Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples
Arulandhu, Alfred J. ; Staats, Martijn ; Hagelaar, Rico ; Voorhuijzen, Marleen M. ; Prins, Theo W. ; Scholtens, Ingrid ; Costessi, Adalberto ; Duijsings, Danny ; Rechenmann, François ; Gaspar, Frédéric B. ; Barreto Crespo, Maria Teresa ; Holst-Jensen, Arne ; Birck, Matthew ; Burns, Malcolm ; Haynes, Edward ; Hochegger, Rupert ; Klingl, Alexander ; Lundberg, Lisa ; Natale, Chiara ; Niekamp, Hauke ; Perri, Elena ; Barbante, Alessandra ; Rosec, Jean Philippe ; Seyfarth, Ralf ; Sovova, Tereza ; Moorleghem, Christoff Van; Ruth, Saskia van; Peelen, Tamara ; Kok, Esther - \ 2017
GigaScience 6 (2017)10. - ISSN 2047-217X
CITES - COI - Customs agencies - cyt b - DNA metabarcoding - Endangered species - matK - Mini-barcodes - rbcL - Traditional medicines
DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance.
Responses in sediment phosphorus and lanthanum concentrations and composition across 10 lakes following applications of lanthanum modified bentonite
Dithmer, Line ; Nielsen, Ulla Gro ; Lurling, Miguel ; Spears, Bryan M. ; Yasseri, Said ; Lundberg, Daniel ; Moore, Alanna ; Jensen, Nicholai D. ; Reitzel, Kasper - \ 2016
Water Research 97 (2016). - ISSN 0043-1354 - p. 101 - 110.
31P NMR - Dissolved organic carbon (DOC) - EXAFS - Full scale - Lake restoration - Lanthanum - Lanthanum modified bentonite - P sequestration
A combined field and laboratory scale study of 10 European lakes treated between 2006 and 2013 with a lanthanum (La) modified bentonite (LMB) to control sediment phosphorus (P) release was conducted. The study followed the responses in sediment characteristics including La and P fractions and binding forms, P adsorption capacity of discrete sediment layers, and pore water P concentrations. Lanthanum phosphate mineral phases were confirmed by solid state 31P MAS NMR and LIII EXAFS spectroscopy. Rhabdophane (LaPO4 · nH2O) was the major phase although indications of monazite (LaPO4) formation were also reported, in the earliest treated lake. Molar ratios between La and P in the sediments were generally above 1, demonstrating excess La relative to P. Lanthanum was vertically mixed in the sediment down to a depth of 10 cm for eight of the ten lakes, and recovery of La in excess of 100% of the theoretical aerial load indicated translocation of the LMB towards the deepest areas of the lakes. Lanthanum was generally recovered from bed sediment samples following sequential chemical extraction from the HCl fraction. Soluble reactive P (SRP) release experiments on intact sediment cores indicated conditions of P retention (with the exception of two lakes) by sediments, indicating effective control of sediment P release, i.e. between two and nine years after treatment.
Consideration of life cycle energy use and greenhouse gas emissions in road infrastructure planning processes: Examples of Sweden, Norway, Denmark and The Netherlands
Miliutenko, Sofiia ; Kluts, Ingeborg ; Lundberg, Kristina ; Toller, Susanna ; BrattebØ, Helge ; Birgisdóttir, Harpa ; Potting, José - \ 2014
Journal of environmental assessment policy and management 16 (2014)4. - ISSN 1464-3332
energy use - environmental assessment - Greenhouse gas (GHG) emissions - life cycle assessment - road infrastructure planning
Energy use and greenhouse gas (GHG) emissions associated with life cycle stages of road infrastructure are currently rarely assessed during road infrastructure planning. This study examines the road infrastructure planning process, with emphasis on its use of Environmental Assessments (EA), and identifies when and how Life Cycle Assessment (LCA) can be integrated in the early planning stages for supporting decisions such as choice of road corridor. Road infrastructure planning processes are compared for four European countries (Sweden, Norway, Denmark, and the Netherlands). The results show that only Norway has a formalised way of using LCA during choice of road corridor. Only the Netherlands has a requirement for using LCA in the later procurement stage. It is concluded that during the early stages of planning, LCA could be integrated as part of an EA, as a separate process or as part of a Cost-Benefit Analysis.
