| 1. |
- Andersson, Oscar
(författare)
-
Följeforskningsprocessen
- 2015
-
Ingår i: Social mobilisering. - Malmö : Universus Press. ; :1, s. 221-259
-
Bokkapitel (populärvet., debatt m.m.)
|
|
| 2. |
|
|
| 3. |
|
|
| 4. |
- Ankarklev, Johan, et al.
(författare)
-
Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates
- 2015
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
-
Tidskriftsartikel (refereegranskat)abstract
- Background: The diarrhea-causing protozoan Giardia intestinalis makes up a species complex of eight different assemblages (A-H), where assemblage A and B infect humans. Comparative whole-genome analyses of three of these assemblages have shown that there is significant divergence at the inter-assemblage level, however little is currently known regarding variation at the intra-assemblage level. We have performed whole genome sequencing of two sub-assemblage AII isolates, recently axenized from symptomatic human patients, to study the biological and genetic diversity within assemblage A isolates. Results: Several biological differences between the new and earlier characterized assemblage A isolates were identified, including a difference in growth medium preference. The two AII isolates were of different sub-assemblage types (AII-1 [AS175] and AII-2 [AS98]) and showed size differences in the smallest chromosomes. The amount of genetic diversity was characterized in relation to the genome of the Giardia reference isolate WB, an assemblage AI isolate. Our analyses indicate that the divergence between AI and AII is approximately 1 %, represented by similar to 100,000 single nucleotide polymorphisms (SNP) distributed over the chromosomes with enrichment in variable genomic regions containing surface antigens. The level of allelic sequence heterozygosity (ASH) in the two AII isolates was found to be 0.25-0.35 %, which is 25-30 fold higher than in the WB isolate and 10 fold higher than the assemblage AII isolate DH (0.037 %). 35 protein-encoding genes, not found in the WB genome, were identified in the two AII genomes. The large gene families of variant-specific surface proteins (VSPs) and high cysteine membrane proteins (HCMPs) showed isolate-specific divergences of the gene repertoires. Certain genes, often in small gene families with 2 to 8 members, localize to the variable regions of the genomes and show high sequence diversity between the assemblage A isolates. One of the families, Bactericidal/ Permeability Increasing-like protein (BPIL), with eight members was characterized further and the proteins were shown to localize to the ER in trophozoites. Conclusions: Giardia genomes are modular with highly conserved core regions mixed up by variable regions containing high levels of ASH, SNPs and variable surface antigens. There are significant genomic variations in assemblage A isolates, in terms of chromosome size, gene content, surface protein repertoire and gene polymorphisms and these differences mainly localize to the variable regions of the genomes. The large genetic differences within one assemblage of G. intestinalis strengthen the argument that the assemblages represent different Giardia species.
|
|
| 5. |
- Franzen, Oscar, et al.
(författare)
-
Draft genome sequencing of Giardia intestinalis assemblage B isolate GS : is human giardiasis caused by two different species?
- 2009
-
Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 5:8, s. e1000560-
-
Tidskriftsartikel (refereegranskat)abstract
- Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16 x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.
|
|
| 6. |
- Jerlström-Hultqvist, Jon, et al.
(författare)
-
Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate.
- 2010
-
Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11, s. 543-
-
Tidskriftsartikel (refereegranskat)abstract
- Background Giardia intestinalis is a protozoan parasite that causes diarrhea in a wide range of mammalian species. To further understand the genetic diversity between the Giardia intestinalis species, we have performed genome sequencing and analysis of a wild-type Giardia intestinalis sample from the assemblage E group, isolated from a pig. Results We identified 5012 protein coding genes, the majority of which are conserved compared to the previously sequenced genomes of the WB and GS strains in terms of microsynteny and sequence identity. Despite this, there is an unexpectedly large number of chromosomal rearrangements and several smaller structural changes that are present in all chromosomes. Novel members of the VSP, NEK Kinase and HCMP gene families were identified, which may reveal possible mechanisms for host specificity and new avenues for antigenic variation. We used comparative genomics of the three diverse Giardia intestinalis isolates P15, GS and WB to define a core proteome for this species complex and to identify lineage-specific genes. Extensive analyses of polymorphisms in the core proteome of Giardia revealed differential rates of divergence among cellular processes. Conclusions Our results indicate that despite a well conserved core of genes there is significant genome variation between Giardia isolates, both in terms of gene content, gene polymorphisms, structural chromosomal variations and surface molecule repertoires. This study improves the annotation of the Giardia genomes and enables the identification of functionally important variation.
|
|
| 7. |
- Abrahamson, Alexandra, et al.
