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 prevention (staying healthy for as long as possible) or treatment (in diseased situations).
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:
You 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 as one 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 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). Towards the end of the course, special emphasis is placed on experiment design and interpretation, as we move away from the textbook to real life scientific problems.
We have switched to the 12th edition of Gilbert: Developmental Biology, since we were informed that students could no longer obtain the 11th edition.
Advanced Nutrition and Human Metabolism (by Cooper and Smith, 6th edition - ISBN-:78-1133104056 OR 8th edition - ISBN 9780357449813, e-book is also an option).
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.
Please note that as a third-year BSc student, we expect you to be able to discriminate between what is important and what is less important/anecdotal (‘hoofd- en bijzaken’).
|
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.
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
- Attendance at the lectures (hoorcolleges) is highly recommended, since these should be fun and informative, are interactive and provide additional examples/background that may not be in the textbook to enhance your learning experience. Our lecture rooms are not equipped with video recording equipment.
- Attendance at the tutorials (werkcolleges) is highly recommended as well, since this is where you will actively engage with the material in preparation for your exams.
Note that all content covered in either the lectures or the tutorials can be tested at the exams.
- Attendance at the practical components (wet-lab experiments and computer/modeling exercises (laptop colleges)) is mandatory, since these will also be evaluated. 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 | |
|
0.4 (40%) Tentamen digitaal (week 4) | Must be ≥ 5, Mandatory |
|
0.1 (10%) Laptop Computer Practicals | Must be ≥ 5, Mandatory |
|
0.1 (10%) Wetlab Practical Mammary Gland & Intestine | Must be ≥ 5, Mandatory |
|
0.4 (40%) Partial Exam #2 (week 8) | Must be ≥ 5, Mandatory |
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] = open exam questions - split across 3 mornings 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 average of these exams also counts 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
Main goal
The main goal of Frontiers I is to build a solid foundation in a variety of topics from (or closely related to) the field of developmental biology, focusing on molecular and cellular interactions in tissue growth and maintenance. Here, we encourage you to actively participate in the lectures and tutorials: ask questions and train yourself in the critical and logical thinking that is required to properly design, execute and interpret scientific experiments.
Course design
Science is becoming increasingly more multi- or even interdisciplinary and research teams are often composed of members with various backgrounds and different areas of expertise. For this reason, we are taking a multidisciplinary, systems biology approach: we cover multilple different topics and biomedical/societal health challenges (e.g. cancer, aging, nutrition). At the end of Frontiers I, each of you should also have some familiarity with the application of computational modeling.
Course structure - the big picture
Knowledge and Insight
In weeks 1 through 6, 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 (including breast cancer as an example) and nutritional challenges (e.g. metabolic disorders and food allergies).
A first partial exam (multiple choice questions) is scheduled at the end of week 4 to test knowledge and insight of the material covered in weeks 1 through 4. This means you are expected to know and recognize specific processes, definitions, structures, etc. (i.e. the basic stuff you should have available as “parate kennis” – or “know from the top of your head” as a 3rd year BSc student of the Frontiers track/minor Biomedical Sciences so you can join in a basic scientific discussion).
Integration and Application of knowledge and skills
Throughout the course, specific 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 this end, wet lab practicals are scheduled in weeks 1 and 5. Computer-aided practicals are scheduled throughout. Both of these are designed to help you process the material from the lectures and self-study, as they connect the theoretical/conceptual knowledge to real-life experimental situations and biological questions.
A second partial exam (open exam questions) is scheduled in week 8 and is spread out over three days to test deeper levels of understanding (i.e. analysis, experiment design and interpretation, etc.). To prepare for this, multiple tutorials (werkcolleges) on experiment design and interpretation are scheduled in week 6 and 7. This exam will test in how far you truly master the material and can creatively apply the knowledge and skills you acquire during the course in a situation you have not yet encountered before. To test if anyone is really reading this syllabus, an easter egg is hidden in this sentence: draw a friendly dinosaur on the cover page of your written exam of 22 October to collect 0.2 (out of 10) extra bonus points.
Note that these assignments cover the entire content of the course (so all of the material from weeks 1-8, including the in class discussions on experiment interpretation and design, the use of different techniques/approaches for specific purposes/to answer specific questions, etc.). This means that the material from weeks 1-4 is again included, but we will be testing your grasp of this material at a more conceptual level (i.e. can you work with the knowledge and skills you acquired).
Course structure - from week to week
Week 1
We will start with an introductory lecture, detailing the set-up of the course and the idea behind the different components and assignments.
We will then immediately dive into developmental biology, starting with a lecture on early development (covering cleavage divisions and gastrulation). This is followed by a lecture on cell communication and cell movement, looking at cell adhesion and motility and pattern formation. We will also zoom in on the molecular signal transduction pathways that control cell proliferation and cell identity, with examples from the MAPK signaling pathway. This includes a lecture on why computational modeling is important and how it complements wet lab experimental biology.
We will then start with a closer look at one of the germ layers, the ectoderm. Focusing on formation of the neural tube and the skin and its appendages (including the mammary gland – wet lab practical), the rest of the week will highlight different cellular behaviors of cells originating from this germ layer.