Groundwater Dependent ecosystems. Part II. Ecosystems services and management in Europe under risk of climate change and land use intensification
Klove, B. ; Allan, A.C. ; Bertrand, G. ; Druzynska, E. ; Ertürk, A. ; Goldscheider, N. ; Henry, S. ; Karakaya, N. ; Karjalainen, T.P. ; Koundouri, P. ; Kupfersberger, K. ; Kvoerener, J. ; Lundberg, A. ; Muotka, T. ; Preda, E. ; Velázquez, M.P. ; Schipper, P.N.M. - \ 2011
Environmental Science & Policy 14 (2011)7. - ISSN 1462-9011 - p. 782 - 793.
water - framework - conservation - perspective - valuation - spain
Groundwater in sufficient amounts and of suitable quality is essential for potable water supplies, crop irrigation and healthy habitats for plant and animal biocenoses. The groundwater resource is currently under severe pressure from land use and pollution and there is evidence of dramatic changes in aquifer resources in Europe and elsewhere, despite numerous policy measures on sustainable use and protection of groundwater. Little is known about how such changes affect groundwater dependent ecosystems (GDEs), which include various aquatic and terrestrial ecosystems above ground and inside the aquifer. Future management must take this uncertainty into account. This paper focuses on multiple aspects of groundwater science, policy and sustainable management. Examples of current management methods and practices are presented for selected aquifers in Europe and an assessment is made of the effectiveness of existing policies such as the European Water Framework Directive and the Habitat Directive in practice and of how groundwaters and GDEs are managed in various conditions. The paper highlights a number of issues that should be considered in an integrated and holistic approach to future management of groundwater and its dependent ecosystems.
The effect of an audience on the gakel-call and other frustration behaviours in the laying hen (Gallus gallus domesticus)
Zimmerman, P.H. ; Lundberg, A. ; Keeling, L.J. ; Koene, P. - \ 2003
Animal Welfare 12 (2003)3. - ISSN 0962-7286 - p. 315 - 326.
male chickens - human-beings - fowl - stimuli - courtship - fear
When thwarted in a behaviour, laying hens show an increase in stereotyped pacing, displacement preening and a specific vocalisation known as the 'gakel-call'. How these behaviours, which might serve as indicators of welfare, are influenced by social factors is not yet known. In this study, we investigated the effect of an audience (another bird or a human) on the expression of the gakel-call and other behaviours indicating frustration. Twenty-four Lohman Brown hens were trained to gain free access to food in a test cage. Sixteen hens were used as test birds and eight as non-test audience birds. The food-deprived test hens were tested for 15 min in a non-thwarting situation (food freely available) and for 15 min in a thwarting situation (food covered but visible). For both situations we investigated four different treatments: no audience in the adjacent cage; a non-thwarted audience bird in the adjacent cage; a thwarted audience bird in the adjacent cage; and finally a human audience. The durations of stereotyped pacing and displacement preening were significantly higher in test birds during thwarting than during non-thwarting; thwarted birds also gave significantly more gakel-calls compared to non-thwarted birds. The test birds, and also the audience birds, gave more gakel-calls when thwarted in the presence of a thwarted conspecific than when in the presence of a non-thwarted bird, but there were no significant differences in stereotyped pacing or displacement preening, which are usually associated with frustration. In conclusion, this study supports the view that the gakel-call signals frustration in laying hens. Furthermore, the state of the audience influences the occurrence of gakel-calls in thwarted hens. Thus, when using the gakel-call as a welfare-indicator, the social aspects of the vocal expression of frustration in laying hens should not be overlooked
|Audience effect on the expression of frustration in the domestic laying hen
Zimmerman, P.H. ; Lundberg, A.S. ; Keeling, L.J. ; Koene, P. - \ 1999
In: Proceedings of the 33rd International Congress of the International Society for Applied Ethology, Lillehammer, Norway - p. 59 - 59.