| 1. |
- Nystedt, Björn, et al.
(författare)
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The Norway spruce genome sequence and conifer genome evolution
- 2013
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 497:7451, s. 579-584
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Tidskriftsartikel (refereegranskat)abstract
- Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (>10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding.
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| 2. |
- Näsström, Thomas, et al.
(författare)
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Synthetic NAC 71-82 Peptides Designed to Produce Fibrils with Different Protofilament Interface Contacts
- 2021
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Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 22:17
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Tidskriftsartikel (refereegranskat)abstract
- Alpha-synucleinopathies are featured by fibrillar inclusions in brain cells. Although α-synuclein fibrils display structural diversity, the origin of this diversity is not fully understood. We used molecular dynamics simulations to design synthetic peptides, based on the NAC 71-82 amino acid fragment of α-synuclein, that govern protofilament contacts and generation of twisted fibrillar polymorphs. Four peptides with structures based on either single or double fragments and capped or non-capped ends were selected for further analysis. We determined the fibrillar yield and the structures from these peptides found in the solution after fibrillisation using protein concentration determination assay and circular dichroism spectroscopy. In addition, we characterised secondary structures formed by individual fibrillar complexes using laser-tweezers Raman spectroscopy. Results suggest less mature fibrils, based on the lower relative β-sheet content for double- than single-fragment peptide fibrils. We confirmed this structural difference by TEM analysis which revealed, in addition to short protofibrils, more elongated, twisted and rod-like fibril structures in non-capped and capped double-fragment peptide systems, respectively. Finally, time-correlated single-photon counting demonstrated a difference in the Thioflavin T fluorescence lifetime profiles upon fibril binding. It could be proposed that this difference originated from morphological differences in the fibril samples. Altogether, these results highlight the potential of using peptide models for the generation of fibrils that share morphological features relevant for disease, e.g., twisted and rod-like polymorphs.
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| 3. |
- Andersson, K, et al.
(författare)
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Colloidal rare earth elements in a boreal river: Changing sources and distributions during the spring flood
- 2006
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Ingår i: Geochimica Et Cosmochimica Acta. - : Elsevier BV. - 0016-7037 .- 1872-9533. ; 70:13, s. 3261-3274
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Tidskriftsartikel (refereegranskat)abstract
- Variations in the physico-chemical speciation of the rare earth elements (REE) have been investigated in a subarctic boreal river during an intense spring flood event using prefiltered (< 100 mu m) samples, cross-flow (ultra)filtration (CFF), flow field-flow fractionation (FIFFF), and diffusive gradients in thin films (DGT). This combination of techniques has provided new information regarding the release and transport of the REE in river water. The colloidal material can be described in terms of two fractions dominated by carbon and iron, respectively. These two fractions, termed colloidal carrier phases, showed significant temporal changes in concentration and size distribution. Before the spring flood, colloidal carbon concentrations were low, the colloids being dominated by relatively large iron colloids. Colloidal concentrations increased sharply during the spring flood, with smaller carbon colloids dominating. Following the spring flood, colloidal concentrations decreased again, smaller carbon colloids still dominating. The REE are transported mainly in the particulate and colloidal phases. Before the spring flood, the REE composition of all measured fractions was similar to local till. During the spring flood, the REE concentrations in the colloidal and particulate fractions increased. The increase was most marked for the lighter REE, which therefore showed a strong enrichment when normalized to local till. Following the spring flood, the REE concentrations decreased again and reverted to a distribution similar to local till. These changes in the concentration and distributions of carbon iron and REE are interpreted in terms of changing hydrological flow paths in soil and bedrock which occur during the spring flood. (c) 2006 Elsevier Inc. All rights reserved.
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| 4. |
- Kaur-Kahlon, G., et al.
