
2 - challenges in the conservation faced by multiple marine populations;
3 - application of NGS technologies in the study of marine conservation.

Mandatory literature

Van Oppen, M.J. and Coleman; Advancing the protection of marine life through genomics, PLoS Biology, 20(10), p.e3001801, 2022
Antil, S., Abraham, J.S., Sripoorna, S., Maurya, S., Dagar, J., Makhija, S., Bhagat, P., Gupta, R., Sood, U., Lal, R. and Toteja, R.,; DNA barcoding, an effective tool for species identification: a review., Molecular biology reports, 50(1), pp.761-775., 2023
Tan, M.P., Wong, L.L., Razali, S.A., Afiqah-Aleng, N., Mohd Nor, S.A., Sung, Y.Y., Van de Peer, Y., Sorgeloos, P. and Danish-Daniel, M.,; Applications of next-generation sequencing technologies and computational tools in molecular evolution and aquatic animals conservation studies: A short review, Evolutionary Bioinformatics, 15, p.1176934319892284., 2019
Goodwin, S., McPherson, J.D. and McCombie, W.R.,; Coming of age: ten years of next-generation sequencing technologies, Nature reviews genetics, 17(6), pp.333-351., 2016
Froufe, E., Gomes-dos-Santos, A., Matos, A., Wilson, J., Malakpourkolbadinezhad, S., Pereira, D.D., Singer, R. and Castro, L.F.C.,; How complex is the hidden species diversity of the teleost Plotosus genus?. , Ichthyological Research, 71(1), pp.163-173., 2024

Teaching methods and learning activities

Problem-Based Learning:

• Students will tackle actual marine conservation challenges that directly relate to the molecular techniques they've learned
• Collaborative problem-solving by working in teams,  brainstorm solutions, and present their findings

Integration of Technologies:

• Students will use softwares designed to analyze biological data, specifically for interpreting sequencing data and identifying unique genetic markers
• Database mining to compare findings to established genetic databases, gaining insights into the relationships between different marine organisms

Field Trip to CIIMAR:

• Students will visit the CIIMAR (Centre for Marine and Environmental Research) to witness firsthand how these molecular techniques are applied in a research setting. They'll have the opportunity to interact with marine scientists and gain valuable insights into their work.

keywords

Natural sciences > Biological sciences > Biology > Genetics
Natural sciences > Biological sciences > Biodiversity > Sustainable exploitation
Natural sciences > Environmental science > Earth science > Marine sciences

Evaluation Type

Distributed evaluation without final exam

Assessment Components

Designation	Weight (%)
Participação presencial	10,00
Apresentação/discussão de um trabalho científico	70,00
Trabalho escrito	10,00
Trabalho laboratorial	10,00
Total:	100,00

Amount of time allocated to each course unit

Designation	Time (hours)
Apresentação/discussão de um trabalho científico	20,00
Frequência das aulas	20,00
Estudo autónomo	20,00
Trabalho escrito	20,00
Trabalho laboratorial	20,00
Total:	100,00

Eligibility for exams

Course Assessment: Student performance will be evaluated based on the following criteria: regular attendance, timely completion of assigned coursework, successful submission of final projects, and the quality of a research poster.
The poster should demonstrate a comprehensive understanding of molecular biology techniques and their application to marine biodiversity studies.

Calculation formula of final grade

The final grade will be calculated based on three components: attendance (10%), participation (20%), and final project (70%).
The final result will be rounded to the nearest integer (out of a maximum of 20 points). A student will be considered to have passed the course with a final grade of 10 or higher.