| 1. |
- Widén Nilsson, Elin, et al.
(författare)
-
Kartdata till PLC6 : Underlagsrapport till Pollution Load Compilation 6 rörande markanvändning, vattenförekomstområden, regionsindelning, jordbruksmarkens jordart, lutning och fosforhalt samt medelvärdesberäkningar
- 2016
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- För att källfördela läckage av kväve och fosfor till Östersjön och Västerhavet behövs en stor mängd geografisk information. Kartunderlaget är därför av mycket stor betydelse. Rapporten syftar till att ge en detaljerad fördjupning i hur de olika kartbaserade underlagsdata till PLC6 togs fram. Särskilt för markanvändningen fördjupas även analysen av resultaten. Hydrologiska vattenförekomstområden har tagits fram baserat på vattenmyndigheternas klassning av vattenförekomster och SVAR-databasen för delavrinningsområden. De ca 23 100 vattenförekomstområdena har grupperats till ca 1100 redovisningsområden, samt vidare till huvudavrinningsområden och havsbassängernas avrinningsområden.Regionsindelning för olika beräkning av läckage från jordbruksmark, skog och öppen mark i olika delar av Sverige har tagits fram baserat på PLC5- indelningen och med ett tillägg av två nya regioner för läckaget från skog och öppen mark. En ny markanvändningskarta har tagits fram, baserad på vägkartan, Jordbruksverkets jordbruksblock och stödsökta grödor, SCB:s tätortskarta, Skogsstyrelsens data på faktiskt avverkad areal, och Corine-data för Norge och Finland. Inom tätorter har SMD-kartan använts för en mer högupplöst klassning till beräkningen av dagvattenbelastning. Jordbruksmarkens jordartsfördelning, fosforhalt i marken och lutning har beräknats baserats på nya kartdata.Beräkningar av varje vattenförekomstområdes centrumkoordinater och medelhöjd har genomförts.Läckageregionernas målavrinning och kvävedeposition har beräknats baserat på vattenförekomstområdenas avrinning respektive rasterdata för depositionen.
|
|
| 2. |
- Bensch, Staffan, et al.
(författare)
-
The genome of Haemoproteus tartakovskyi and its relationship to human malaria parasites
- 2016
-
Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 8:5, s. 73-1361
-
Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships among hemosporidian parasites, including the origin of Plasmodium falciparum, the most virulent malaria parasite of humans, have been heavily debated for decades. Studies based on multiple-gene sequences have helped settle many of these controversial phylogenetic issues. However, denser taxon sampling and genome-wide analyses are needed to confidently resolve the evolutionay relationships among hemosporidian parasites. Genome sequences of several Plasmodium parasites are available but only for species infecting primates and rodents. To root the phylogenetic tree of Plasmodium, genomic data from related parasites of birds or reptiles are required. Here, we use a novel approach to isolate parasite DNA from microgametes and describe the first genome of a bird parasite in the sister genus to Plasmodium, Haemoproteus tartakovskyi Similar to Plasmodium parasites, H. tartakovskyi has a small genome (23.2 Mb, 5,990 genes) and a GC content (25.4%) closer to P. falciparum (19.3%) than to Plasmodium vivax (42.3%). Combined with novel transcriptome sequences of the bird parasite Plasmodium ashfordi, our phylogenomic analyses of 1,302 orthologous genes demonstrate that mammalian-infecting malaria parasites are monophyletic, thus rejecting the repeatedly proposed hypothesis that the ancestor of Laverania parasites originated from a secondary host shift from birds to humans. Genes and genomic features previously found to be shared between P. falciparum and bird malaria parasites, but absent in other mammal malaria parasites, are therefore signatures of maintained ancestral states. We foresee that the genome of H. tartakovskyi will open new directions for comparative evolutionary analyses of malarial adaptive traits.
|
|
| 3. |
- Hellgren, Olof, et al.
(författare)
-
De novo synthesis of thiamine (vitamin B1) is the ancestral state in Plasmodium parasites – evidence from avian haemosporidians
- 2018
-
Ingår i: Parasitology. - 0031-1820. ; 145:8, s. 1084-1089
-
Tidskriftsartikel (refereegranskat)abstract
- Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria. Here we show that the genes essential for the de novo synthesis of thiamine are found also in avian Plasmodium species. Importantly, they are also present in species phylogenetically basal to all mammalian and avian Plasmodium parasites, i.e. Haemoproteus. Furthermore, we found that these genes are expressed during the blood stage of the avian malaria infection, indicating that this metabolic pathway is actively transcribed. We conclude that the ability to synthesize thiamine is widespread among haemosporidians, with a recent loss in the rodent malaria species.
|
|
| 4. |
- Hellgren, Olof, et al.
(författare)
-
De novo synthesis of thiamine (vitamin B1) is the ancestral state in Plasmodium parasites – evidence from avian haemosporidians
- 2017
-
Ingår i: Parasitology. - : Cambridge University Press (CUP). - 0031-1820 .- 1469-8161. ; 145:8, s. 1084-1089
-
Tidskriftsartikel (refereegranskat)abstract
- Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria. Here we show that the genes essential for the de novo synthesis of thiamine are found also in avian Plasmodium species. Importantly, they are also present in species phylogenetically basal to all mammalian and avian Plasmodium parasites, i.e. Haemoproteus. Furthermore, we found that these genes are expressed during the blood stage of the avian malaria infection, indicating that this metabolic pathway is actively transcribed. We conclude that the ability to synthesize thiamine is widespread among haemosporidians, with a recent loss in the rodent malaria species.
|
|
| 5. |
|
|
| 6. |
- Videvall, Elin, et al.
