Degree | Type | Year | Semester |
---|---|---|---|
2500250 Biology | OB | 3 | 1 |
Although no official prerequisite exists, students are advised to review concepts that refer to the microbial world, previously studied. Likewise, it is convenient to have a good knowledge of the courses previously studied in the degree of Biology.
In order to take this course it is necessary that the student has passed the tests of Safety and Biosafety that he/she will find in the corresponding Moodle space. It is necessary to present, the first day of class, the printed pdf documents generated when passing the tests. Also, it is necessary to know and accept the operating rules of the laboratories of the Faculty of Biosciences. In addition, it is imperative that the student follows the rules of work indicated by the teaching staff. For safety reasons, if the two tests have not been passed, or the student does not wear a lab coat and safety glasses, access to the lab will not be allowed.
This is a mandatory course of the third year of the Degree in Biology, which introduces students to the basic knowledge of prokaryotic and viral diversity, with special emphasis on their structural and ecophysiological characteristics, as well as their biotechnological importance, and in the need for constant updating of information through the bibliographic databases.
The main objective of the scourse is to provide the basic training for the study of the microbial diversity, physiology and metabolism of the main groups of prokaryotes and viruses.
The specific objectives of the course are the following:
Theory
Prokariotic Diversity
1. Introduction to prokaryotic diversity
What do we mean by prokayotic diversity? Functional diversity as a concept.
2. Phylogeny and microbial systematics
Molecular phylogeny. The species concept for prokaryotes. Classification, nomenclature and identification. Classification systems. Polyphasic taxonomy: phenotypic, genotypic and phylogenetic methods. Classification units. Bergey´s Manual of Systematic Bacteriology. Culture collections.
3. Diversity of Archaea
Structural particularities of archaea. Phylogeny and metabolism. Main physiological groups and key genera. Applied importance.
4. Diversity of Bacteria
Ecophysiological characteristics of the different groups. Main phototrophic, chemolithotrophic and chemoorganotrophic groups and their significance. Key genera.
5. Extension of prokaryotic diversity
What do we know about the diversity of prokaryotes? Current tools available to assess the hidden diversity of bacteria and archaea.
Viral diversity
6. Introduction: virology and its origins
Relevant facts in the history of virology. The eradication of the smallpox and the risk of re-emergence. Clinical and biotechnological aspects of virology. Bioterrorism.
7. Virus nature and virological methodology
Strict parasitism, multiplication and transmission. Viral diversity. The viral cycle. Obtaining viral particles. Quantitative analysis of viral particles. Detection of viral components and applications in the diagnostic methodology. Biological security Contention levels:P1 to P4.
8. Virions: viral particles and their genomes
The viral particle. Functions of the capsid. Morphology of viral particles. Sites of binding to receptors. Chemical composition, structure and organization of the viral genome: structural and non-structural genes. Principles of complexity of viral genomes and genome reduction. Recombination, reorganization and phenotypic mixing.
9. The viral cycle
Cellular recognition. Internalization. Decapsidation. Cell shutdown. Synthesis of RNA, DNA and viral proteins: temporal sequences. Cytopathic effects. Release of viral particles. Apoptosis. Cell transformation and oncogenesis. Productive and non-productive infections. Lithic cycles vs. lysogenic cycles.
10. Origin and evolution of viruses
Origin of viruses; Regressive and progressive theories. Mechanisms of diversity generation. Mutation frequencies and relative abundance of mutants. Mutation fixation. Viral replicase and copy fidelity. Variability and evolution in RNA viruses and retroviruses. Viral quasispecies. Evolution and evolutionary potential. Founder effects and bottlenecks. Genetic and antigenic divergence; influenza virus. Analysis of viral phylogeny.
11. Principles of viral taxonomy
First classifications of viruses: Baltimore classification of animal viruses. The International Committee of Virus Taxonomy and the classification system. Viral properties used in taxonomy.
12. Double-stranded DNA viruses (Classe I)
The life cycle of polyomaviruses and papilomaviruses. Medical aspects: cell transformation and oncogenesis. The life cycle of adenoviruses. Medical aspects: recombinant adenoviruses. The life cycle of herpesviruses. Medical aspects: latent infections. Diseases caused by herpesvirus. The life cycle of poxviruses. Medicalaspects: the smallpox virus. Eradication of smallpox. Bioterrorism.
