Università Roma Tre

BACTERIOLOGY UNIT

Introduction to and history of Microbiology
Functional diversity and distribution of microorganisms, main discoveries in the microbiology field, present and future biotechnological applications of microorganisms.

Structure and functions of bacterial cells
Structure of the prokaryotic cell. Cell division: binary fission. Cytoplasm, cytoplasmic inclusions and sub-cellular organelles. Cytoplasmic membrane and cell wall in Bacteria and Archaea. Mechanisms involved in protein secretion and cell wall biogenesis. Surface appendages: flagella and pili. Bacterial motility and chemotaxis. Cell differentiation in bacteria and sporulation. Microbial communities: biofilms. Bacterial metabolism: chemoorganotrophs, chemolithotrophs and phototrophs. Bacterial cultures and methods for bacterial cell count. Antibiotics: activity and mechanisms of action. Evolution and mechanisms of antibiotic resistance.

Bacterial genetics and regulation of gene expression
Structure of the bacterial genome. Operons. Pangenome of bacterial species. Mobile genetic elements: plasmids and transposable elements. Horizontal gene transfer: transformation, conjugation, transduction. Structure-function of bacterial RNA polymerase. Transcriptional and post-transcriptional regulation of gene expression. Examples of global regulators: catabolite repression and quorum sensing.

Principles of bacterial taxonomy
The concept of bacterial species. Bacterial identification: culture- and molecular-based approaches. Molecular clocks and phylogenetic analysis. Characterization of complex microbial communities.

Laboratory practice
- Gram staining
- Viable cell count by plating assays
- Determination of the minimum inhibitory concentration and minimum bactericidal concentration of antibiotics
- Antibiogram (Kirby-Bauer assays)

Madigan, Martinko. Brock. Biology of microorganisms. Pearson.

The textbook must be integrated with the slides of the lessons and the protocols of the exercises that will be provided by the teacher.

What are viruses and how do they replicate. Types of capsids and their function, types of genomes and phases of the viral multiplication cycle.
Definition of viral species and quasi-species and introduction to viral taxonomy
Acute, latent and persistent infections: definition and examples
David Baltimore's breakdown of viruses into 7 replication classes and the differences between classes.
Virus titration, cultivation and isolation methodologies
Attack mechanisms and viral penetration
The size of the viral genomes and their distinctive characteristics compared to the cellular genomes
Genetic variability in DNA and RNA viruses in comparison.
Replication cycle of some DNA phages (T4, lambda, φX174 and M13 as examples of Baltimore class I and II phages). The host's restriction against phage infections.
Both phages and animal viruses can transduce cellular genes with different mechanisms.
SV40 and human papillomaviruses, two small dsDNA animal viruses of Baltimore class I viruses): replication cycle, definition of host and permissive and non-permissive cells, promotion of oncogenesis.
Introduction to innate antimicrobial immunity and PAMPs, induction of type I interferons and introduction to their mechanism of action.
Antibodies: structure and function, monoclonal and polyclonal antibodies, use in microbiology
The definition of serotype and genotype and methods used to define them (neutralization test and genome sequencing)
Notes on the humoral and cellular adaptive immune response against microbial infections: role of B, Tc and Th lymphocytes; differences between primary and secondary immune response to infections.
Replicative cycle of three different positive ssRNA viruses in comparison (i.e., poliovirus, hepatitis C virus, phage Qβ or MS2) as examples of Baltimore class IV viruses). Introduction to coronaviruses and the viral pandemics of the XIX and XX centuries.
The Vesicular Stomatitis Virus and the flu virus in comparison (examples of Baltimore class V viruses)
Retroviruses as example of Baltimore class VI viruses: oncogenic retroviruses and the AIDS virus. Why the hepatitis B virus (Baltimore class VII) is defined an upside down retrovirus.
Antimicrobial vaccines (the story: Jenner and smallpox, Pasteur and rabies; examples of anti-viral and antibacterial vaccines used today: anti-tetanus, -polio, -pertussis, -hepatitis B, -HPV, -flu)
practical laboratory exercises:
1. introduction to animal cell cultures
2. hemagglutination test as a titration or serological identification test

Use PDF files of lessons and exercise present in the Moodle platform and the following textbook: N. J. Dimmock, A. J. Easton, K. N. Leppard - Introduction to Modern Virology - Seventh edition 2016 -Wiley Blackwell - ISBN 978-1-119-97810-7 or later editions.
Consult the web site viralzone.expasy.org.