(författare)
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Response of a coastal tropical pelagic microbial community to changed salinity and temperature
- 2016
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Ingår i: Aquatic Microbial Ecology. - 0948-3055 .- 1616-1564. ; 77:1, s. 37-50
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Tidskriftsartikel (refereegranskat)abstract
- Studies on the responses of tropical microbial communities to changing hydrographic conditions are presently poorly represented. We present here the results from a mesocosm experiment conducted in southwest (SW) coastal India to investigate how changes in temperature and salinity may affect a coastal tropic microbial community. The onset of algal and bacterial blooms, the maximum production and biomass, and the interrelation between phytoplankton and bacteria were studied in replicated mesocosms. The treatments were set up featuring ambient conditions (28 °C, 35 PSU), hyposalinity (31 PSU), warming (31 °C) and a double manipulated treatment with warming and hyposalinity (31 °C, 31 PSU). The hyposaline treatment had the most considerable influence manifested as significantly lower primary production, and the most dissimilar microphytoplankton species community. The increased temperature acted as a catalyst in the double manipulated treatment and higher primary production was maintained. We investigated the dynamics of the microbial community with a structural equation model approach, and found a significant interrelation between phytoplankton biomass and bacterial abundance. Using this methodology, it became evident that temperature and salinity changes, individually and together, mediate direct and indirect effects that influence different compartments of the microbial loop. In the face of climate change, we suggest that in relatively nutrient replete tropical coastal zones, salinity and temperature changes will affect nutrient assimilation with subsequent significant effects on the quantity of microbial biomass and production.
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| 5. |
- Andersson, Stefan, et al.
(författare)
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Reproduktion, pollination och spridning
- 2008
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Ingår i: Botanik - systematik, evolution, mångfald. - 9789144043043 ; , s. 233-276
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Bokkapitel (refereegranskat)
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| 6. |
- Franzen, Oscar, et al.
(författare)
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Draft genome sequencing of Giardia intestinalis assemblage B isolate GS : is human giardiasis caused by two different species?
- 2009
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Ingår i: PLoS Pathogens. - : Public Library of Science (PLoS). - 1553-7366 .- 1553-7374. ; 5:8, s. e1000560-
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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.
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| 7. |
- Jerlström-Hultqvist, Jon, et al.
(författare)
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Genome analysis and comparative genomics of a Giardia intestinalis assemblage E isolate.
- 2010
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 11, s. 543-
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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.
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| 8. |
- Matsson, Ingvar, et al.
(författare)
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LOKET - a gamma-ray spectroscopy system for in-pool measurements of thermal power distribution in irradiated nuclear fuel
- 2006
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 569:3, s. 872-882
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Tidskriftsartikel (refereegranskat)abstract
- An important issue in the operations of nuclear power plants is the independent validation of core physics codes like e.g. Westinghouse PHOENIX-4/POLCA-7. Such codes are used to predict the thermal power distribution down to single node level in the core. In this paper, a dedicated measurement system (LOKET) is described and experimental results are discussed. The system is based on a submergible housing, containing a high-resolution germanium detector, allowing for measurements in-pool. The system can be transported to virtually any nuclear power plant's fuel storage pool for measurements in-pool during outage. The methodology utilises gamma radiation specific for La-140, whose decay is governed by the parent Ba-140, reflecting a weighted average power distribution, representative for the last weeks of operation of the core. Good agreements between measured power distribution and core physics calculations (Ba distribution) have been obtained during a series of experiments at Leibstadt NPP in Switzerland and Cofrentes NPP in Spain (BWRs) for both fuel assemblies and single fuel rods. The system has proven as a very useful tool for the experimental validation of core calculations also for the most complex fuel designs and challenging core configurations. Experimental errors (on the 1 - sigma level), has been demonstrated below +/- 2% on nodal level for assembly measurements.
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| 9. |
- Matsson, Ingvar, et al.
(författare)
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On-site Gamma-ray Spectroscopic Measurements of Fission Gas Release in Irradiated Nuclear Fuel
- 2007
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Ingår i: Applied Radiation and Isotopes. - : Elsevier BV. - 0969-8043 .- 1872-9800. ; 65:1, s. 36-45
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Tidskriftsartikel (refereegranskat)abstract
- An experimental, non-destructive in-pool, method for measuring fission gas release (FGR) in irradiated nuclear fuel has been developed. Using the method, a significant number of experiments have been performed in-pool at several nuclear power plants of the BWR type. The method utilises the 514 keV gamma-radiation from the gaseous fission product Kr-85 captured in the fuel rod plenum volume. A submergible measuring device (LOKET) consisting of an HPGe-detector and a collimator system was utilised allowing for single rod measurements on virtually all types of BWR fuel. A FGR database covering a wide range of burn-ups (up to average rod burn-up well above 60 MWd/kgU), irradiation history, fuel rod position in cross section and fuel designs has been compiled and used for computer code benchmarking, fuel performance analysis and feedback to reactor operators. Measurements clearly indicate the low FGR in more modern fuel designs in comparison to older fuel types.
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| 10. |
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