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- Agües Paszkowsky, Núria, et al.
(författare)
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Vegetation and Drought Trends in Sweden’s Mälardalen Region – Year-on-Year Comparison by Gaussian Process Regression
- 2020
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Ingår i: 2020 Swedish Workshop on Data Science (SweDS). - : IEEE. - 9781728192048
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Konferensbidrag (refereegranskat)abstract
- This article describes analytical work carried out in a pilot project for the Swedish Space Data Lab (SSDL), which focused on monitoring drought in the Mälardalen region in central Sweden. Normalized Difference Vegetation Index (NDVI) and the Moisture Stress Index (MSI) – commonly used to analyse drought – are estimated from Sentinel 2 satellite data and averaged over a selection of seven grassland areas of interest. To derive a complete time-series over a season that interpolates over days with missing data, we use Gaussian Process Regression, a technique from multivariate Bayesian analysis. The analysis show significant differences at 95% confidence for five out of seven areas when comparing the peak drought period in the dry year 2018 compared to the corresponding period in 2019. A cross-validation analysis indicates that the model parameter estimates are robust for temporal covariance structure (while inconclusive for the spatial dimensions). There were no signs of over-fitting when comparing in-sample and out-of-sample RMSE.
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| 4. |
- Brännvall, Mathias, et al.
(författare)
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Evidence for induced fit in bacterial RNase P RNA-mediated cleavage
- 2007
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 372:5, s. 1149-1164
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Tidskriftsartikel (refereegranskat)abstract
- RNase P with its catalytic RNA subunit is involved in the processing of a number of RNA precursors with different structures. However, precursor tRNAs are the most abundant substrates for RNase P. Available data suggest that a tRNA is folded into its characteristic structure already at the precursor state and that RNase P recognizes this structure. The tRNA D-/T-loop domain (TSL-region) is suggested to interact with the specificity domain of RNase P RNA while residues in the catalytic domain interact with the cleavage site. Here, we have studied the consequences of a productive interaction between the TSL-region and its binding site (TBS) in the specificity domain using tRNA precursors and various hairpin-loop model substrates. The different substrates were analyzed with respect to cleavage site recognition, ground-state binding, cleavage as a function of the concentration of Mg2+ and the rate of cleavage under conditions where chemistry is suggested to be rate limiting using wild-type Escherichia coli RNase P RNA, M1 RNA, and M1 RNA variants with structural changes in the TBS-region. On the basis of our data, we conclude that a productive TSL/TBS interaction results in a conformational change in the M1 RNA substrate complex that has an effect on catalysis. Moreover, it is likely that this conformational change comprises positioning of chemical groups (and Mg2+) at and in the vicinity of the cleavage site. Hence, our findings are consistent with an induced-fit mechanism in RNase P RNA-mediated cleavage.
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| 6. |
- Brännvall, Mathias, 1973-
(författare)
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Metal ion cooperativity in Escherichia coli RNase P RNA
- 2002
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- RNase P is an essential ribonuclease responsible for removal of the 5’ leader of tRNA precursors. Bacterial RNase P consists of an RNA subunit and a small basic protein. The catalytic activity is associated with the RNA subunit, i.e. bacterial RNase P RNA is a ribozyme. The protein subunit is, however, essential for activity in vivo. RNase P RNA, as well as the holoenzyme, requires the presence of divalent metal ions for activity. The aim of this thesis was to increase our understanding of the catalytic mechanism of RNase P RNA mediated cleavage. The importance of the nucleotides close to the cleavage site and the roles of divalent metal ions in RNase P RNA-catalyzed reaction were investigated. Escherichia coli RNase P RNA (M1 RNA) was used as a model system.It was shown that different metal ions have differential effects on cleavage site recognition. Cleavage activity was rescued by mixing metal ions that do not promote cleavage activity by themselves. This suggests that efficient and correct cleavage is the result of metal ion cooperativity in the RNase P RNA-mediated cleavage reaction. The results suggested that one of the metal ions involved in this cooperativity is positioned in the vicinity of a well-known interaction between RNase P RNA and its substrate. Based on my studies on how different metal ions bind to RNA and influence its activity we raise the interesting possibility that the activity of biocatalysts that depend on RNA for activity are up- or downregulated depending on the intracellular concentrations of the bulk biological metal ions Mg2+ and Ca2+.The nucleotides upstream of the cleavage site in the substrate were found to influence the cleavage efficiency. This was not exclusively due to intermolecular base pairing within the substrate but also dependent on the identities of the nucleotides at position –2 and –1. The strength of the base pair at position –1/+73 was demonstrated to affect cleavage efficiency. These observations are in keeping with previous suggestion that the nucleotides close to the cleavage site are important for RNase P cleavage. We conclude that the residue at -1 is a positive determinant for cleavage by RNase P. Hence, my studies extend our understanding of the RNase P cleavage site recognition process.
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| 7. |
- Brännvall, Mathias, et al.
(författare)
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Metal ion cooperativity in ribozyme cleavage of RNA
- 2001
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - 0027-8424 .- 1091-6490. ; 98:23, s. 12943-12947
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Tidskriftsartikel (refereegranskat)abstract
- Combinations of chemical and genetic approaches were used to study the function of divalent metal ions in cleavage of RNA by the ribozyme RNase P RNA. We show that different divalent metal ions have differential effects on cleavage site recognition and rescue of cleavage activity by mixing divalent metal ions that do not promote cleavage by themselves. We conclude that efficient and correct cleavage is the result of cooperativity between divalent metal ions bound at different sites in the RNase P RNA-substrate complex. Complementation of a mutant RNase P RNA phenotype as a result of divalent metal ion replacement is demonstrated also. This finding together with other data indicate that one of the metal ions involved in this cooperativity is positioned near the cleavage site. The possibility that the Mg2+/Ca2+ ratio might regulate the activity of biocatalysts that depend on RNA for activity is discussed.
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