(författare)
-
Gill EROD in monitoring of CYP1A inducers in fish : A study in rainbow trout (Oncorhynchus mykiss) caged in Stockholm and Uppsala waters
- 2007
-
Ingår i: Aquatic Toxicology. - : Elsevier BV. - 0166-445X .- 1879-1514. ; 85:1, s. 1-8
-
Tidskriftsartikel (refereegranskat)abstract
- The gill filament 7-ethoxyresorufin O-deethylase (EROD) assay was evaluated as a monitoring tool for waterborne cytochrome P4501 A (CYP1A) inducers using rainbow trout (Oncorhynchus mykiss) caged in urban area waters in Sweden. To compare the CYP1A induction response in different tissues, EROD activity was also analyzed in liver and kidney microsomes. Immunohistochemistry was used to localize CYP1A protein in gill and kidney. In two separate experiments fish were caged at sites with fairly high expected polyaromatic hydrocarbon (PAH) contamination. In the first experiment, gill EROD activities were analyzed in fish exposed for 1-21 days in a river running through Uppsala. The reference site was upstream of Uppsala. In the second, gill, liver and kidney EROD activities were analyzed in fish exposed for 1-5 days in fresh or brackish waters of Stockholm and in a reference lake 60 km north of Stockholm. Fish exposed for 5 days followed by 2 days of recovery in tap water in the laboratory were also examined. The gill consistently showed a higher EROD induction compared with the liver and the kidney. After I day of caging, gill EROD activity was markedly induced (6-17-fold) at all sites examined. Induction in gill was pronounced (5-7-fold) also in fish caged at the reference sites. In the 21-day exposure study gill EROD activity remained highly induced throughout the experiment (26-fold at most) and the induced CYP1A protein was exclusively confined to the gill secondary lamellae. In the 5-day exposure experiment, EROD activity peaked after I day and then declined in both gill and liver, while CYP1A immunostaining in the gill remained intense over the 5-day period. In the kidney, CYP1A staining was weak or absent. We conclude that gill EROD activity is a more sensitive biomarker of exposure to waterborne CYP1A inducers than EROD activity in liver and kidney.
|
|
| 8. |
|
|
| 9. |
- Agertz, Oscar, et al.
(författare)
-
Vintergatan - i. The origins of chemically, kinematically, and structurally distinct discs in a simulated milky way-mass galaxy
- 2021
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 503:4, s. 5826-5845
-
Tidskriftsartikel (refereegranskat)abstract
- Spectroscopic surveys of the Milky Way's stars have revealed spatial, chemical, and kinematical structures that encode its history. In this work, we study their origins using a cosmological zoom simulation, VINTERGATAN, of a MilkyWay-mass disc galaxy. We find that in connection to the last major merger at z ∼ 1.5, cosmological accretion leads to the rapid formation of an outer, metal-poor, low-[α/Fe] gas disc around the inner, metal-rich galaxy containing the old high-[α/Fe] stars. This event leads to a bimodality in [α/Fe] over a range of [Fe/H]. A detailed analysis of how the galaxy evolves since z ∼ 1 is presented. We demonstrate the way in which inside-out growth shapes the radial surface density and metallicity profile and how radial migration preferentially relocates stars from the inner disc to the outer disc. Secular disc heating is found to give rise to increasing velocity dispersions and scale heights with stellar age, which together with disc flaring explains several trends observed in the MilkyWay, including shallower radial [Fe/H] profiles above the mid-plane.We show how the galaxy formation scenario imprints non-trivial mappings between structural associations (i.e. thick and thin discs), velocity dispersions, α-enhancements, and ages of stars; e.g. the most metal-poor stars in the low-[α/Fe] sequence are found to have a scale height comparable to old high-[α/Fe] stars. Finally, we illustrate how at low spatial resolution, comparable to the thickness of the galaxy, the proposed pathway to distinct sequences in [α/Fe]-[Fe/H] cannot be captured.
|
|
| 10. |
- Andersson, Eric P., et al.
(författare)
-
INFERNO : Galactic winds in dwarf galaxies with star-by-star simulations including runaway stars
- 2023
-
Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 521:2, s. 2196-2214
-
Tidskriftsartikel (refereegranskat)abstract
- The formation and evolution of galaxies have proved sensitive to the inclusion of stellar feedback, which is therefore crucial to any successful galaxy model. We present INFERNO, a new model for hydrodynamic simulations of galaxies, which incorporates resolved stellar objects with star-by-star calculations of when and where the injection of enriched material, momentum, and energy takes place. INFERNO treats early stellar kinematics to include phenomena such as walkaway and runaway stars. We employ this innovative model on simulations of a dwarf galaxy and demonstrate that our physically motivated stellar feedback model can drive vigorous galactic winds. This is quantified by mass and metal loading factors in the range of 10–100, and an energy loading factor close to unity. Outflows are established close to the disc, are highly multiphase, spanning almost 8 orders of magnitude in temperature, and with a clear dichotomy between mass ejected in cold, slow-moving (T ≲ 5 × 104 K, v < 100 km s-1) gas and energy ejected in hot, fast-moving (T > 106 K, v > 100 km s-1) gas. In contrast to massive disc galaxies, we find a surprisingly weak impact of the early stellar kinematics, with runaway stars having little to no effect on our results, despite exploding in diffuse gas outside the dense star-forming gas, as well as outside the galactic disc entirely. We demonstrate that this weak impact in dwarf galaxies stems from a combination of strong feedback and a porous interstellar medium, which obscure any unique signatures that runaway stars provide.
|
|
