| 1. |
- Andersson, Anders, et al.
(författare)
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Global analysis of mRNA stability in the archaeon Sulfolobus
- 2006
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 7:10, s. R99-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Transcript half-lives differ between organisms, and between groups of genes within the same organism. The mechanisms underlying these differences are not clear, nor are the biochemical properties that determine the stability of a transcript. To address these issues, genome-wide mRNA decay studies have been conducted in eukaryotes and bacteria. In contrast, relatively little is known about RNA stability in the third domain of life, Archaea. Here, we present a microarray-based analysis of mRNA half-lives in the hyperthermophilic crenarchaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, constituting the first genome-wide study of RNA decay in archaea. Results: The two transcriptomes displayed similar half-life distributions, with medians of about five minutes. Growth-related genes, such as those involved in transcription, translation and energy production, were over-represented among unstable transcripts, whereas uncharacterized genes were over-represented among the most stable. Half-life was negatively correlated with transcript abundance and, unlike the situation in other organisms, also negatively correlated with transcript length. Conclusion: The mRNA half-life distribution of Sulfolobus species is similar to those of much faster growing bacteria, contrasting with the earlier observation that median mRNA half-life is proportional to the minimal length of the cell cycle. Instead, short half-lives may be a general feature of prokaryotic transcriptomes, possibly related to the absence of a nucleus and/or more limited post-transcriptional regulatory mechanisms. The pattern of growth-related transcripts being among the least stable in Sulfolobus may also indicate that the short half-lives reflect a necessity to rapidly reprogram gene expression upon sudden changes in environmental conditions.
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| 2. |
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| 3. |
- Jiao, Xiang, et al.
(författare)
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Structural Alterations from Multiple Displacement Amplification of a Human Genome Revealed by Mate-Pair Sequencing
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:7, s. e22250-
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Tidskriftsartikel (refereegranskat)abstract
- Comprehensive identification of the acquired mutations that cause common cancers will require genomic analyses of large sets of tumor samples. Typically, the tissue material available from tumor specimens is limited, which creates a demand for accurate template amplification. We therefore evaluated whether phi29-mediated whole genome amplification introduces false positive structural mutations by massive mate-pair sequencing of a normal human genome before and after such amplification. Multiple displacement amplification led to a decrease in clone coverage and an increase by two orders of magnitude in the prevalence of inversions, but did not increase the prevalence of translocations. While multiple strand displacement amplification may find uses in translocation analyses, it is likely that alternative amplification strategies need to be developed to meet the demands of cancer genomics.
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| 4. |
- Moruz, Luminita, 1982-, et al.
(författare)
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Mass Fingerprinting of Complex Mixtures : Protein Inference from High-Resolution Peptide Masses and Predicted Retention Times
- 2013
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 12:12, s. 5730-5741
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Tidskriftsartikel (refereegranskat)abstract
- In typical shotgun experiments, the mass spectrometer records the masses of a large set of ionized analytes but fragments only a fraction of them. In the subsequent analyses, normally only the fragmented ions are used to compile a set of peptide identifications, while the unfragmented ones are disregarded. In this work, we show how the unfragmented ions, here denoted MS1-features, can be used to increase the confidence of the proteins identified in shotgun experiments. Specifically, we propose the usage of in silico mass tags, where the observed MS1-features are matched against de novo predicted masses and retention times for all peptides derived from a sequence database. We present a statistical model to assign protein-level probabilities based on the MS1-features and combine this data with the fragmentation spectra. Our approach was evaluated for two triplicate data sets from yeast and human, respectively, leading to up to 7% more protein identifications at a fixed protein-level false discovery rate of 1%. The additional protein identifications were validated both in the context of the mass spectrometry data and by examining their estimated transcript levels generated using RNA-Seq. The proposed method is reproducible, straightforward to apply, and can even be used to reanalyze and increase the yield of existing data sets.
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| 5. |
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| 6. |
- Rosenlund, David, et al.
(författare)
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Historically restricted or historically empowered? : Differences in access to historical content knowledge between low- and high-SES pupils
- 2024
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Ingår i: Curriculum Journal. - : John Wiley & Sons. - 0958-5176 .- 1469-3704. ; 35:2, s. 220-236
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Tidskriftsartikel (refereegranskat)abstract
- In the study presented in this article, the aim is to further the understanding regarding the differences between pupils (aged 15–16) from schools with low or high socio-economic status (SES), regarding the amount and diversity of content knowledge in history that they have acquired by the end of compulsory schooling. Following a definition of historical content knowledge, we situate the concept in relation to other aspects of the history school subject. This is done to visualize historical content knowledge's central role in more complex aspects of the subject. The empiri-cal material used in the study is pupils' responses on both selected and constructed response items on the Swedish national test in history. In the study, a com-bination of qualitative and quantitative approaches is used. The results show not only that pupils in low- SES schools provide fewer examples of historical content knowledge. We can also establish that the historical content knowledge of pupils from high-SES schools represents several perspectives while there are few perspectives present in the responses from pupils in low-SES schools. The results are used to discuss how the differences between pupils in low- and high-SES schools may affect their possibilities for educational success and active participation in society.
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| 7. |
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| 8. |
- Selander, Jenny, et al.
(författare)
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Long-Term Exposure to Road Traffic Noise and Myocardial Infarction
- 2009
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Ingår i: Epidemiology. - : Lippincott Williams & Wilkins, Inc. - 1044-3983 .- 1531-5487. ; 20:2, s. 272-279
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Tidskriftsartikel (refereegranskat)abstract
- Background: An association has been reported between long-term exposure to road traffic noise and the risk of myocardial infarction (MI), but the evidence is limited and inconclusive. No previous study has simultaneously analyzed the role of exposure to noise and air pollution from road traffic in the risk of MI. Methods: A population-based case-control study on MI was conducted 1992-1994 in Stockholm County. Participants answered a questionnaire and underwent a physical examination. Residential exposure to noise and air pollution from road traffic between 1970 and 1992-1994 was assessed for 3666 participants (1571 cases of MI and 2095 controls), based on residential history combined with information on traffic intensity and distance to nearby roads. Information was also obtained on factors potentially affecting the relationship between noise exposure and MI, such as noise annoyance. Results: The correlation between long-term individual exposure to noise and air pollution from traffic was high (r = 0.6). The adjusted odds ratio for MI associated with long-term road traffic noise exposure of 50 dBA or higher was 1.12 (95% confidence interval = 0.95-1.33). In a subsample, defined by excluding persons with hearing loss or exposure to noise from other sources, the corresponding odds ratio was 1.38 (1.11-1.71), with a positive exposure-response trend. No strong effect modification was apparent by sex or cardiovascular risk factors, including air pollution from road traffic. Conclusions: The results lend some support to the hypothesis that long-term exposure to road traffic noise increases the risk for MI.
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