SLU-network for DNA-barcoding
We started a SLU-network for DNA-barcoding in 2014 for researchers and analysts working within environmental monitoring and assessment at SLU, using DNA-barcoding in their work or are planning for it. DNA-barcoding is a method to separate certain taxa within a group of organisms from other taxa by using short sequences of DNA from certain parts of the DNA. The aim of the network is the exchange of knowledge, and the exploitation of possibilities for the use of DNA-barcoding within environmental monitoring and assessment.
Maria Kahlert from the Department of Aquatic Sciences and Assessment took the initiative for this network, which got funding from Fomar (fund for development of methods and communication/knowledge exchange).
SWEBOL - Swedish network for DNA-barcoding
EDNA - open forum for researchers and stakeholders to discuss molecular methods for the use in environmental assessment
COST DNAqua-net - network to discuss molecular methods for the use in environmental assessment and monitoring of European water bodies
Barcoding in environmental assessment (Miljöövervakningsdagarna 2015) (in Swedish)
Spår av DNA avslöjar abborren (P1 radio, in Swedish)
Barcoding for environmental monitoring (Temadag miljöanalys 18.11.2014) (in Swedish)
"Streckkodning av gener" in Miljötrender November 2014 (in Swedish)
Swedish Museum of Natural History, Bi-lagan nr 1 mars 2014:
DNA-streckkodning – så går det till (Johannes Bergsten) (in Swedish)
Konsten att göra en höna av en fjäder – DNA-streckkoder i praktiken (Markus Englund) (in Swedish)
DNA-nyckeln (in Swedish)
SLU-researchers in the network
Please feel free to join!
Andrea Belgrano, Dept. of Aquatic Resources, Inst. of Marine Research Lysekil
Ulf Bergström, Dept. of Aquatic Resources
Anna Berlin, Dept. Forest Mycology and Pathology, barcoding of fungi
Johanna Boberg, Dept. Forest Mycology and Pathology, barcoding of fungi (cooperation within department)Patrik Bohman, Dept. of Aquatic Resources, Inst. of Freshwater Research Drottningholm, crayfish, freshwater, eDNA
Michelle Cleary, Southern Swedish Forest Research Centre, barcoding of forest pathogen funghi
Erik Degerman, Dept. of Aquatic Resources, fish
Stina Drakare, Dept. of Aquatic Sciences and Assessment, phytoplankton and their use in biomonitoring (publication about phytoplankton and barcoding)
Lennart Edsman, Dept. of Aquatic Resources, Inst. of Freshwater Research Drottningholm (genetic noble crayfish and singla crayfish, eDNA of crayfish and crayfish deseases)
Ann-Britt Florin, Dept. of Aquatic Resources, Inst. of Coastal Research Öregrund
Hanna Friberg, Dept. Forest Mycology and Pathology, plant pathogenic fungi
Ulf Grandin, Dept. of Aquatic Sciences and Assessment, vegetation, biodiversity, ecosystem services
Kerstin Holmgren, Dept. of Aquatic Resources, fish
David Huyben, Dept. of Animal Nutrition and Management, fish gut microbes
Maria Kahlert, Dept. of Aquatic Sciences and Assessment, benthic diatoms and their use in biomonitoring (Foma project in cooperation with INRA, France)
Karl Lundström, Dept. of Aquatic Resources, barcoding for diet analysis of seals (plans for diet analysis of more organisms, e.g. cormorants) and seal eDNA in water samples. Cooperation with Swedish Museum of Natural History.
Kirsten Miller Dept. of Ecology, using molecular techniques to understand
trophic interactions (largely in agroecosystems)
Kamyar Mogodiniyai Kasmaei, Dept, of Animal Nutrition and Management, Silage biochemistry and microbiology
Ruth Nichols, Dept. Forest Mycology and Pathology, food webs, molecular ecology, ungulate browsing ecology
Diem Nguyen, Dept. Forest Mycology and Plant Pathology, forest tree diversity and fungal community
Jonas Oliva. Dept. Forest Mycology and Pathology, pathogen funghi
Stefan Palm, Dept. of Aquatic Resources, fish
Göran Spong, Dept. of Wildlife, Fish and Environmental Studies, barcoding, sekvence analyses, development of diagnostic SNP-panels
Johan Stendahl, Dept. of Soil Sciences, barcoding of soil microfauna for environmental monitoring
Malin Strand, The Swedish Species Information Centre, barcoding of ribbon-worms
Astrid Taylor, Dept. of Ecology, barcoding of Oribatida
1. First network meeting at the Swedish Museum of natural history, Stockholm on 21 January 2014 at the seminar "DNA-based species and individual identification – coordination, new opportunities, and applications in society". Get to know participants from SLU, discussion of options and plans with the network, mixer with external actors.
2. Establishment of email-list for easier exchange of information ("email@example.com").
3. Establishment of network-website, and Wikipedia information on DNA-barcoding in Swedish.
4. First internal network meeting 4/3 2014 at SLU, Aquatic Sciences and Assessment, and Forest Mycology and Pathology. Introduction of all partners, visit to DNA-laboratory.
5. Exchange of Foma- and Formas-applications for support and constructive criticism from the network (spring 2014)
6. Exchange of practical experiences with DNA-sampling, -extraction, -sequencing and costs (spring 2014).
7. Brainstorming about future activities of the network (fall 2014)
8. Common application regarding NJ-Faculty's upcoming strategic investments (fall 2014)
9. Common information to the article "Barcoding of genes" in Miljötrender November 2014
10. Participation & co-organization of the “temadag miljöanalys” (theme day environmental monitoring) 18.11.2014: Lecture about DNA- barcoding basics, workshop with stakeholders about barcoding and future needs.
11. Participation & co-organization of FOMA seminar at SLU Aqua 3.12.2014. "Fish, crayfish and mussels as eDNA in environmental monitoring (in English)"
12. Participation & co-organization of FoSW Lunch seminar "Molecular based ecological inventories - revisiting ecology" by Dr. Alain Francs, INRA-UMR BioGeCo-Bordeaux, 11.12.2014, MVM, SLU, followed by meeting on barcoding-pipelines.
- SciLifeLab workshop 5 February 2015. SciLifeLab informed about its possibilities, followed by a discussion with participants on own needs. Lecturers: Olga Vinnere Petterson and Christian Tellgren-Roth. Feel free to contact Olga directly for further discussion, also video meetings possible: Olga.Pettersson@scilifelab.uu.se
SciLifeLab homepage: http://www.scilifelab.se/
SciLifeLab presentation 5/2 2015, see:
- DNA barcoding workshop 16 April
- SciLifeLab workshop on biodiversity and evolution 1 June
- Knowledge gaps for developing DNA barcoding for environmental assessment
- DNA extraction workshop for beginners
Organisms in SLU's barcoding-projects