At the end of week 1, you will not only have engaged with the material in the form of lectures, laptop tutorials and wet lab practicals, but will also have had your first experience in connecting the molecular, cellular and tissue level. This will continue throughout the course.
Week 2
Following up on our introduction to early development, we will zoom into the role of epigenetic gene regulation in establishing and maintaining gene expression patterns. We will also explore the genetic circuitry underlying pattern formation and synthetic gene wiring – including tools and technologies to experimentally manipulate gene expression and the epigenetic landscape. This will also include a hands on tutorial on ongoing/recent research in this area in addition to lectures and computer practicals.
Week 3
We will start with a closer look at the second germ layer, the endoderm. Focusing on the intestine, we will discuss its development and its maintenance in the adult by tissue resident stem cells.
The remainder of the week will look at this complex organ system in more depth, focusing on the intestine, its inhabitants (our microbiota), and its biological function: the uptake of nutrients. We also discuss the presence of biomarkers in the human body and their role in diagnostics.
Week 4
Continuing our journey through the intestine, we will discuss nutrition and intestinal (patho)physiology, including obesity and inflammatory bowel disease.
At the end of the week, you will take a multiple choice exam to test your knowledge and insight of the material taught so far.
A final question hour and two days of self study are scheduled prior to this first exam. The material for this exam is the content of all the lectures (hoorcolleges) and tutorials (werkcolleges) up to that point.
The wet lab practical and computational practicals are graded separately.
To be absolutely clear: You are NOT allowed to access any material (books, notes, internet browsers, phones, etc.) during the exam and it is forbidden to use anything other than your own brain and memory!
Week 5
We will take a closer look at stem cells and stem cell assays and we will discuss how the Wnt-signaling pathway controls stem cell maintenance and differentiation. The precarious balance maintained by stem cells can be disrupted with very different outcomes: uncontrolled cell proliferation (as observed in cancer) and tissue degeneration (as observed in aging). In a second wet-lab practical, we will try to identify intestinal stem cells.
In a couple of tutorials and computer practicals, we will try to uncover general principles of stem cell growth. How can you track their behavior, and what does it take to do this? Here you will experience first-hand the need for modeling in understanding complex cell behavior and the integration with experimental approaches.
We also start with the first of a series of tutorials (werkcolleges) on experiment design and interpretation.
Week 6
We discuss the last of the three germlayers, the mesoderm. We then focus on dynamic changes in cell behavior. Focusing on the neural crest, we discuss how cells can travel long distances during development before arriving at their final destination and meeting their final fate.
We also discuss the influence of hormones and the environment on cell behavior and development.
During development, cells also often need to switch their phenotype. An example is EMT, or epithelial to mesenchymal transition, which is also a property of metastasizing cancer cells. We discuss how cell identity is not fixed, looking at reprogramming and transdifferentiation from a cancer and regenerative medicine perspective.
We also spend one day on an exciting new area of scientific research, namely that of "synthetic embryos", where aspects of early development are recapitulated in vitro. You will explore and discuss the scientific, legal and ethical/societal implications.
Altogether, we are branching out to place the molecular and cellular details and principles you have encountered thus far in a broader context.
Week 7
We start with a look at a real-life PhD project with an interactive lecture by a senior PhD student. Ask them anything!
We also look at nutrition and the response of our bodies to feeding and fasting, with a special emphasis on insulin signaling.
The rest of the week is filled with tutorials on experiment design and interpretation to help you prepare for the partial exam in week 8. Plenty of time is reserved for self study to help you prepare for the following week as will.
Week 8
The partial exam in week 8 is spread out across three days/assignments (open questions).
The first assignment will test the materials taught by Thijs van Boxtel/Caitrin Crudden/Renee van Amerongen
The second assignment will test the materials taught by Pernette Verschure
The third assignment will test the materials taught by Stanley Brul/Wouter de Jonge/Hilde Herrema/Paul Lucassen
All of the lectures/tutorials and the associated materials (including book chapters) constitute the exam material. More detailed information will be provided by Thijs van Boxtel, Pernette Verschure and Stanley Brul via Canvas.
For the assignments in week 8, students are allowed to bring one piece of A4 paper with their own handwritten notes (front and back).
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.
Overall, students find this course intellectually challenging. They feel encouraged to actively participate and find the workload manageable. Last year, the course scored particularly high when it came to the intended learning outcomes (namely whether students felt that they had developed research skills and whether they had learned about new/current scientific theories and developments). We hope to continue all of this in 2024-2025!
In the 2023-2024 evaluation, some students asked for more structure in the course design. To this end, we have expanded the section of this course manual dealing with course structure to give students an overview of how the different topics fit together and what the underlying principles are that the course focuses on. It also gives a detailed week-by-week breakdown.
Some students also commented that the instructions for some of the final exams in week 8 could be improved. To this end, all teachers have been asked to re-align the content of the tutorials (werkcolleges) in weeks 5-7 in preparation for these final exams.
Staff