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- Jallow, Muminatou, et al.
(författare)
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Genome-wide and fine-resolution association analysis of malaria in West Africa.
- 2009
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; , s. 657-665
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Tidskriftsartikel (refereegranskat)abstract
- We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 x 10(-7) to P = 4 x 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.
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| 3. |
- Lindgren, Paula, et al.
(författare)
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Organic geochemistry of the Haughton Impact Structure
- 2008
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Konferensbidrag (populärvet., debatt m.m.)abstract
- The Haughton Impact Structure (HIS) formed 39 Ma ago. The target rocks include Lower Palaeozoic aged limestone that contain small quantities of solvent extractable organic matter. The target bedrock, hydrothermal deposits and limestone clasts within impact melt breccias all yield fossil organic matter that has been thermally matured to varying degrees. But unusually for a terrestrial impact crater, molecular biomarkers survive. While many other impact structures on Earth (e.g. Gardnos) possess lithologies with associated organic carbon, thermal maturation prior or subsequent to the impact has destroyed any biomarkers that were present (note that this is not necessarily due to the impact itself). In other instances the biomarkers present are found in hydrocarbon accumulations and have migrated through the structure (e.g. Siljan). The HIS is unique in not experiencing subsequent regional metamorphism, furthermore the sedimentary organic matter is mostly present within the target rocks as inclusions of organic matter and not a free continuous petroleum phase (it has not migrated).The extraction and analysis of biomarkers from impactites from the HIS radically alters how an organic geochemist, looking to detect ancient molecular evidence of life, views the surface of a planetary body. For craters of a certain diameter (23 km), impact cratering, far from being an agent that obliterates the biomarker fossil record, can be shown to be a geological process more akin to tectonic activity: it has the potential to exhume geological formations that would otherwise be buried – albeit at the cost of a relatively minor increase in thermal maturity.
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| 4. |
- Martin, Francis, et al.
(författare)
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The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
- 2008
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 452:7183, s. 7-88
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Tidskriftsartikel (refereegranskat)abstract
- Mycorrhizal symbioses -- the union of roots and soil fungi -- are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants1,2. Boreal, temperate, and montane forests all depend upon ectomycorrhizae1. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of 2 ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here, we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-million-base genome assembly contains ~ 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features most notably a battery of effector-type small secreted proteins (SSP) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific proteins likely play a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell walls, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus which enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem in order to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.
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