12 EC
Semester 1, period 1
50521FB12Y
The emphasis of this course is on basic (or fundamental) biomedical research. How does research progress at the boundary of the known and unknown? This requires specific knowledge of the systems you are studying (at the molecular, cellular and tissue level) as well as the skills and creativity to design and interpret experiments. All with the aim of unraveling biology's mysteries and - in the long run - to come up with novel solutions to improve human health, either in the context of health (prevention) or disease (treatment).
With this in mind, we will connect basic research endeavors to some of today’s biggest societal health challenges throughout this course. Students will
In this course, we will encounter and discuss a diversity of topics, organized around the following three themes:
Students will learn
The course starts by giving students a solid foundation in developmental biology, focusing on complex multicellular animals. Taking the three germ layers (ectoderm, endoderm and mesoderm) as a starting point, students will learn the fundamental principles of cell communication and cell movement, tissue patterning and gene regulation. Healthy cell behavior will continuously be compared to diseased situations, with a more in depth focus on aging (including stem cells and their promise for regenerative medicine), cancer formation (taking breast cancer, melanoma and neuroblastoma as an example) and nutritional challenges (e.g. metabolic disorders and food allergies). In two wet-lab practicals, students will get the opportunity to connect the materials from the textbook and the lecture to real tissues observed in an experimental setting.
Along the way, students will learn to understand functional mechanisms of epigenetic gene regulation, including dynamics and heterogeneity to explain how cells adapt to perturbations. We will focus on approaches and methods to study the different levels of gene regulation and epigenetics at average (i.e. 'bulk') and single cell resolution. We will also discuss tools to interfere with epigenetic gene regulation and the rational design of cell systems to wire systems behaviour. Gene wiring and related gene expression behaviour will be explored in a computational practical. This knowledge will be the basis to understand deregulated, pathological cell behaviour and disease development and responsiveness to treatment.
Interkingdom interactions, involving microbiota (bacteria and fungi) and the microbiome (the genomes of the microbiota), and its role in neurological development, the establishment of normal metabolism/ prevention of obesity, as well as the prevention of inflammatory diseases of the gut, will be presented and discussed by experts in the field. Students are expected to use their knowledge of metabolism and its regulation to ask critical probing questions on cause-consequence relationships in this field where systems biology approaches are commonly used.
In the time leading up to the exam(s), students will get ample opportunity to process and actively engage with the material. Special emphasis will be placed on the integration of different knowledge areas, by combining insights from wet-lab experiments and synthetic biology approaches with computational modeling. To achieve this, the material will be presented in the form of lectures (hoorcollege) and directly applied in tutorials (werkcollege) and practicals (either wet-lab experiments or computer excercises).
We have switched to the 12th edition of Gilbert: Developmental Biology, since we were informed that students could no longer obtain the 11th edition.
Make sure to bring a lab coat, lab journal, pen and pencils to the wet lab practicals! You will receive a manual during the practical.
you will be asked to install R on your personal laptop
Additional information/materials, hand-outs and papers will be posted on Canvas.
The learning material will be presented in the form of lectures (hoorcollege). This will be alternated with tutorials (werkcollege) and practicals (either wet-lab experiments or computer excercises), allowing students to process and actively engage with the material. Due to the small group size, all of the lectures and tutorials are highly interactive to help students develop their scientific reasoning skills.
Students are expected to actively engage with and process the material during the time allocated for self-study ('zelfstudie'). Please note that in the Datanose schedule, the time that should be allocated to self-study is not explicitly indicated! It is your responsibility to use the open time slots for this purpose.
|
Activiteit |
Aantal uur |
|
Hoorcollege & werkcollege & question hours/feedback sessions |
106 |
|
Practicals & laptop tutorials |
60 |
|
Deeltentamen I / |
2 |
|
Deeltentamen II / |
3 x 4 hrs* |
|
Zelfstudie / Self study |
186 |
During contact hours, the material will be presented in the form of lectures (hoorcollege) and directly applied in tutorials (werkcollege) and practicals (either wet-lab experiments or computer/modeling exercises). Students are expected to actively engage with and process the material during the time allocated for self-study.
The details of the final take home assignment are still being worked out and will be communicated as soon as possible.
You will develop your critical thinking and analytical skills as we move away from the text book into 'real world' examples and papers in the tutorials ('werkcolleges') and practicals. This requires active participation on your part: we will cover a lot of different topics, but rather than just absorbing the material, we encourage you to ask questions and to dig deeper. How do biomedical scientists go about finding the answers to their questions? How do you design and interpret an experiment? How do you formulate a logical scientific argument? Which experimental approaches and techniques do you pick to address a specific biological question? How do you design experiments for different scales of complexity (molecules, cells, tissues, organisms, environmental interactions)?
