6 EC
Semester 1, period 3
5043THPM6Y
1. Global content
Theory
Although microorganisms are invisible to the naked eye, their role in nature and in economic life is immense. Not only are they important because their total mass on Earth far exceeds that of all higher eukaryotes combined, they also display many unique physiological traits that have not been detected in eukaryotes and that have an enormous impact on the physical state of our planet. In addition, microorganisms have a major impact on the health and disease of both plants and animals, including us. Finally, they are crucial for the processing of many different types of food and production in the biotech and biopharmaceutical industry. The huge diversity in structure, physiology, cellular differentiations and underlying molecular regulatory mechanisms, and their capacity to grow fast and to adapt to the most extreme environmental conditions, are topics that will be addressed in the lectures.
Because of their many unique capabilities, such as extracting energy for growth from organic resources and also from minerals and light, micro-organisms play an important role around the globe, from the deep oceans to freshwater environments, snow on mountains to tropical forest soils, from growth-supporting plant and intestinal microbiomes to the production of daily foods, like beer, bread, yoghurt etc., life-saving antibiotics and many biopharmaceuticals, and they play crucial roles in many diseases and are responsible for the related global antimicrobial resistance problem. In this course, the diversity of molecular mechanisms that underly the enormous capacity and impact of bacteria will be illustrated by discussing (i) the role of different heterotrophic microorganisms in soil essential for carbon cycling, (ii) the role of nitrogen-fixing cyanobacteria in the oceans, (iii) examples of food processing in industrial biotechnology, and mineral extraction in mining, (iv) the conserved regulation mechanisms that support the cellular differentiations underlying many of these and other, e.g. disease-related processes, and (v) the modern molecular biology and next-generation sequence tools used to investigate these mechanisms.
Literature study
To illustrate the latest key developments in microbiology, the students will read several high-impact research papers published in 2022. They will present and discuss these papers with their peers. A vital aim of this exercise is to help the student read and understand modern research papers in molecular and ecological microbiology.
Practical
Working with microorganisms requires specific abilities to work safely while preventing unwanted contamination. Acquiring these abilities is incorporated in the practical work of two small research projects that each student will carry out, one in an IBED laboratory and one in a SILS laboratory. A range of projects will be offered from the fields of aquatic microbiology, microbial ecology, molecular microbiology, and microbial physiology. The projects will be carried out by 2 to 4 students and will be supervised by PhD students, postdocs, and technicians of the two institutes. Participants will learn how contemporary knowledge about microorganisms is translated into fundamental research questions and will gather hands-on experience. The results of these practicals will be presented by the students to peers and instructors in a mini-symposium.
2. Intended learning outcomes
After finishing the course, students will be able to:
3. Teaching methods
Staff members of SILS-MMP (Molecular Microbial Physiology) and IBED-FAME (Freshwater and Marine Ecology) will give the lectures and the 'werkcolleges'. Teaching is based on the book Brock Biology of Microorganisms (15th edition), Madigan, Martinko, Bender, Buckley and Stahl eds. Global Edition, Pearson.
The course contains three parts.
4. Attendance
Attendance to the lectures is highly recommended as absence frequently coincides with failure in the written exam. Attendance to the literature study and the practical projects is mandatory, as written in the general Teaching and Examination Regulations. (OER Deel B, Artikel 4.8).
5. Assignments
In the literature study, every student must read two papers given to him/her. One paper is presented in a short, 10-minute PowerPoint presentation according to the instructions on Canvas. For the other paper, which is presented by one of the other students, the student must prepare at least three questions for discussion; the discussion will be 5 minutes.
In the practical, assistants will assign a research question to a team of two to four students and discuss how to deal with it in laboratory practice. The students will make a plan, organize the materials, do the experiments (usually based on written protocols), collect results, and analyse and visualise the data. The students must take the so-called empirical cycle into account. The results of each project will be presented in a short PowerPoint presentation to peers and lecturers.
1. Course materials
PowerPoint slides of the lecturers
Canvas serves for the exchange of details about these materials and other aspects of the course.
2. Timetable and course structure
The up-to-date timetable can be found in DataNose. A more detailed schedule will be provided via Canvas.