13. Single-stranded DNA viruses (Classe II)
The life cycle of parvoviruses. Medical aspects: Parvovirus B19.
14. Doubled-stranded RNA viruses (Classe III)
The life cycle of reoviruses. Medical aspects: rotavirus.
15. Single-stranded RNA viruses (+) (Classe IV)
The life cycle of picornaviruses. Medical aspects: poliovirus, rhinovirus and the virus of hepatitis A. The life cycle of flaviviruses. Medical aspects: hepatitis C virus, dengue virus and Zika virus. The life cycle of coronaviruses. Medical Aspects: SARS,MERS and COVID-19.
16. Single-stranded RNA Viruses (-) (Classe V)
The life cycle of rhabdoviruses. Medical aspects: rabies virus. The life cycle of paramyxoviruses. Medical aspects: measles and mumps. The life cycle of orthomyxoviruses. Medical aspects: the flu viruses. The influenza pandemic of 1918. Origin of epidemics and pandemics: antigenic drift and antigenic shift. Avian flu and its transmission to humans. The life cycle of filoviruses. Medical aspects: Ebola virus.
17. Retroviruses (Classe VI)
The life cycle of retroviruses. Medical aspects: oncogenesis. The Lentivirus genus: The human immunodeficiency viruses.
18. Hepadnavirus (Classe VII)
The life cyclce of hepadnaviruses: DNA retrovirus. Medical aspects: the hepatitis B virus.
Problems / Seminars
1. Methods of isolation of microorganisms
2. Techniques of microscopic observation
3. Methods of identification and characterization of microorganisms
4. Work sessions with scientific articles
Laboratory work
1. Isolation of microorganisms from natural environments
2. Identification: biochemical and physiological tests
3. Preparation and quantification of viral lysates
4. Neutralization of viruses
*Unless the requirements enforced by the health authorities demand a prioritization or reduction of these contents.
The course consists of three modules, which have been programmed in an integrated way so that the student will have to relate throughout the course the content and activities programmed in order to achieve the skills indicated in this guide.
Several learning strategies will be combined:
Theory classes: Student must acquire the scientific and technical knowledge of this course by attending these classes and complementing them with the autonomous study of the topics explained. At the beginning of the course, students will be given a detailed calendar of the topics that will be worked on throughout the course, as well as the bibliography that they will have to consult to prepare each theory class and for the autonomous study of the topics explained. Within this module, classes will be based on master or expository lectures and in a brief discussion of the same.
Seminars/case resolution classes: The purpose of these sessions is: a) working methodological aspects, b) facilitating the understanding of the knowledge presented in the theoretical classes, c) enable the student to design basic experiments id) make a bridge between the participatory theoretical classes and the practical work of the laboratory, with the aim of integrating the theoretical knowledge with the practitioners. The student will work on specific practical cases that will have to be developed during the course. In addition, the bibliography that will be consulted and the relation of each session with the subjects treated in the participative theoretical classes will also be indicated.
Laboratory work: The objectives of these activities are: a) facilitate the understanding of the knowledge exposed to the theory classes, b) apply the knowledge developed in the sessions of seminars/case resolution, c) acquire manual skills, d) interpret results and e) acquire the ability to work with microorganisms. Class attendance is compulsory in order to be able to acquire the skills of the course. In order to take this course it is necessary that the student has passed the tests of Safety and Biosafety that he/she will find in the corresponding Moodle space. It is mandatory to present, the first day of class, the printed pdf documents generated when passing the tests. Also, it is necessary to know and accept the operating rules of the laboratories of the Faculty of Biosciences. In addition, it is imperative that the student follows the rules of work indicated by the teaching staff. For safety reasons, if the two tests have not been passed, or the student does not wear a lab coat and safety glasses, access to the lab will not be allowed.Finally,in order to achieve good performance and acquire the competencies corresponding to this activity, it is essential that the student make a comprehensive reading of the proposed practices before their completion.
Additional information
In order to support the training activities indicated above, classroom tutoring sessions canbe programmed at the requestofthe students. Likewise, the students will be able to carry out individual tutorials in the office of the professors Jose Luis Corchero Nieto (IBF-112.1) and Maira Martínez-Alonso (C3-329).
