| 1. |
- Albaugh, Timothy J, et al.
(författare)
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Do biological expansion factors adequately estimate stand-scale aboveground component biomass for Norway spruce?
- 2009
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Ingår i: Forest Ecology and Management. - : Elsevier BV. - 0378-1127 .- 1872-7042. ; 258:12, s. 2628-2637
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Tidskriftsartikel (refereegranskat)abstract
- We developed site specific component (stem, branch, and foliage) biomass functions for two sites in Sweden (64° and 57° North latitude) where four treatments (control, irrigated, fertilized, irrigated plus fertilized) were applied in the existing Norway spruce stands (Picea abies L. Karst.) for 17 years. We tested for site effects in the component biomass equations and compared site specific biomass estimates to those generated using published functions ( Lehtonen et al., 2004 and Wirth et al., 2004). Site effects were significant for all components and indicated it would be unlikely to generate equations that well estimate biomass across the Norway spruce range as implicitly indicated in our efforts to generate species biomass expansion factors. We rejected our hypothesis that the published functions would well estimate component biomass for control plots. The published functions did not compare well with site specific component biomass estimates for the other treatments; both published functions well estimated stem mass up to stem mass of 25 Mg ha−1, beyond which stem mass was overestimated, and both functions over and under estimated foliage and branch mass. Nor did the published functions compare well with each other, with stem, foliage and branch mass estimate differences of 12, 55, −8% and 11, 77, and 59% for the southern and northern sites, respectively, when averaged over all treatments and years. Adding limiting resources through fertilization increased stem, foliage and branch mass 57, 11, 18% and 120, 37, and 69% at the southern and northern sites, respectively, which would increase carbon sequestration and available stemwood and bioenergy materials. We recommend that more effort is spent in process-based modeling to better predict mass at a given site and ultimately provide better estimates of carbon sequestration and bioenergy material production changes.
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| 2. |
- Elmlund, Hans, et al.
(författare)
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Cryo-EM Reveals Promoter DNA Binding and Conformational Flexibility of the General Transcription Factor TFIID
- 2009
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 17:11, s. 1442-1452
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Tidskriftsartikel (refereegranskat)abstract
- The general transcription factor IID (TFIID) is required for initiation of RNA polymerase II-dependent transcription at many eukaryotic promoters. TFIID comprises the TATA-binding protein (TBP) and several conserved TBP-associated factors (TAFs). Recognition of the core promoter by TFIID assists assembly of the preinitiation complex. Using cryo-electron microscopy in combination with methods for ab initio single-particle reconstruction and heterogeneity analysis, we have produced density maps of two conformational states of Schizosaccharomyces pombe TFIID, containing and lacking TBP. We report that TBP-binding is coupled to a massive histone-fold domain rearrangement. Moreover, docking of the TBP-TAF1(N-terminus) atomic structure to the THID map and reconstruction of a TAF-promoter DNA complex helps to account for TAF-dependent regulation of promoter-TBP and promoter-TAF interactions.
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| 3. |
- Linder, Tomas, et al.
(författare)
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A family of putative transcription termination factors shared amongst metazoans and plants.
- 2005
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Ingår i: Current genetics. - : Springer Science and Business Media LLC. - 0172-8083 .- 1432-0983. ; 48:4, s. 265-9
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Tidskriftsartikel (refereegranskat)abstract
- The human mitochondrial transcription termination factor (mTERF) is involved in the regulation of transcription of the mitochondrial genome. Similarity searches and phylogenetic analysis demonstrate that mTERF is a member of large and complex protein family (the MTERF family) shared amongst metazoans and plants. Interestingly, we identify three novel MTERF genes in vertebrates, which all encode proteins with predicted mitochondrial localization. Members of the MTERF family have so far not been detected in fungi, supporting the notion that mitochondrial transcription regulation may have evolved separately in yeast and animal cells.
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| 4. |
- Linder, Tomas
(författare)
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Conserved structure-function relationships in the mediator complex
- 2007
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The Mediator complex is an essential multiprotein coregulator of RNA polymerase II (pol II)- dependent transcription in fungi and metazoans. Mediator interacts directly with both pol II and sequence-specific transcriptional regulators and thus acting as a bridge between the two. We have performed a comparative biochemical and functional characterisation the Mediator in the two ascomycete yeasts S. cerevisiae and S. pombe to address to what degree subunit architecture and specific regulatory functions have been conserved between these two species. In Paper I we identified the Med31 protein as a stable subunit of Mediator in S. cerevisiae and S. pombe. We defined a highly conserved central motif in the Med31 protein that appeared to be required but not sufficient for the association of Med31 with the rest of the Mediator complex. In Paper II we investigated the structural basis for the global shutdown of pol II-dependent transcription in the S. cerevisiae MED17 temperature sensitive allele srb4-138. We found that the srb4-138 allele disrupts the interaction between the head and middle domains both in vitro and in vivo. This suggested that the global shutdown of transcription in srb4-138 cells at the non-permissive temperature is caused by destabilisation of the core Mediator complex. In Paper III we characterised the architecture of the S. pombe Cdk8 module by biochemical means and addressed its relationship to the non-essential Med1 subunit. We found that the Med1 subunit is closely linked both structurally and functionally with the Cdk8 module. Electron microscopy of wildtype and Δmed1 Mediator resolved the position of the Med1 subunit as proximal to the Cdk8 module within the pol II-binding cleft of the core Mediator complex. Expression profiling of Δmed1 cells showed significant overlap with the changes seen in cells lacking either Med12 or Med13. In Paper IV we carried out a comprehensive functional characterisation of the S. pombe Mediator complex and identified two distinct morphological pathways that require different parts of the Mediator for their proper regulation. Head domain-linked mutants tended to grow as hyphae due to their inability to express genes required for proper cell separation after mitosis. Mutants of the Cdk8 module aggregated into large clumps due to impaired repression of genes that code for cell surface agglutinins. Comparison with similar studies done in S. cerevisiae revealed that both regulatory roles for these subcomplexes are conserved.
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| 5. |
- Zhu, Xuefeng, et al.
(författare)
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Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions
- 2006
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Ingår i: Molecular Cell. - : Elsevier BV. - 1097-2765 .- 1097-4164. ; 22:2, s. 169-178
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Tidskriftsartikel (refereegranskat)abstract
- Mediator exists in a free form containing the Med12, Med13, CDK8, and CycC subunits (the Srb8-11 module) and a smaller form, which lacks these four subunits and associates with RNA polymerase II (Pol II), forming a holoenzyme. We use chromatin immunoprecipitation (ChIP) and DNA microarrays to investigate genome-wide localization of Mediator and the Srb8-11 module in fission yeast. Mediator and the Srb8-11 module display similar binding patterns, and interactions with promoters and upstream activating sequences correlate with increased transcription activity. Unexpectedly, Mediator also interacts with the downstream coding region of many genes. These interactions display a negative bias for positions closer to the 5' ends of open reading frames (ORFs) and appear functionally important, because downregulation of transcription in a temperature-sensitive med17 mutant strain correlates with increased Mediator occupancy in the coding region. We propose that Mediator coordinates transcription initiation with transcriptional events in the coding region of eukaryotic genes.
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