Microbial Genomics
Code: 100983 ECTS Credits: 6| Degree | Type | Year | Semester |
|---|---|---|---|
| 2500502 Microbiology | OT | 4 | 2 |
Contact
- Name:
- Daniel Yero Corona
- Email:
- daniel.yero@uab.cat
Use of Languages
- Principal working language:
- spanish (spa)
- Some groups entirely in English:
- No
- Some groups entirely in Catalan:
- No
- Some groups entirely in Spanish:
- Yes
Other comments on languages
Although the working language is Spanish, students can also participate in Catalan or English, and do the exams or other exercises in any of the three languages.Prerequisites
It is recommended to have coursed Molecular Biology of Prokaryotes, Bioinformatics and Genetic Engineering of Microorganisms.
Objectives and Contextualisation
The main objective of this course is to broaden the vision of microbial genomics and the molecular and bioinformatics techniques used as well as their current and future applications.
Competences
- Act with ethical responsibility and respect for fundamental rights and duties, diversity and democratic values.
- Communicate orally and in writing.
- Develop creativity and initiative.
- Develop critical reasoning skills in the field of study and in relation to the social context.
- Know and use -omics tools (genomics, transcriptomics, proteomics, metagenomics, etc.).
- Make changes to methods and processes in the area of knowledge in order to provide innovative responses to society's needs and demands.
- Obtain, select and manage information.
- Take account of social, economic and environmental impacts when operating within one's own area of knowledge.
- Take sex- or gender-based inequalities into consideration when operating within one's own area of knowledge.
- Use bibliography or internet tools, specific to microbiology or other related disciplines, both in English and in the first language.
- Work individually or in groups, in multidisciplinary teams and in an international context.
Learning Outcomes
- Act with ethical responsibility and respect for fundamental rights and duties, diversity and democratic values.
- Apply and interpret the omic tools solve problems related to the biology and evolution of microorganisms.
- Apply the different omic tools to solving problems related to molecular biology and genetic improvement of microorganisms.
- Communicate orally and in writing.
- Develop creativity and initiative.
- Develop critical reasoning skills in the field of study and in relation to the social context.
- Discuss the contribution of the omics to the revision of concepts and paradigms in microbiology.
- Identify and interpret microbial metabolism from genomic information.
- Make changes to methods and processes in the area of knowledge in order to provide innovative responses to society's needs and demands.
- Obtain, select and manage information.
- Take account of social, economic and environmental impacts when operating within one's own area of knowledge.
- Take sex- or gender-based inequalities into consideration when operating within one's own area of knowledge.
- Understand the applications of the omics to the study of microbial diversity.
- Use bibliography or internet tools, specific to microbiology or other related disciplines, both in English and in the first language.
- Work individually or in groups, in multidisciplinary teams and in an international context.
Content
The student will work on the following contents:
- Methods for the study of genomics
- Genomic analysis
- Prokaryotic species concept and taxogenomics
- Structural genomics and evolution of genomes
- Comparative genomics. Core and accessory genome and pangenome
- Functional genomics: from genome to function
- Population genomics of microorganisms
- Metagenomics, pathogenomics and other omics
- Current challenges of microbial genomics and case studies.
Methodology
This course will be taught following the problem-based learning method (PBL). The class group will be divided into small groups that will independently work three problems. In the last module the teams could choose between two different problems. Each of the problems will last approximately 15 sessions, including the evaluation tests.
The student's role will be to actively participate in the working group, to assign group moderator roles, spokesperson and activities coordinator to the group members. They should also work individually to research, select and manage the information to share, discuss and re-elaborate the new knowledge with their workgroup. Finally, the group will present and discuss with the rest of the class the knowledge acquired, its application in the context of the problem and in other contexts.
The role of professors will be to facilitate the learning process, stimulate group discussions and critical thinking, provide the necessary tools for students to build knowledge and guide them. If necessary, some participatory master classes can be performed. As supervised activities and to support the learning activities indicated above, individual and collective mentoring will be possible. At the beginning of the course, teachers will explain to the students the organization of the subject and will give the working guidelines.
Annotation: Within the schedule set by the centre or degree programme, 15 minutes of one class will be reserved for students to evaluate their lecturers and their courses or modules through questionnaires.
