Microbiology - Toxicology

2019-2020

Course Objective

The course provides basic knowledge and understanding of (medical)
microbiology and toxicology, supplemented, extended and illustrated with
experiments, models and current topics. A total of 22 specific learning
objectives are defined: microbiology (1-10); medical microbiology
(11-14); toxicology (15-19); wet and dry practicals, plus exercises
(20); computer modelling-workgroups (21); literature workgroups (22).

After successful completion of the course, the student can:
1. review the history of microbiology on the basis of major discoveries.
2. describe the methods used to make microorganisms visible and explain
the underlying principles.
3. illustrate the prokaryotic and eukaryotic microbial diversity using
classification criteria.
4. identify and characterise the structures and functions of parts of
the cytoplasm, membranes and cell walls of prokaryotes.
5. identify the processes of prokaryotic cell division and population
growth, reproduce the ways to measure growth, and characterise the
effects of environmental factors on growth.
6. explain the concepts of (anaerobic) respiration and fermentation in
prokaryotes.
7. identify and characterise the distinctive processes of viruses and
subviral particles.
8. reproduce and apply the principles of microbial culturing methods.
9. identify and describe the methods and principles of Systems
Microbiology.
10. identify and characterise physical, chemical and biological agents
for the control of microorganism growth.
11. identify and characterise positive and negative interactions between
humans and microorganisms.
12. name and characterise a number of diagnostic microbiology methods.
13. reproduce the concepts of epidemiology and characterise the
different ways of transmission of microbic diseases.
14. characterise a number of specific microbial diseases: lyme, malaria,
plague, tetanus and cholera.
15. develop and interpret dose-response curves, and apply derived
concepts in the context of a risk assessment.
16. explain what toxicokinetics is and reason along the lines of the
absorption, distribution, metabolism, elimination (ADME) model.
17. indicate how exposure to toxic substances may lead to acute or
delayed effects.
18. identify current toxic substance groups and characterise their
mechanisms of action, with particular attention to microbial toxins and
food contaminants.
19. name the Paracelsian paradigm, and apply it in risk assessments of
substances, with special attention to essential nutrients, mutagenic
substances and endocrine disruptors.
20. independently perform basic microbiological-experimental techniques,
critically consider these techniques, and reproduce the associated
calculations.
21. use and (de)construct computer models of toxicological dose-response
curves, microbial growth curves and immunological herd-immunity, and
understand the underlying mathematics.
22. reproduce and explain theory related to the two topics (obesity;
human microbiome) discussed in the two seminar workgroups.

Course Content

The course consists of two-thirds microbiology and one-third toxicology.
In the course, basic (medical) microbiological and toxicological theory
is taught and illustrated with computer and laboratory experiments;
these parts cover most of the course. With regard to (medical)
microbiology, the negative effects of micro-organisms on humans will be
amply covered (e. g. infectious diseases), but attention will also be
paid to the positive effects on humans. In toxicology, the negative
effects of toxic substances will also be treated and compared to
positive characteristics of toxic substances (e. g. combating pathogens
and disease vectors with biocides and pesticides). In addition, the
potential occurrence of toxic substance in the context of the food
matrix (e. g. breast milk, fatty fish) will be considered.
Students will not only acquire theoretical knowledge from lectures and
study books but also hands-on experience during workgroups and
practicals.
In the in-depth part of the course, attention will be paid to the
overlap between the two (Microbiology and Toxicology) disciplines, as
well as to the contemporary systems-perspective within (medical)
microbiological and toxicological contexts. Systems-(micro)biological
and systems-toxicological aspects will be treated in relation to the use
of mathematical and computer models. Two different seminar workgroups
will also be devoted to considering microbiology and toxicology from a
system perspective. One seminar workgroup will focus on the theme
'obesity', where attention will be paid to the influence of early
exposure to obesogenic chemicals (toxicology). A second workgroup will
focus on 'human microbiomics' as a theme, in particular to discuss
recent developments that are not yet covered by textbooks.
In the practicals, students will acquire knowledge about experimental
techniques and learn how to process and interpret the measurement and
results they obtain. These laboratory practicals consist of nine
"wet"-experiments and one "dry" computer-based experiment (virtual
calux). By carrying out wet experiments, students also acquire practical
and basic laboratory skills that are essential for their further
studies. In addition, special lectures and seminars will focus on
'microbiological numeracy skills'.
As part of the mathematical line of the first year, the use and
construction of basic mathematical models in (medical) microbiology and
toxicology will be dealt with during Practical Computer Classes. Here
the emphasis will be on obtaining a first understanding of model-based
quantitative approaches. The models that the students will make and
study (using Microsoft Excel) will deal with the following topics: 1. a
logistic description of the dose-response curve in toxicology; 2. a
model-based description of exponential microbial growth under nutrient
limitation; 3. a model-based description of herd immunity. During a
regular workgroup, further attention will be paid to toxicokinetics
(using a first-order kinetics model) and risk analysis.

