Munin: Browsing Artikler, rapporter og annet (arktisk og marin biologi) by Author

Analysing diet of small herbivores : the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

Valentini, Alice; Soininen, Eeva Marjatta; Coissac, Eric; Ims, Rolf Anker; Miquel, Christian; Yoccoz, Nigel Gilles; Gielly, Ludovic; Brochmann, Christian; Brysting, Anne K.; Sønstebø, Jørn H.; Taberlet, Pierre (Journal article; Tidsskriftartikkel; Peer reviewed, 20-Aug-2009)

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Integrated approaches to drainage basin nutrient inputs and coastal eutrophication: an introduction

Wassmann, Paul; Olli, Kalle (Chapter; Bokkapittel, 06-Jan-2005)

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Abstract:

Ingress Eutrophication is an increase in primary production due to increased nutrient supply and its consequences. In its widest sense eutrophication means any increase of nutrient availability that increases primary production. Frequently, however, eutrophication is understood exclusively as the consequence of nutrient input by anthropogenic activities. The primary consequence of eutrophication in aquatic environments is an enhancement of algal productivity and accumulation of algal biomass. Secondary consequences are changes in community structure of plankton and benthos. Man-induced eutrophication or changes in biodiversity are nothing new: they are a well-known consequence of human culture. Eutrophication phenomena accompanied all human settlements. Even in the early days of mankind human activities resulted in ecosystem changes. Several large animals such as the mammoth survived the glacial periods, but not the last one. It has been suggested that Neolithic hunters decimated this species to extinction. Similar suggestions have also been made regarding other large mammals that did not continue to exist after the last glacial. The main sewage canal in the city of Rome, ‘cloaca’, has given rise to a number of expression regarding sewage pathways in numerous languages. Since classical and medieval times there have been ‘clean-ups’ of unsanitary, plague-ridden cities. Eutrophication is thus the oldest environmental problem of human civilization and not a recent phenomenon. However, with the significant increase of human population over recent decades, eutrophication has developed from a more or less local to a global issue. Due to changes in human living conditions and the declining number of people employed in agriculture, the population in the coastal zone increases steadily. The nutrient concentration increases continually from small streams over rivers and larger lakes to the estuaries. The consequences of this, such as discoloured waters, ‘rotten’ bottom water, odour and reduced fishing yields are obvious to even a casual observer. The combined effect of increasing human population and movement to the coastal zone, the environmental pressure on rivers, estuaries and shelf regions results in an ever-increasing pressure on the entire coastal zone (Figure 1). Consequently, eutrophication turns into an escalating global phenomenon as long as the human population increases. Homo sapiens has thus a vital impacton nature that is part of its culture. As a consequence of that we have to distinguish between natural and cultural eutrophication. In most of this text the term eutrophication stands for cultural eutrophication.

URI:

http://hdl.handle.net/10037/2371

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Drainage basin nutrient inputs and eutrophication: an integrated approach

Olli, Kalle; Wassmann, Paul (Book; Bok, 06-Jan-2005)

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Abstract:

Eutrophication is an increase in primary production due to increased nutrient supply and its consequences. In its widest sense eutrophication means any increase of nutrient availability that increases primary production. Frequently, however, eutrophication is understood exclusively as the consequence of nutrient input by anthropogenic activities. The primary consequence of eutrophication in aquatic environments is an enhancement of algal productivity and accumulation of algal biomass. Secondary consequences are changes in community structure of plankton and benthos. Man-induced eutrophication or changes in biodiversity are nothing new: they are a well-known consequence of human culture. Eutrophication phenomena accompanied all human settlements. Even in the early days of mankind human activities resulted in ecosystem changes. Several large animals such as the mammoth survived the glacial periods, but not the last one. It has been suggested that Neolithic hunters decimated this species to extinction. Similar suggestions have also been made regarding other large mammals that did not continue to exist after the last glacial. The main sewage canal in the city of Rome, ‘cloaca’, has given rise to a number of expression regarding sewage pathways in numerous languages. Since classical and medieval times there have been ‘clean-ups’ of unsanitary, plague-ridden cities. Eutrophication is thus the oldest environmental problem of human civilization and not a recent phenomenon. However, with the significant increase of human population over recent decades, eutrophication has developed from a more or less local to a global issue. Due to changes in human living conditions and the declining number of people employed in agriculture, the population in the coastal zone increases steadily. The nutrient concentration increases continually from small streams over rivers and larger lakes to the estuaries. The consequences of this, such as discoloured waters, ‘rotten’ bottom water, odour and reduced fishing yields are obvious to even a casual observer. The combined effect of increasing human population and movement to the coastal zone, the environmental pressure on rivers, estuaries and shelf regions results in an ever-increasing pressure on the entire coastal zone (Figure 1). Consequently, eutrophication turns into an escalating global phenomenon as long as the human population increases. Homo sapiens has thus a vital impacton nature that is part of its culture. As a consequence of that we have to distinguish between natural and cultural eutrophication. In most of this text the term eutrophication stands for cultural eutrophication.