In the schedule below, you will find the relation between the number of ECTS and the study load.
|
Lectures |
21 hours |
|
Literature study |
8 hours |
|
Practical projects |
80 hours |
|
Exam |
4 hours |
|
Presentations |
8 hours |
|
Self-study |
47 hours |
|
Total ECS 6 x 28 |
168 hours |
3. Assessment and inspection of assessed work
A student has passed the course when the weighted final grade is 5.5 or above, both for the exam and the practical each.
Knowledge about the contents of the lectures will be tested in a written exam which consists of 30 multiple-choice questions and three open questions. Marking of the practical will be based on practical skills, overview and data handling (grading by the assistant), and half on the oral presentation (grading by all assistants and lecturers that come to listen).
|
Component |
Deadline |
Weight % |
Minimum grade |
Compensation |
Resit (grade doesn’t expire, expires, resit is possible) * |
|
Written Exam |
19/01/2023 |
50% |
5.5 |
No |
|
|
Practical 1 |
03/02/2023 |
25% |
5.5 |
No |
|
|
Practical 2 |
03/02/2023 |
25% |
5.5 |
No |
|
|
|
|
|
|
|
|
* Grades for interim components are valid until the end of the academic year.
For at least twenty working days after the announcement of the results of a written examination, the student can, on request, inspect his/her assessed work, the questions and assignments set, as well as the standards applied for marking. The place and time will be announced via Blackboard (from the Teaching and Examination Regulations).
4. Fraud and plagiarism
This course uses the rules and regulations on fraud and plagiarism control of the University of Amsterdam. Plagiarism or fraud means copying the work of another student or copying scientific sources (for example, from books and magazines and the Internet) without mentioning the source. Plagiarism is prohibited. It is carefully monitored and strictly acted upon. Upon suspicion of plagiarism, it will be mentioned to the Examinations Board. When the Examinations Board is certain that there has been plagiarized, then this can lead to a maximum exclusion of all education for an entire calendar year. For more information on fraud and plagiarism rules of the University of Amsterdam, see www.uva.nl/plagiarism.
5. Application and further information
Course registration is via the web form. Information on the registration procedure will be emailed to the students concerned.
Number of participants
Maximum of 24 students
6. Contact
|
Coordinator/Lecturer |
Freshwater and Marine Ecology / IBED |
|
Name |
Prof. dr. Gerard Muijzer |
|
Address: Science Park 904 |
Room C4.227 |
|
|
g.muijzer@uva.nl |
|
|
|
|
Lecturer |
Bacterial Cell Biology / SILS |
|
Name |
Prof. dr. Leendert Hamoen |
|
|
L.W.Hamoen@uva.nl |
|
|
|
|
Lecturer |
Bacterial Cell Biology / SILS |
|
Name |
dr. Gauvav Dugar |
|
|
|
|
|
|
|
Lecturer |
Freshwater and Marine Ecology / IBED |
|
Name |
dr. Merijn Schuurmans (Merijn) |
|
|
j.m.schuurmans@uva.nl |
Will be handed out
Powerpoints, key concepts and terms, videos
Activity | Hours | |
Practicum | 80 | |
Presentatie | 8 | |
Tentamen | 4 | |
Werkcollege | 40 | |
Self study | 36 | |
Total | 168 | (6 EC x 28 uur) |
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
If you cannot attend a tutorial or practicum, please inform the coordinator T.denBlaauwen@uva.nl or the practicum coordinator J.M.Schuurmans@uva.nl, respectively. If the lecture is live, please do a Corona self test every morning before you leave and if in doubt, do not attend. All lectures are recorded and will be made available on canvas.
| Item and weight | Details |
|
Final grade | |
|
0.5 (100%) Tentamen |
Knowledge about the contents of the lectures will be tested in a written exam and a minimum score of 5.6 should be acquired. The two practicals are obligatory and contribute each 25 % to the final grade, and each of them should be passed. Marking of the practical will be based on practical skills, overview and data handling (grading by the assistant), and half on the oral presentation (grading by all assistants and lecturers that come to listen).
A model for the content of the exam answers that are required will be available after the exam.
The practical course will be in a small group depending on the total number of students and each member of the group will participate in the presentation of the practical work.
The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl
| College rooster power of microbes 2023 | ||||||
| datum | tijd | docent | topic | |||
The schedule for this course is published on DataNose.