Activities
| Title | Hours | ECTS | Learning Outcomes |
|---|---|---|---|
| Type: Directed | |||
| Problem-based learning | 40 | 1.6 | 1, 12, 11, 3, 13, 6, 5, 8, 9, 10, 7, 2, 4, 15, 14 |
| Type: Supervised | |||
| Tutorship | 3 | 0.12 | 3, 13, 8, 7, 2 |
| Type: Autonomous | |||
| Integrate information and generate hypotheses | 20 | 0.8 | 6, 5, 10, 15 |
| Preparation of the work plans, reports and oral presentations | 21 | 0.84 | 3, 13, 6, 5, 8, 7, 2, 4, 15 |
| Reading specialized texts | 40 | 1.6 | 10, 14 |
| Search and management of information | 20 | 0.8 | 10, 14 |
Assessment
The evaluation of the subject consists of three modules associated with each of the proposed problems. The evaluation of each module will be made according to the following distribution:
1. Individual written exam: Consistent in a specific written test where the course-specific competencies, concepts and methodologies worked on each problem is assessed. The maximum score is 5 points out of 10 for each problem.
2. Deliveries and/or reports associated with the problem. The report may consist of a written assignment and/or an oral presentation. In some cases, co-evaluations of other students' submissions and/or reports will be carried out. The maximum mark for this section is 4 points out of 10 for each problem, distributed in the different deliveries. The number and specific weight of each delivery, report, and/ or co-evaluation activity will be indicated in the problem presentation session.
3. Self-evaluation of the group: the working group should evaluate its functioning in solving the problem. The maximum mark is 0.5 points out of 10.
4. Individual self-evaluation: each member of the group should evaluate himself/herself and the rest of his/her classmates. The maximum mark is 0.5 points out of 10.
To pass each module the student must obtain at least a score of 4.5 points out of 10 in the individual written exam. If the student does not pass any of the individual written tests, he/she will perform a retake examination. To be eligible for the retake process, the student should have been previously evaluated in a set of activities equaling at least two-thirds of the final score of the course or module.
The absence without justification or non-profit of the classroom sessions may substract up to 1 point from the final grade of the subject. To pass the subject, it is mandatory to attend a minimum of 20 classroom sessions, including attendanceat theworking sessions of the class group, whose date of celebration will be established during the course development.
The students pass the course when the average mark of the evaluation activities is equal to or greater than 5.
The student will be graded as "Non-evaluable" if the weight of all conducted evaluation activities is less than 67% of t final score.
Assessment Activities
| Title | Weighting | Hours | ECTS | Learning Outcomes |
|---|---|---|---|---|
| Case 1 Individual written exam | 20% | 1.5 | 0.06 | 3, 13, 5, 8, 7, 2, 4 |
| Case 2 individual written exam | 20% | 1.5 | 0.06 | 3, 13, 5, 8, 7, 4 |
| Case 3 individual written exam | 20% | 1.5 | 0.06 | 3, 13, 5, 8, 7, 2, 4 |
| Evaluation of deliveries and / or reports associated | 30% | 0 | 0 | 1, 12, 11, 3, 13, 6, 5, 8, 9, 10, 7, 2, 4, 15, 14 |
| Individual self-evaluation | 5% | 0.5 | 0.02 | 6, 5, 10, 4, 15, 14 |
| Workgroup's self-evaluation | 5% | 1 | 0.04 | 6, 5, 10, 4, 15, 14 |
Bibliography
It is the responsibility of the student to seek the bibliography necessary for the resolution of the problems raised. To do this he/ she can be advised by the teachers. Still the following textbooks are recommended for basic concepts on genomics concepts and case studies.
- Genome and Genomics: From Archaea to Eukaryotes. Chaitanya, K. V. 2019. Singapore: Springer Singapore Pte. Limited. https://bibcercador.uab.cat/permalink/34CSUC_UAB/1c3utr0/cdi_askewsholts_vlebooks_9789811507021
- The Pangenome Diversity, Dynamics and Evolution of Genomes / Edited by Hervé Tettelin, Duccio Medini. Ed. Hervé. Tettelin and Duccio. Medini. 1st ed. 2020. Cham: Springer International Publishing. https://bibcercador.uab.cat/permalink/34CSUC_UAB/1eqfv2p/alma991010360498206709
- Population Genomics: Microorganisms Edited by Martin F. Polz, Om P. Rajora. Ed. Martin F. Polz and Om P. Rajora. 1st ed. 2019. Cham: Springer International Publishing. https://bibcercador.uab.cat/permalink/34CSUC_UAB/1eqfv2p/alma991010404004706709
- Bacterial Pathogenomics. Editor(s):Mark J. Pallen Editor-in-chief, Karen E. Nelson, Gail M. John Wiley & Sons, Inc., 2014. https://bibcercador.uab.cat/permalink/34CSUC_UAB/1eqfv2p/alma991010350952606709
- Microbial Functional Genomics. Zhou, Jizhong, Dorothea K Thompson, and James M Tiedje. 2004. Hoboken: John Wiley & Sons, Incorporated. https://bibcercador.uab.cat/permalink/34CSUC_UAB/1c3utr0/cdi_proquest_ebookcentral_EBC3056645
Software
There is no specific software for this subject