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- L. B. Almeida, Bilena, et al.
(författare)
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The transcription factor network of E. coli steers global responses to shifts in RNAP concentration
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 50:12, s. 6801-6819
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Tidskriftsartikel (refereegranskat)abstract
- The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
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- Launiainen, S, et al.
(författare)
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Vertical variability and effect of stability on turbulence characteristics down to the forest floor of a pine forest.
- 2007
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Ingår i: Tellus. Series B: Chemical and Physical Meteorology. - : Stockholm University Press. - 0280-6509 .- 1600-0889. ; 59, s. 919-936
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Tidskriftsartikel (refereegranskat)abstract
- Among the fundamental problems in canopy turbulence, particularly near the forest floor, remain the local diabatic effects and linkages between turbulent length scales and the canopy morphology. To progress on these problems, mean and higher order turbulence statistics are collected in a uniform pine forest across a wide range of atmospheric stability conditions using five 3-D anemometers in the subcanopy. The main novelties from this experiment are: (1) the agreement between second-order closure model results and measurements suggest that diabatic states in the layer above the canopy explain much of the modulations of the key velocity statistics inside the canopy except in the immediate vicinity of the trunk space and for very stable conditions. (2) The dimensionless turbulent kinetic energy in the trunk space is large due to a large longitudinal velocity variance but it is inactive and contributes little to momentum fluxes. (3) Near the floor layer, a logarithmic mean velocity profile is formed and vertical eddies are strongly suppressed modifying all power spectra. (4) A spectral peak in the vertical velocity near the ground commensurate with the trunk diameter emerged at a moderate element Reynolds number consistent with Strouhal instabilities describing wake production.
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- Acosta Navarro, Juan Camilo, et al.
(författare)
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Global emissions of terpenoid VOCs from terrestrial vegetation in the last millennium
- 2014
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Ingår i: Journal of Geophysical Research - Atmospheres. - : Wiley-Blackwell. - 2169-897X .- 2169-8996. ; 119:11, s. 6867-6885
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Tidskriftsartikel (refereegranskat)abstract
- We investigated the millennial variability (1000 A.D.-2000 A.D.) of global biogenic volatile organic compound (BVOC) emissions by using two independent numerical models: The Model of Emissions of Gases and Aerosols from Nature (MEGAN), for isoprene, monoterpene, and sesquiterpene, and Lund-Potsdam-Jena-General Ecosystem Simulator (LPJ-GUESS), for isoprene and monoterpenes. We found the millennial trends of global isoprene emissions to be mostly affected by land cover and atmospheric carbon dioxide changes, whereas monoterpene and sesquiterpene emission trends were dominated by temperature change. Isoprene emissions declined substantially in regions with large and rapid land cover change. In addition, isoprene emission sensitivity to drought proved to have significant short-term global effects. By the end of the past millennium MEGAN isoprene emissions were 634 TgC yr-1 (13% and 19% less than during 1750-1850 and 1000-1200, respectively), and LPJ-GUESS emissions were 323 TgC yr-1(15% and 20% less than during 1750-1850 and 1000-1200, respectively). Monoterpene emissions were 89 TgC yr-1(10% and 6% higher than during 1750-1850 and 1000-1200, respectively) in MEGAN, and 24 TgC yr-1 (2% higher and 5% less than during 1750-1850 and 1000-1200, respectively) in LPJ-GUESS. MEGAN sesquiterpene emissions were 36 TgC yr-1(10% and 4% higher than during 1750-1850 and 1000-1200, respectively). Although both models capture similar emission trends, the magnitude of the emissions are different. This highlights the importance of building better constraints on VOC emissions from terrestrial vegetation.
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- Smolander, Olli Pekka, et al.
(författare)
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Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map
- 2022
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Ingår i: GigaScience. - : Oxford University Press (OUP). - 2047-217X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Background: The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results: The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92-94% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions: The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.
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