The student will have at the Moodle space all the documentation delivered by the teacher for the good monitoring of the course. He / she will also be able to consult the teaching space of the Degree Coordination to obtain updated information.
*The proposed teaching methodology may experience some modifications depending on the restrictions to face-to-face activities enforced by health authorities.
Title | Hours | ECTS | Learning Outcomes |
---|---|---|---|
Type: Directed | |||
Laboratory work | 12 | 0.48 | 1, 3, 2, 9, 15, 14, 12, 13 |
Seminar/case resolution classes | 8 | 0.32 | 1, 9, 10, 15, 14, 12, 13, 4, 5, 18 |
Theory lectures | 31 | 1.24 | 17, 6, 1, 8, 7, 9, 10, 11 |
Type: Supervised | |||
Individual/group tutorials | 2 | 0.08 | 17, 6, 8, 7, 15, 11, 4 |
Type: Autonomous | |||
Bibliografy search | 9 | 0.36 | 16, 15, 4, 18 |
Estudy | 50 | 2 | 6, 1, 8, 7, 11, 4 |
Preparation and writing of works | 20 | 0.8 | 17, 6, 1, 8, 7, 9, 10, 16, 15, 12, 13, 11, 4, 18 |
Text reading | 12 | 0.48 | 1, 8, 7, 10, 11, 4 |
The evaluation of the course will be individual and continued through the following tests:
Assessment of the theory classes module (60% of the global mark): During the course, two written exams of this module will be programmed. Each of the tests will have a weight of 50% of the module's mark, but the average will only be used if the test score is equal or superior to 5; otherwise, the student will have to carry out a second-chance examination of the failed written test.
Each test will consist of short answer questions, aimed at assessing whether the key conceptual objectives have been achieved, and/or multiple choice test questions which will allow to avaluate a large part of the contents.
Assessment of the seminar/case resolution classes module (20% of the overall mark): The evaluation will include the following aspects:
Written test (10% of the overall mark).
Oral presentation of the work done (10% of the overall mark).
Only the average will be made if the score of the tests is equal or superior to 5.
Assessment of lab work module (20% of the global mark): The evaluation will include the following aspects:
Completion of a questionnaire and monitoring of pracical skiils acquired which will consist of the delivery of different practical results to the teaching staff during the laboratory sessions (2% of the overall mark).
Oral presentation of the practical results (8% of the overall mark)
Written test (10% of the overall mark), which will consist of multiple choice test questions.
Only the average will be made if the mark of the tests is equal or superior to 5.
*Student’s assessment may experience some modifications depending on the restrictions to face-to-face activities enforced by health authorities.
Final Considerations:
*Student’s assessment may experience some modifications depending on the restrictions to face-to-face activities enforced by health authorities.
Title | Weighting | Hours | ECTS | Learning Outcomes |
---|---|---|---|---|
Laboratory work assessment | 20 | 1 | 0.04 | 1, 3, 2, 9, 14 |
Seminar/case resolution assessment | 20 | 1 | 0.04 | 1, 9, 10, 14, 12, 13, 4, 5, 18 |
Theory assessment I | 30 | 2 | 0.08 | 17, 6, 8, 7, 16, 15, 11 |
Theory assessment II | 30 | 2 | 0.08 | 17, 6, 8, 7, 16, 15, 11 |
Recommended books:
- James W. Brown. 2015. Principles of microbial diversity. 1ª ed. ASM Press.
- Madigan MT, Martinko JM, Bender KS, Buckley DH, Stahl DA. 2015. Brock Biología de los Microorganismos. 14ª ed. Pearson Education.
- Madigan MT, Martinko JM, Bender KS, Buckley DH, Stahl DA. 2015. Brock Biología de los Microorganismos. 14ª ed. Pearson Education. http://www.ingebook.com/ib/NPcd/IB_BooksVis?cod_primaria=1000187&codigo_libro=5850
- Madigan MT, Bender KS, Buckley DH, Sattley WM, Stahl DA. 2019. Brock Biology of Microorganisms. 15th ed. Pearson SA.