Teaching Methods

Formal lectures (LE): 32 hours
Mathematics lectures: 2 hours (compulsory)
Practicals (wet- and dry-experiments, PT A and B): 19 hours (compulsory)
Practical Computer Classes (PCC): 8 hours (compulsory)
Seminars (Lectures) Microbiology (SE): 3 hours (compulsory)
Seminar Workgroups (SG): 6 hours (compulsory)

Method of Assessment

(i) Practical: the list of results of the most important experiments is
drawn up in pairs and evaluated by the teaching assistant as
satisfactory/unsatisfactory.
(ii) Attendance at the compulsory practicals and seminars (there are NO
opportunities to make up for missed days) will be recorded, and assessed
as satisfactory/unsatisfactory. In principle, full attendance is
expected. In exceptional cases, absence may be compensated for by
writing and submitting a satisfactory report (topic to be specified), no
later than 8 working days after the end of the course.
(iii) Completion of compulsory assignments will be recorded and assessed
as satisfactory/unsatisfactory. In the event of unsatisfactory
completion, a student will be given one chance to resubmit the
assignment(s) in question, no later than 8 working days after the end of
the course.
(iv) A single multiple-choice digital test at the end of the course. A
substantial part of the questions (approximately one-third) will be
about the practicals and the seminars and seminar workgroups. The grade
for the digital exam is also the final grade for the course as a whole,
provided that all assignments (and report where applicable) have been
assessed as satisfactory. If one or more assignments or reports are
evaluated as unsatisfactory, the consequence may be that the course as a
whole must be redone in the next academic year, regardless of the score
for the digital (multiple-choice) exam. Students will only be allowed to
do the regular resit, if all assignments (and report where applicable)
have been assessed as satisfactory.

Literature

1. Microbiology text book: Madigan, Bender, Buckley, Sattley and Stahl.
2019. Brock Biology of Microorganisms (fifteenth global edition),
Pearson.
2. Environmental Toxicology – Open online textbook. Hyperlink will be
provided during the course.
3. MicTox practical syllabus (theory, experiments and calculations).
4. All PowerPoint slides used in the lectures.
5. Topics to be treated during the Seminars (workgroups and lectures)
and Practical Computer Classes.

Target Audience

Compulsory course for first-year BSc students Biomedical Sciences.

Additional Information

For the 'wet'-practicals, a lab coat is required.

Custom Course Registration

You need to sign up via VUnet.

Explanation Canvas

All communication for during the course will be done via Canvas. You are
therefore requested to check the Canvas website of the course
(preferably every day) and also check your mail in the Canvas inbox. If
you want to send an e-mail yourself, you have to do so via Canvas.
Canvas will be used as THE ONLY communication channel for the course.

Recommended background knowledge

a. Students may take advantage of the knowledge acquired during the
courses Genetics, Biochemistry and Cell Biology in the period
September-December of the first year.
b. Knowledge of cellular processes of eukaryotic macroorganisms will
serve as contrast for the knowledge of similar processes in prokaryotic
microorganisms that students gain within MicTox.
c. Basic knowledge of Excel is required.

General Information

Course Code AB_1139
Credits 6 EC
Period P3
Course Level 100
Language of Tuition English
Faculty Faculty of Science
Course Coordinator dr. J.H. van Heerden
Examiner dr. J.H. van Heerden
Teaching Staff dr. ir. T.H.M. Hamers
dr. M.P. Bergman
dr. D. Molenaar
prof. dr. W. Bitter
dr. J.H. van Heerden

Practical Information

You need to register for this course yourself

Last-minute registration is available for this course.

Teaching Methods Study Group*, Lecture, Practical*, Computer lab*, Seminar*

*You cannot select a group yourself for this teaching method, you will be placed in a group.

Target audiences

This course is also available as: