12 EC
Semester 1, period 1
5042ECO12Y
The emerging field of ecological genomics strives to uncover the genetic and molecular mechanisms influencing organisms’ responses and adaptations to their natural environments. Achieving this aim requires a good understanding of both ecologically important phenotypes and 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, we will focus on the ways in which ecogenomics aims to unite genomic and ecological approaches, which are: (1) to explore the natural variation found within model or crop species, (2) to analyze close relatives with a broader range of phenotypes (e.g. comparative genomics), and (3) to generate new genomic resources for the species of interest. We will explore the underlying principles of genomics and how they are being applied for each of these three approaches. We will specifically focus on ecogenomic studies of abiotic and biotic stress responses and the regulation and modification of signalling cascades. Specific approaches that will be discussed and demonstrated include: genome sequencing, genetic mapping, expression analysis (microarrays and transcriptomics), proteomics, 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 studies.
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, and "Plant Physiology and Development" by Taiz and Zeiger.
Gain practical experience in and understanding of genomics approaches and their application to fundamental questions in evolution and ecology.
After finishing this course, the student is able to:
· Explain theoretical knowledge in the field of Ecogenomics
· Carry out a large scale genomics research project, using analytical techniques.
· Apply knowledge of recent literature and critically evaluate literature
· Implement theoretical background in the design and interpret results of an ecogenomics research project
|
Activiteit |
Aantal uur |
|
Computerpracticum |
43 |
|
Excursie |
8 |
|
Hoorcollege |
34 |
|
Practicum |
70 |
|
Tentamen |
3 |
|
Vragenuur |
2 |
|
Werkcollege |
26 |
|
Zelfstudie |
150 |
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
Attendance at lectures is highly recommended. Attendance during practical components is mandatory (from Teaching and Examination Regulations).
| Item and weight | Details |
|
Final grade | |
|
50% Tentamen | Must be ≥ 5 |
|
40% Practical report | |
|
10% Assigments papers (presentation and questions) |
A student has passed the course when each partial examination is graded with a 5.0 or higher and when the weighted final grade is 5.5 of higher.
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 primary research papers with a group of students, individually graded
Oral presentations
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.uva.nl/plagiarism
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Het rooster van dit vak is in te zien op 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