(författare)
-
Major shifts in gut microbiota during development and its relationship to growth in ostriches
- 2019
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 28:10, s. 2653-2667
-
Tidskriftsartikel (refereegranskat)abstract
- The development of gut microbiota during ontogeny is emerging as an important process influencing physiology, immunity and fitness in vertebrates. However, knowledge of how bacteria colonize the juvenile gut, how this is influenced by changes in the diversity of gut bacteria and to what extent this influences host fitness, particularly in nonmodel organisms, is lacking. Here we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiome in ostriches (Struthio camelus, n = 66, repeatedly sampled) over the first 3 months of life and its relationship to growth. We found a gradual increase in microbial diversity with age that involved multiple colonization and extinction events and a major taxonomic shift in bacteria that coincided with the cessation of yolk absorption. Comparisons with the microbiota of adults (n = 5) revealed that the chicks became more similar in their microbial diversity and composition to adults as they aged. There was a five-fold difference in juvenile growth during development, and growth during the first week of age was strongly positively correlated with the abundance of the genus Bacteroides and negatively correlated with Akkermansia. After the first week, the abundances of six phylogenetically diverse families (Peptococcaceae, S24-7, Verrucomicrobiae, Anaeroplasmataceae, Streptococcaceae, Methanobacteriaceae) were associated with subsequent reductions in chick growth in an age-specific and transient manner. These results have broad implications for our understanding of the development of gut microbiota and its associations with animal growth.
|
|
| 7. |
- Videvall, Elin, et al.
(författare)
-
The Avian Transcriptome Response to Malaria Infection.
- 2015
-
Ingår i: Molecular biology and evolution. - : Oxford University Press (OUP). - 0737-4038 .- 1537-1719. ; 32:5, s. 1255-1267
-
Tidskriftsartikel (refereegranskat)abstract
- Malaria parasites are highly virulent pathogens which infect a wide range of vertebrates. Despite their importance, the way different hosts control and suppress malaria infections remains poorly understood. With recent developments in next generation sequencing techniques, however, it is now possible to quantify the response of the entire transcriptome to infections. We experimentally infected Eurasian siskins (Spinus spinus) with avian malaria parasites (Plasmodium ashfordi), and used high-throughput RNA-sequencing to measure the avian transcriptome in blood collected before infection (day 0), during peak parasitemia (day 21 post infection), and when parasitemia was decreasing (day 31). We found considerable differences in the transcriptomes of infected and uninfected individuals, with a large number of genes differentially expressed during both peak and decreasing parasitemia stages. These genes were overrepresented among functions involved in the immune system, stress response, cell death regulation, metabolism, and telomerase activity. Comparative analyses of the differentially expressed genes in our study to those found in other hosts of malaria (human and mouse), revealed a set of genes that are potentially involved in highly conserved evolutionary responses to malaria infection. By using RNA-sequencing we gained a more complete view of the host response, and were able to pinpoint not only well documented host genes, but also unannotated genes with clear significance during infection, such as microRNAs. This study shows how the avian blood transcriptome shifts in response to malaria infection, and we believe it will facilitate further research into the diversity of molecular mechanisms that hosts utilize to fight malaria infections.
|
|
| 8. |
- Videvall, Elin, et al.
(författare)
-
The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression
- 2017
-
Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X.
-
Tidskriftsartikel (refereegranskat)abstract
- Malaria parasites (Plasmodium spp.) include some of the world's most widespread and virulent pathogens. Our knowledge of the molecular mechanisms these parasites use to invade and exploit hosts other than mice and primates is, however, extremely limited. It is therefore imperative to characterize transcriptome-wide gene expression from non-model malaria parasites and how this varies across host individuals. Here, we used high-throughput Illumina RNA-sequencing on blood from wild-caught Eurasian siskins experimentally infected with a clonal strain of the avian malaria parasite Plasmodium ashfordi (lineage GRW2). By using a multi-step approach to filter out host transcripts, we successfully assembled the blood-stage transcriptome of P. ashfordi. A total of 11 954 expressed transcripts were identified, and 7 860 were annotated with protein information. We quantified gene expression levels of all parasite transcripts across three hosts during two infection stages – peak and decreasing parasitemia. Interestingly, parasites from the same host displayed remarkably similar expression profiles during different infection stages, but showed large differences across hosts, indicating that P. ashfordi may adjust its gene expression to specific host individuals. We further show that the majority of transcripts are most similar to the human parasite Plasmodium falciparum, and a large number of red blood cell invasion genes were discovered, suggesting evolutionary conserved invasion strategies between mammalian and avian Plasmodium. The transcriptome of P. ashfordi and its host-specific gene expression advances our understanding of Plasmodium plasticity and is a valuable resource as it allows for further studies analysing gene evolution and comparisons of parasite gene expression.
|
|
