Umeå Plant Science Centre

Department of Plant Physiology, Umeå University

MOLECULAR ECOLOGY, 15ECTS

Spring 2016 22/03 – 05/06

Course teachers
Course leader / BA / Benedicte Albrectsen /
NS
PI
SP / Nathaniel Street
Pelle Ingvarsson
Stefano Papazian /

BW / Bernard Wessels /

Course Book: “An Introduction to Molecular Ecology”, 2nd Edition, 2008. Trevor Beebee & Graham Rowe, Oxford University Press. ISBN13: 978-0-199-29205-9.

Webpage: Cambro

Literature: Additional material will be provided on Cambro electronically during the course.

NB: Due to our policy of environmental awareness, paper hand-outs will NOT be provided!

Examination: Lab reports, discussions, project writing, presentation, and defence.

Grading:

< 60 % correct = Underkänd(U), >60% correct = Godkänd (G) and 80% correct = Väl godkänd(VG)

Date/Time Lecture WEEK 12 Teacher Location

Tues 22/03

10:00-11:45 / L1.Course start, Introduction and Registration / BA /

C3-28-41

Wed 23/03

09:00-11:00
13:00-15:00 / L2. Genomics II: Microarrays – then and now
L3. Genomics III: Sequencing technologies / NS
NS /

N430

N410

Thurs 24/03

09:00-11:00

13:00-15:00

/ L4. Genomics IV: Genome assembly and annotation
L5. Genomics V: DNA variation analysis / NS

BS/NS

N430

N410

Fri 25/03

/ Reading (Good Friday)

Date/Time Lecture WEEK 13 Teacher Location

Week 13

/ Reading (Easter Break)

Date/Time Lecture WEEK 14 Teacher Location

Mon 04/04

/ L6. Genomics IV: Genome assembly and annotation
L7. Statistics I: Chemometrics Methods / NS
JT/NS /

N430

N300

Tues 05/04

09.00-11.00 / L8. Statistics II: Statistical analysis of expression data
L9. Statistics III: Statistics and analyses of RNA-seq / PR/NS
ND/NS /

N300

N430

Wed 06/04

/ Reading /

Thurs 07/04

09.00-10.00
10.15-12.00 / L10. Metabolomics I
L11. Metabolomics II / TM/NS
TM/NS /

N300

Fri 08/04

12.00-14.00 / Population Genetics package – 21/4 / PI / C3-28-41

Date/Time Lecture WEEK 15 Teacher Location

Mon 11/04

10:00-11:00

11:00-14:00

/ Cutting edge seminar Magnus Nordborg
Work on project / MN
PI / KB3A9
C3-28-41

Tues 12/04-

Thur 14/04

/ Work on project / PI /

EMG/UPSC

To be announced

Fri 15/04

10:30-13:00

/ Discussion, selected papers in “Population genetics” / PI / C4-30-23

Date/Time Lecture WEEK 16 Teacher Location

Mon 18/04

Thur 21/04

/ Work on project
Room C4-30-23 reserved 21/4: 12.00-16.00 / PI / EMG/UPSC
To be announced

Fri 22/04

10:00-12:00 / Lab intro I: Plant – Herbivore Interactions
and Lab Me-JA treatment / SP/BW / KB4C10 Wallenberg GH

Date/Time Lecture WEEK 17 Teacher Location

Mon 25/04

10:00-12:00
13:00 - 17:00 / Lab intro II. DNA/RNA extraction, Lab security
Lab: START caterpillars experiment / SP/BW /

KB4C10 Wallenberg GH

Tues 26-27/04

/ Paper reading

Thurs 28/04

9:00-17:00 / Lab: END caterpillars experiment
Remove and weigh caterpillars, Collect leaves / SP/BW / Wallenberg GH

Fri 29/04

9:00-17:00 / Lab: Grinding leaves
Lab: RNA extraction
Lab: cDNA synthesis / SP/BW /

KB4C9

Date/Time Lecture WEEK 18 Teacher Location

Mon 02/05

9:00-17:00

/ Lab: q-PCR / SP/BW /

KB4C9

Tues 03/05

9:00-17:00

/ Lab: Collect results from qPCR
Lab: Analyse results
Questions and Wrap up /

SP/BW

/ KB4C9

Wed 04/05

12:00-14:00 / Chemical Ecology in a Genomic Era
Preparations for presentations Monday / BA /

C4-30-23

Thurs 05/05

12:00-14:00 / Chemical Ecology in a Genomic Era, / BA / C4-30-23

Fri 06/05

12:00-14:00 / Chemical Ecology in Genomic Era, / BA /

C3-28-41

Date/Time Lecture WEEK 19 Teacher Location

Mon 09/05

09:00-15:00 / Lab presentations / BA/SP/BW / C3-28-41

Tues 10/05

11:00-13:00 / PBL: GMO and beyond / BA / C3-28-41

Wed 11/05

/ reading /

BA

Thurs 12/05

12:00-14:00 / PBL: GMO and beyond / BA /

C3-28-41

Fri 13/05

/ Lab reports dead line to SP / SP /

Date/Time Lecture WEEK 20 Teacher Location

Mon 16-

Fri 20/05

/ PBL: Metagenomics
Room C3-28-41 reserved 16/05: 9.00-12.00
& 20/05: 12.00-14.00 / BA / EMG/UPSC
To be announced

Date/Time Lecture WEEK 21 Teacher Location

Mon 23-

Fri 27/05

/ PBL: Cutting edge
Room C3-28-41 reserved 23/05: 9.00-12.00 / BA / EMG/UPSC

To be announced

Date/Time Lecture WEEK 22 Teacher Location

Mon 30-31/05

/ UPSC days (special schedule)

Wed 01/06

09:00-15:00 / PBL: Cutting edge presentations / BA /

C3-28-41

Thurs 02/06

12.00-16.00 / PBL: Cutting edge reports / BA /

C3-28-41

Fri 03/06

12.00-13.00 / Evaluation day / BA /

C3-28-41

Lecture rooms

All lectures will be held in the KBC environment, and most lectures will be held within the UPSC part of the building complex. There may be minor changes to the schedule, so make sure to check the newest version which will always be available on Cambro.

Course webpage

The course starts off with registration and introduction on Thursday March 22, 2016 in C3-28-41 at 10.00. Please let me know if you are unable to attend the registration and introduction, but still intend to follow the course.

The course textbook is “An Introduction to Molecular Ecology”, 2nd Edition, 2008. Trevor Beebee & Graham Rowe, Oxford University Press. ISBN13: 978-0-199-29205-9.

We encourage you to obtain a copy prior to the start of the course.

All material provided during the course will be available at the course site in Cambro. For instance lectures or parts of them, study questions and background material (scientific papers and other online resources). In order to look at or download these papers, you will most often need to be situated on the University network. Due the restricted access to the journals, these are only available as full-text through the Umeå University Library (http://www.ub.umu.se/) subscriptions.

You must be registered on the course in order to access the course site in Cambro.

Information will be added both before the course starts and during the course. If any material is missing, please inform me.

You are most welcome to contact me if you have any questions regarding the course.

Course Coordinator:

Benedicte Albrectsen

e-mail:

Phone: +46 90-786 7011 // +46 70 338 49 19

Molecular Ecology Spring 2016