URI:

http://hdl.handle.net/10037/2389

File(s) in this item: 1

book.pdf (17.04Mb)

Pelagic eutrophication in the Gulf of Riga

Wassmann, Paul (Chapter; Bokkapittel, 06-Jan-2005)

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Abstract:

Quantitative estimates of the fluxes and dynamics in the nutrient load on marine environments, their distribution and channelling through the food web and the effect on the increase of new production, are fundamental and constitute a prerequisite for the planning of actions for water protection measures. The Gulf of Riga is no exception. The Gulf is a semi-enclosed part of the eastern Baltic Sea, surrounded by Estonia and Latvia and has one major outlet, the Irbe Straight Sound, and one minor one, the Muhu Sound. The Gulf of Riga has a surface area of 19,000 km2, is up to 67 m deep, has a relatively simple topography and a volume of 420 km3 (Figure 19.1). The Gulf is eutrophicated and most of the pollution loads in the Gulf can be attributed to human activities in the drainage basin, which covers 135,700 km2, or more than seven times the surface area of the Gulf itself. In pelagic environments the fate of organic matter produced by an increased supply of nutrients, the regulation of vertical flux and in particular the pelagicbenthic coupling are not well known in general, let alone in the Gulf of Riga. Since the beginning of this century Estonian, Latvian, Lithuanian and Russian scientists have already carried out a substantial body of work in various disciplines in the Gulf of Riga and its drainage area (summarised by Ojaveer 1995). From 1993–1997 Nordic and Baltic scientists joined forces in an international project, the ‘Environmental Research in the Baltic Sea’, also referred to as the ‘Gulf of Riga Project’ (GoR). The objective was to study environmental problems in the Gulf and its drainage area, and to determine their impact on the rest of the Baltic Sea in general and the Baltic Proper in particular (Figure 19.2). The investigations reviewed here aim at to understand the Gulf of Riga as an ecosystem by analysing 1. the dynamics of the runoff of nutrients and their supply to the Gulf, 2. the distribution of nutrients in the Gulf, 3. the production and distribution of plankton and organic matter and 4. the processes involved in settling and the vertical export of organic matter. This chapter rests upon 14 publications from the project ‘Pelagic eutrophication and sedimentation’ (Wassmann & Tamminen, 1999); see also J. Mar. Syst, Vol 23.

URI:

http://hdl.handle.net/10037/2388

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article.pdf (690.3Kb)

Evaluation of three commercial bovine ELISA kits for detection of antibodies against Alphaherpesviruses in reindeer (Rangifer tarandus tarandus)

Das Neves, Carlos G.; Yoccoz, Nigel G.; Roger, Matthieu; Rimstad, Espen; Tryland, Morten (Journal article; Tidsskriftartikkel; Peer reviewed, 09-Mar-2009)

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Abstract:

Background: The genus Varicellovirus (family Herpesviridae subfamily Alphaherpesvirinae) includes a group of viruses genetically and antigenically related to bovine herpesvirus 1 (BoHV-1) among which cervid herpesvirus 2 (CvHV-2) can be of importance in reindeer. These viruses are known to be responsible for different diseases in both wild and domestic animals. Reindeer are a keystone in the indigenous Saami culture and previous studies have reported the presence of antibodies against alphaherpesviruses in semi-domesticated reindeer in northern Norway. Mortality rates, especially in calves, can be very high in some herds and the abortion potential of alphaherpesvirus in reindeer, unlike in bovines, remains unknown. ELISA kits are the most used screening method in domestic ruminants and given the close genetic relationship between viruses within this genus, it might be possible to use such kits to screen cervids for different alphaherpesviruses. We have compared three different commercial ELISA kits in order to validate its use for reindeer and CvHV-2.
Methods: Three commercial bovine ELISA kits (A, B and C), using either indirect (A) or blocking (B and C) ELISA techniques to detect antibodies against BoHV-1 were tested with sera from 154 reindeer in order to detect antibodies against CvHV-2. A Spearman's rank-based coefficient of correlation (ρ) was calculated. A dilution trial was performed for all kits. A virus neutralization test using both BoHV-1 and CvHV-2 was carried out.
Results: Seroprevalence was almost the same with all kits (40–41%). Despite a similar qualitative score, quantitatively kits classified samples differently and a strong correlation was only identified between Kits B and C. Blocking kits performed better in both repeatability and in the dilution trial. The virus neutralization results confirmed the ELISA results to a very high degree. Neutralizing titres ranged from 1:2 to 1:256 and from 0 to 1:16 against CvHV-2 and BoHV-1 respectively.
Conclusion: Results show that the genetic and antigenic similarity between BoHV-1 and CvHV-2 enables the use of a bovine gB blocking ELISA kit to screen reindeer. The use of an ELISA kit is both cheaper and time saving, allowing screening of large populations. This study revealed a high number of positive animals against CvHV-2 and its impact and distribution in the general population should be further evaluated.

URI:

http://hdl.handle.net/10037/2173

File(s) in this item: 1

article.pdf (867.6Kb)

Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome

Zhuang, Xuan; Yang, Chun; Fevolden, Svein-Erik; Cheng, Chi-Hing Christina (Journal article; Tidsskriftartikkel; Peer reviewed, 2012)

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Abstract:

Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing. We recovered some of the missing AFGP coding sequences and reconstructed a partial AFGP locus in the Atlantic cod genome, bringing to light that not all repetitive sequences lack protein coding information. Also, reliance on genomes of model organisms as reference for annotating protein-coding gene content of a newly sequenced non-model species could lead to omission of novel genetic traits.

URI:

http://hdl.handle.net/10037/4993

File(s) in this item: 1

article.pdf (1.478Mb)

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Abstract:	We present an accurate, fast, simple and non-destructive photographic method to estimate wax ester and lipid content in single individuals of the calanoid copepod genus Calanus and test this method against gas-chromatographic lipid measurements.
URI:	http://hdl.handle.net/10037/4416