Molecular Microbiology

Code:

B4036

Acronym:

B4036

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2023/2024 - 2S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Master in Cell and Molecular Biology

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:BCM	18	Official Study Plan until 2023/2024	1	-	6	42	162

Teaching language

Portuguese

Objectives

The objectives of Molecular Microbiology, must translate the specific skills that are expected to be developed by the students, namely: • Plan, execute and interpret experiments. • Familiarization with routine techniques in microbiology and biology molecular (culture of microorganisms, cloning, gel electrophoresis of agarose and polyacrylamide, new generation sequencing etc.). • Familiarization with databases of genomic information and protein and bioinformatics tools (Blast, ClustalW, Primer3, SILVAngs, etc.). • Autonomy in search of scientific literature on a particular topic and using the free tools such as PubMed of NCBI also available in the Virtual Library of UP, in particular the Web of Knowledge. • Develop the capacity of oral and written communication. • Develop the capacity of synthesis and critical thinking.

Learning outcomes and competences

Mastering of routine techniques in Microbiology and Molecular Biology and experimental design. Understanding of the different regulation levels of gene expression  (transcription, translation and post-translation) and the use of eDNA tools for studying microbiomes in natural environments, using case studies.

Working method

Presencial

Program

The Molecular Microbiology syllabus aims at bringing students closer to the research area.

Students will benefit from the material resources used in research, and will have access to the specific skills of different research groups, as well as to the knowledge already built and translated into scientific publications. This approach to a research environment is fundamental to ensure access to resources that otherwise would not be available. The laboratory activities incorporate themes of fundamental research versus applied research in microbiology.

 

The basic organization of genetic information in bacteria, the regulation at the transcription and translation levels and the mechanisms involved will be studied and discussed. As a case study, the molecular mechanisms for the import and export of K+ in Bacillus subtilis will be addressed, with particular emphasis on Ktr channels, the role of c-di-AMP and regulatory proteins. In the laboratory classes, an E. coli strain deficient in the K+ import systems will be complemented with  a plasmid containing sequences that encode the KtrA and/or the KtrB protein and altered versions of the KtrA protein. The growth of the various strains in different K+ concentrations will be evaluated and the results will be analyzed and discussed taking into account the previously acquired knowledge.

 
One component of the program is the integration of innovative environmental DNA (eDNA) methodologies for studying complex microbial communities that inhabit natural environments. Environmental samples will be collected and processed in the laboratory to isolate eDNA. The sequencing results obtained through the Illumina platform will be analyzed by using specific bioinformatic pipelines (e.g. SILVAngs) to study the structure and diversity of the microbial community inhabiting these complex environmental samples.

Finally, the program will include a component dedicated to the isolation of bacteriophages from environmental samples and methodologies used in the study of the diversity of natural microbial communities, as well as in the comparison of bacterial isolates, in particular Lactococcus garvieae isolates, which will be compared by "Pulsed Field Gel Electrophoresis".

Mandatory literature

Hurst, C.J., R.L. Crawford, J.L. Garland, D.A. Lipson, A.L. Mills & L.D. Stetzenbach; Manual of environmental microbiology, ASM Press, Washington, D.C., 2007. ISBN: 978-1-55581-379-6
Kutter, E. & A. Sulakvelidze; Bacteriophages. Biology and Applications., CRC Press, 2005. ISBN: 0-8493-1336-8

Teaching methods and learning activities

Introductory lectures to the research topics, laboratory classes, presentation of results and discussion using a framework (scientific articles and case studies).

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Exame	70,00
Prova oral	15,00
Trabalho escrito	15,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	120,00
Frequência das aulas	42,00
Total:	162,00

Eligibility for exams

Attendance of 75% of the classes.

Calculation formula of final grade

Final examination - 70% (14 points)
Oral presentation - 15% (3 points)
written report - 15% (3 points)

Observations

Jury: Paula Tamagnini, José Américo Sousa, Catarina Magalhães