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- Birney, Ewan, et al.
(author)
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Prepublication data sharing
- 2009
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 461:7261, s. 168-170
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Journal article (peer-reviewed)abstract
- Rapid release of prepublication data has served the field of genomics well. Attendees at a workshop in Toronto recommend extending the practice to other biological data sets.
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| 3. |
- Chiu, CH, et al.
(author)
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Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution
- 2004
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In: Genome Research. - : Cold Spring Harbor Laboratory. - 1549-5469 .- 1088-9051. ; 14:1, s. 11-17
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Journal article (peer-reviewed)abstract
- The study of Hox clusters and genes provides insights into the evolution of genomic regulation of development. Derived ray-finned fishes (Actinopterygii, Teleostei) such as zebrafish and pufferfish possess duplicated Hox clusters that have undergone considerable sequence evolution. Whether these changes are associated with the duplication(s) that produced extra Hox clusters is unresolved because comparison with basal lineages is unavailable. We sequenced and analyzed the HoxA cluster of the bichir (Polypterus senegalus), a phylogenetically basal actinopterygian. Independent lines of evidence indicate that bichir has one HoxA cluster that is mosaic in its patterns of noncoding sequence conservation and gene retention relative to the HoxA clusters of human and shark, and the HoxAalpha and HoxAbeta clusters of zebrafish, pufferfish, and striped bass. HoxA cluster noncoding sequences conserved between bichir and euteleosts indicate that novel cis-sequences were acquired in the stem actinopterygians and maintained after cluster duplication. Hence, in the earliest actinopterygians, evolution of the single HoxA cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after HoxA cluster duplication.
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- Dewar, R. C., et al.
(author)
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Why does leaf nitrogen decline within tree canopies less rapidly than light? An explanation from optimization subject to a lower bound on leaf mass per area
- 2012
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In: Tree Physiology. - : Oxford University Press (OUP). - 0829-318X .- 1758-4469. ; 32:5, s. 520-534
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Journal article (peer-reviewed)abstract
- A long-established theoretical result states that, for a given total canopy nitrogen (N) content, canopy photosynthesis is maximized when the within-canopy gradient in leaf N per unit area (N-a) is equal to the light gradient. However, it is widely observed that N-a declines less rapidly than light in real plant canopies. Here we show that this general observation can be explained by optimal leaf acclimation to light subject to a lower-bound constraint on the leaf mass per area (m(a)). Using a simple model of the carbon-nitrogen (C-N) balance of trees with a steady-state canopy, we implement this constraint within the framework of the MAXX optimization hypothesis that maximizes net canopy C export. Virtually all canopy traits predicted by MAXX (leaf N gradient, leaf N concentration, leaf photosynthetic capacity, canopy N content, leaf-area index) are in close agreement with the values observed in a mature stand of Norway spruce trees (Picea abies L. Karst.). An alternative upper-bound constraint on leaf photosynthetic capacity (A(sat)) does not reproduce the canopy traits of this stand. MAXX subject to a lower bound on m(a) is also qualitatively consistent with co-variations in leaf N gradient, m(a) and A(sat) observed across a range of temperate and tropical tree species. Our study highlights the key role of constraints in optimization models of plant function.
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| 5. |
- Franklin, Oskar, et al.
(author)
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Modeling carbon allocation in trees : a search for principles
- 2012
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In: Tree Physiology. - : Oxford University Press (OUP). - 0829-318X .- 1758-4469. ; 32:6, s. 648-666
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Research review (peer-reviewed)abstract
- We review approaches to predicting carbon and nitrogen allocation in forest models in terms of their underlying assumptions and their resulting strengths and limitations. Empirical and allometric methods are easily developed and computationally efficient, but lack the power of evolution-based approaches to explain and predict multifaceted effects of environmental variability and climate change. In evolution-based methods, allocation is usually determined by maximization of a fitness proxy, either in a fixed environment, which we call optimal response (OR) models, or including the feedback of an individual's strategy on its environment (game-theoretical optimization, GTO). Optimal response models can predict allocation in single trees and stands when there is significant competition only for one resource. Game-theoretical optimization can be used to account for additional dimensions of competition, e.g., when strong root competition boosts root allocation at the expense of wood production. However, we demonstrate that an OR model predicts similar allocation to a GTO model under the root-competitive conditions reported in free-air carbon dioxide enrichment (FACE) experiments. The most evolutionarily realistic approach is adaptive dynamics (AD) where the allocation strategy arises from eco-evolutionary dynamics of populations instead of a fitness proxy. We also discuss emerging entropy-based approaches that offer an alternative thermodynamic perspective on allocation, in which fitness proxies are replaced by entropy or entropy production. To help develop allocation models further, the value of wide-ranging datasets, such as FLUXNET, could be greatly enhanced by ancillary measurements of driving variables, such as water and soil nitrogen availability.
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| 8. |
- Verlaan, Dominique J., et al.
(author)
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Targeted screening of cis-regulatory variation in human haplotypes
- 2009
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In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 19:1, s. 118-127
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Journal article (peer-reviewed)abstract
- Regulatory cis-acting variants account for a large proportion of gene expression variability in populations. Cis-acting differences can be specifically measured by comparing relative levels of allelic transcripts within a sample. Allelic expression (AE) mapping for cis-regulatory variant discovery has been hindered by the requirements of having informative or heterozygous single nucleotide polymorphisms (SNPs) within genes in order to assign the allelic origin of each transcript. In this study we have developed an approach to systematically screen for heritable cis-variants in common human haplotypes across >1,000 genes. In order to achieve the highest level of information per haplotype studied, we carried out allelic expression measurements by using both intronic and exonic SNPs in primary transcripts. We used a novel RNA pooling strategy in immortalized lymphoblastoid cell lines (LCLs) and primary human osteoblast cell lines (HObs) to allow for high-throughput AE. Screening hits from RNA pools were further validated by performing allelic expression mapping in individual samples. Our results indicate that >10% of expressed genes in human LCLs show genotype-linked AE. In addition, we have validated cis-acting variants in over 20 genes linked with common disease susceptibility in recent genome-wide studies. More generally, our results indicate that RNA pooling coupled with AE read-out by second generation sequencing or by other methods provides a high-throughput tool for cataloging the impact of common noncoding variants in the human genome.
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