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
- Attendance at the lectures is highly recommended, since these are interactive and provide additional examples that may not be in the textbook. Our lecture rooms are not equipped with video recording equipment.
- Attendance during tutorials and practical components (wet-lab experiments and computer/modeling exercises) is mandatory. Students that still end up missing one of the tutorials/practicals will have to make up for this in a personal assignment to be decided upon by the responsible teacher.
- Students that are repeating the course ('recidivisten') can get a 'vrijstelling' for the wet lab practical, provided that they successfully passed these components in the year before. They are however expected to attend the computer practicals again. Please note that this 'vrijstelling' only holds for one year. After this, all course components must be taken again.
| Item and weight | Details |
|
Final grade | |
|
4 (40%) Tentamen digitaal | |
|
1.3333 (13%) Partial assignment I week 8 | |
|
1.3333 (13%) Partial assignment II week 8 | |
|
1.3333 (13%) Partial assignment III week 8 | |
|
1 (10%) Wetlab practical | |
|
1 (10%) Laptop Tutorials |
To pass this course, students must obtain a final grade ≥ 5.5.
This final grade (scale from 1 to 10, rounded off to halves) is calculated as follows:
(0.4 * [partial exam 1] = tentamen digitaal, multiple choice questions at the end of week 4)
+
(0.4 * [partial exam 2] = take home assignments in week 8)
+
(0.1 * [computer assignment] = all laptop tutorials)
+
(0.1 * [wetlab practical] = your answers and lab journal record)
Please note the following:
Contact the course coordinator to make an appointment for inspection.
Up to twenty working days after the announcement of the results of the written examination, students can request to inspect their work and the standards applied for marking. Contact the course coordinator via e-mail to make an appointment.
Students will work in teams of 2 (or alone depending on lab occupancy). At the end of the practical, each individual student must hand in the completed questions (found in the practical hand-out), demonstrating that they properly understood and interpreted the experiments. They will receive a grade based on these answers, as well as their professional attitude during the practical and their experimental record keeping (counting towards 10% of the final grade of the course). Students that fail the practical must complete an alternative assignment to be decided upon by the responsible teacher. Details will be provided during the wet-lab practical.
At the end of each computer practical, students must hand in their answers to a set of questions. Together, these answers will count towards 10% of the final grade of the course. Details on these assignments will be provided during the computer practicals.
This course has two partial exams: A multiple choice exam at the end of week 4 (counting towards 40% of the final grade) and three assignments in week 8. The assignments in week 8 are open book (but paper and paper notes only, no laptops/internet) and their average also count towards 40% of the final grade. Details will be provided during the course.
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
In weeks 1 through 7, students will obtain a solid foundation in cell and developmental biology, focusing on complex multicellular animals. Taking the three germ layers (ectoderm, endoderm and mesoderm) as a starting point, students will learn the fundamental principles of cell communication and cell movement, tissue patterning and (epi)genetic regulation. Healthy cell behavior will continuously be compared to diseased situations, with a more in depth focus on aging (including stem cells and their promise for regenerative medicine), cancer formation (taking breast cancer, melanoma and glioma as an example) and nutritional challenges (e.g. metabolic disorders and food allergies). Special emphasis will be placed on the integration of different knowledge areas, by combining insights from wet-lab experiments and synthetic biology approaches with computational modeling.
Wet lab practicals are scheduled in weeks 1 and 5.
Computer-aided practicals are scheduled throughout.
A first partial exam (multiple choice questions) is scheduled at the end of week 4 to test knowledge and insight.
A second partial exam (take home assignments) is scheduled in week 8 to test deeper levels of understanding (i.e. analysis, experiment design and interpretation, etc.). To prepare for this, multiple werkcolleges on experiment design and interpretation are scheduled in weeks 5 through 7.
The schedule for this course is published on DataNose.
Frontiers I is part of the Frontiers in Medical Biology track and the Minor Biomedical Sciences: From basic biology to booming business.
The course is taught in English.
This course is well evaluated (receiving an 8.0 in the 2020-2021 student evaluation). Students find the course academically challenging and interesting. Overall, students are highly motivated to commit themselves to the material and they always indicate to have learned a lot about a variety of different topics.
We stress that this is a 3rd year course and that, as a result, students are expected to take control of their learning experience (e.g. students are expected to be able to discriminate between "hoofd- en bijzaken", to ask for more explanation when things are unclear, to be able to adapt to the different teaching styles of individual lecturers) and to actively work on developing a critical academic attitude (e.g. to be self-critical, to reflect on their work, to process feedback, to practice in formulating scientific problems/questions and solutions). The smaller group size is well suited for scientific discussions and interaction with the teachers, so use this opportunity!
We make minor adjustments to the course on a continuous basis (e.g. by updating and changing topics to keep up with the rapid advances in the field). Some examples of changes implemented based on student feedback/course evaluation end self-evaluation):