12 EC
Semester 1, period 2
5042ECO12Y
The field of ecological genomics strives to uncover the genetic and molecular mechanisms influencing the response and adaptation of organisms to their natural environments. Achieving this requires a good understanding of ecologically important phenotypes and needs a species with a well-developed genomic tool-kit. Molecular biological and genomic tools have primarily been developed for mammalian and agricultural model organisms (such as yeast and Arabidopsis) representing a narrow spectrum of phenotypes, whereas many organisms that are the focus of ecological research have had limited genomic resources devoted to them.
In this course, you will learn how ecogenomics unites genomic and ecological approaches by exploring the natural variation in model or crop species and their relatives. We will explore the underlying principles of genomics and how they are being applied in ecogenomics. We will focus on ecogenomic studies of abiotic and biotic stress responses . Specific approaches that will be discussed and demonstrated include: genome sequencing, genetic mapping, expression analysis (transcriptomics), metabolomics and epigenomics. Specific analytical techniques that will be done “hands-on” will include: the use of genomic databases and tools, quantitative trait loci (QTL) analysis, stress physiology experiments, comparative sequence analysis, promoter analysis and genome-wide association mappping.
Several textbooks will be used by the lecturers, including "Molecular Biology of the Cell" by Alberts et al, "Evolutionary Analysis" by Freeman & Herron, "A Primer of Genome Science" by Gibson and Muse. Other reading materials are provided on Canvas.
A practical manual will be provided through Canvas at the start of the course.
Selected reviews and primary literature are available on Canvas.
|
Activiteit |
Aantal uur |
|
Computerpracticum |
43 |
|
Excursie |
8 |
|
Hoorcollege |
30 |
|
Practicum |
71 |
|
Tentamen |
3 |
|
Vragenuur |
2 |
|
Werkcollege |
20 |
|
Zelfstudie |
150 |
In the course you will learn how omics and data analysis tools and mapping can be used to unravel mechanisms underlying the interaction of organisms with their environment; you will use these techniques to design an ecogenomics experiment, execute that experiment, analyse the data, and create a report in which you analyse and interpret these data.
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
Attendance at lectures is highly recommended. Attendance during practical components is mandatory. The latter also applies to all (computer) practicals and tutorials. If you are unable to participate due to personal circumstances (such as illness or special family circumstances), please contact the course coordinator by e-mail. The course coordinator will then discuss with you whether there are options to participate/contribute in an alternative way (e.g. online) or compensate your absence later. If you are not able to follow education for a long time (longer than 1 week), please also contact the study advisor.
NB Covid-19: Stick to the RIVM guidelines at all times, even if this means that you have to miss one or more mandatory classes. In this case too, please contact the course coordinator directly so that a solution can be found together.
| Item and weight | Details |
|
Final grade | |
|
0.5 (50%) Tentamen | Must be ≥ 5 |
|
0.4 (40%) Practical | Mandatory |
|
0.1 (10%) Journal club | Mandatory |
|
Final grade after retake | |
|
0.5 (50%) Hertentamen | Must be ≥ 5 |
|
0.4 (40%) Practical | |
|
0.1 (10%) Journal club |
The final grade is composed of the exam (0.5), the practical (report, presentation, attitude)(0.4) and the journal club (0.1). A student has passed the course when the exam scores 5.0 or higher and the weighted final grade is 5.5 or higher. If the practical report is submitted after the deadline without a good reason the maximum grade that can be obtained is 6.0. If the practical report is of insufficient quality the student will be given the opportunity to improve it; the maximum grade that can then be obtained is 6.0.
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 Teaching and Examination Regulations).
Presentation about research papers with a group of students, individually graded
Oral presentations about practical results
Written report of 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
| Weeknummer | Onderwerpen | Studiestof |
| 1 | ||
| 2 | Formative assessment | See Canvas |
| 3 | Formative assessment | See Canvas |
| 4 | Formative assessment | See Canvas |
| 5 | ||
| 6 | ||
| 7 | ||
| 8 | Practical report |
The schedule for this course is published on DataNose.
The course is meant for 3rd year Biology students. Content of the 2nd year UvA Biology courses will be considered as known. Students from outside the UvA, who did not follow these courses, should contact the course coordinator before registration.
Maximum 30 students
We have introduced formative assessment and make available a practice exam to prepare the students for the exam. We have introduced a tutorial on statistical analysis to support the students in their data analysis. We have introduced extra classes/tutorials on GWAS to strengthen the background of the students on that topic. The Canvas page of the course has been restructured and the learning objectives reformulated.