BIOL4410 Environmental DNA sequencing

Credit
6 points
Offering
(see Timetable)
AvailabilityLocationMode
Semester 1UWA (Perth)Face to face
Details for undergraduate courses
  • Honours option in Conservation Biology; Zoology [Bachelor of Science (Honours)]
Content
This unit focuses on the ecological questions relevant to zoologists that can be addressed with DNA sequencing technologies. The unit will be divided into three components. The first part of the unit will be a block of lectures taught in one week that will describe DNA amplicon sequencing and the range of ecological and evolutionary questions that can be addressed by this group of technologies. The second part of the unit will be a short practical project also of a week, involving one day of experimental planning, one of fieldwork in groups of ~4 students for environmental DNA sampling from water, soil or other substrates on or near the UWA Crawley campus and three days of laboratory work to generate a DNA library for sequencing. The third part of the unit will take place 6-8 weeks later after DNA sequencing has been completed and will involve analysing the DNA sequence data with a standardised set of software tools, then analysis of the biological information that the environmental DNA provides. A group oral and visual presentation of the results of this work will required. An essay on an application of DNA sequencing to a different ecological question will be assigned to each student. This will be assigned at the end of the first week of lectures and will allow students to explore a specific application in depth and demonstrate the extent of their understanding of the area in detail
Outcomes
Students are able to (1) plan an effective ecological experiment that will involve DNA sequencing analysis; (2) conduct effective biological sampling leading to appropriate DNA samples for analysis; (3) generate amplicons by PCR appropriate for the ecological question; (4) process amplicons to create a DNA library for high throughput sequencing; (5) conduct bioinformatic analysis of a simple DNA library; and (6) analyse results from DNA sequencing.
Assessment
Indicative assessments in this unit are as follows: (1) online tests during course and final online exam; (2) oral presentation as a group; and (3) essay on a specific topic. Further information is available in the unit outline.

Supplementary assessment is not available in this unit.
Unit Coordinator(s)
Simon Jarman
Unit rules
Prerequisites:
Second year UWA genetics
or
equivalent
Approved quota: 20—academic merit.
Contact hours
Block teaching of lectures and fieldwork over two weeks. Block teaching of bioinformatic analysis, biological data analysis and group presentation over 1 week, 8 weeks after initial block.
lectures x 15hrs, fieldwork x 8hrs, lab work x 24hrs, analysis x 40hrs, prep delivery & group presentation x 15hrs, essay prep x 48hrs
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