- Martín A, Béjar V, Gutiérrez JC, Llagostera M, Quesada E. 2019. Microbiología Esencial. 1ª ed. Editorial Médica Panamericana. https://www.medicapanamericana.com/VisorEbookV2/Ebook/9788491102427
- Ogunseitan O. 2008. Microbial diversity. Form and function in Prokaryotes. Blackwell Publishing. https://onlinelibrary.wiley.com/book/10.1002/9780470750490
- Staley JT, Reysenbach AL. 2002. Biodiversity of microbial life: foundation of earth's biosphere. Willey-Liss, Inc, New York.
- Willey J, Sherwood LM, Woolverton CJ. 2008. Microbiología de Prescott, Harley y Klein. 7ª ed. MacGraw-Hill.
- Willey JM, Sherwood LM, Woolverton CJ. 2017. Prescott's Microbiology. 10th ed. MacGraw-Hill.
- Cann A J. 2016. Principles of molecular virology. (6th Ed). Academic Press. London.
- Cann A J. 2012. Principles of molecular virology. (5th Ed). Academic Press. London. https://www.sciencedirect.com/science/book/9780123849397
- Cann A J. 2009. Principios de virologia molecular. Acribia, DL.
- Flint SJ, Rall GF, Racaniello VR, Skalka AM, Enquist LW. 2015. Principles of virology: Molecular biology, pathogenesis and control. (4rd Ed). ASM Press. Washington.
- Flint SJ, Rall GF, Racaniello VR, Skalka AM, Enquist LW. 2015. Principles of virology, V.1, ASM Press, Washington DC. https://ebookcentral.proquest.com/lib/uab/reader.action?docID=6037145
- Flint SJ, Rall GF, Racaniello VR, Skalka AM, Enquist LW. 2015. Principles of virology, V.2, ASM Press, Washington, DC. https://ebookcentral.proquest.com/lib/uab/reader.action?docID=6029122
- Wagner EK, HewlettMJ, Bloom DC, Camerini D. 2008. Basic virology. 3rd Ed. Blackwell Science, Massachusetts
- Dimmock NJ, Easton AJ, Leppard KN. 2016. Introduction to modern virology. (7th Ed). Blackwell Publishing. Oxford.
- Oxford JS, Kellam P, Collier L. 2016. Human virology. (5th Ed). Oxford University Press. Oxford.
- Collier L, Oxford J. 2014. Virología humana : texto para estudiantes de medicina, odontología y microbiología. 3ª Ed. McGraw-Hill, México. http://www.ingebook.com/ib/NPcd/IB_BooksVis?cod_primaria=1000187&codigo_libro=5244
- Shors T. 2009. VIRUS. Estudio molecular con orientación clínica. Bogotà-Madrid.
- Louten J. 2016. Essential human virology. Elsevier
- Tennant P, Fermin G, Foster JE. 2018. Viruses; molecular biology, host interactions, and applications to biotechnology. Academic Press. https://www.sciencedirect.com/science/book/9780128112571
- E. Domingo. 2015. Virus as Populations: Composition, Complexity, Dynamics, and Biological Implications. Academic Press. https://www.sciencedirect.com/science/book/9780128163313
Complementary books:
- The Prokaryotes.
Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (Editors). 2013-14.The Prokaryotes. Fourth Edition. 11 vol. Springer, New York.
- The Prokaryotes: a handbook on the biology of bacteria
Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (Editors). 2006. Third Edition. 7 vol. Springer, New York. https://link.springer.com/search?query=the+prokaryotes&facet-content-type=%22ReferenceWork%22&from=SL
- Bergey's Manual® of Systematic Bacteriology
Garrity G (Ed.) 2001-2012. Bergey's Manual of Systematic Bacteriology. Second Edition. 5 vol. Springer,
Volume package:
- Bergey's Manual® of Systematics of Archaea and Bacteria
Whitman WB (Ed.). 2015. Bergey's Manual of Systematics of Archaea and Bacteria (digital Ed.). First Edition. John Wiley & Sons, Inc. http://wileyonlinelibrary.com/ref/bergeysmanual
- Encyclopedia of virology
Granoff A, Webster RG. 2008. Encyclopedia of virology (on-line Ed.)Academic Press. London. http://www.sciencedirect.com/science/referenceworks/0122270304
Useful Websites: