| 1. |
- Frohlich, Michael W., et al.
(author)
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Molecular phylogenetics of Euploca (Boraginaceae) : homoplasy in many characters, including the C-4 photosynthetic pathway
- 2022
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In: Botanical journal of the Linnean Society. - : Oxford University Press (OUP). - 0024-4074 .- 1095-8339. ; 199:2, s. 497-537
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Journal article (peer-reviewed)abstract
- We present a phylogenetic analysis using plastid (matK, rbcL) and nuclear (nrITS) DNA for diverse Euploca spp. (formerly Heliotropium section Orthostachys) from the worldwide distribution of a genus and including species encompassing the wide physiological and morphological diversity of the genus. Our results indicate that some remarkably complex features arose multiple times in parallel in Euploca, including attributes of its subsections under section Orthostachys, notably plants that, above ground, consist almost entirely of inflorescences. To elucidate in greater detail the distribution of C-4 species in Euploca and Heliotropium s.s., we made > 800 delta C-13 determinations, including some from the traditional genus Tournefortia. We greatly increase the number of proven C-4 species in Euploca, but found none outside Euploca. Of the tested Euploca spp., c. 28% are C-3 or intermediate in carbon fixation pathway. Our phylogenetic results indicate four parallel/convergent acquisitions of C-4 photosynthesis or fewer origins with subsequent loss in some species.
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| 2. |
- Hendriks, Kasper P., et al.
(author)
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Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
- 2023
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In: Current Biology. - : Elsevier. - 0960-9822 .- 1879-0445. ; 33:19, s. 4052-4068
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Journal article (peer-reviewed)abstract
- The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Bras-sicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To eval-uate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moder-ate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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| 3. |
- Kawabe, Akira, et al.
(author)
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Centromere Locations and Associated Chromosome Rearrangements in Arabidopsis lyrata and A. thaliana
- 2006
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In: Genetics. - Baltimore, MD, USA : The Genetics Society. - 0016-6731 .- 1943-2631. ; 173:3, s. 1613-1619
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Journal article (peer-reviewed)abstract
- We analyzed linkage and chromosomal positions of genes in A. lyrata ssp. petraea that are located near the centromere (CEN) regions of A. thaliana, using at least two genes from the short and long arms of each chromosome. In our map, genes from all 10 A. thaliana chromosome arms are also tightly linked in A. lyrata. Genes from the regions on the two sides of CEN5 have distant map localizations in A. lyrata (genes on the A. thaliana short-arm genes are on linkage group AL6, and long-arm genes are on AL7), but genes from the other four A. thaliana centromere regions remain closely linked in A. lyrata. The observation of complete linkage between short- and long-arm centromere genes, but not between genes in other genome regions that are separated by similar physical distances, suggests that crossing-over frequencies near the A. lyrata ssp. petraea centromere regions are low, as in A. thaliana. Thus, the centromere positions appear to be conserved between A. thaliana and A. lyrata, even though three centromeres have been lost in A. thaliana, and the core satellite sequences in the two species are very different. We can now definitively identify the three centromeres that were eliminated in the fusions that formed the A. thaliana chromosomes. However, we cannot tell whether genes were lost along with these centromeres, because such genes are absent from the A. thaliana genome, which is the sole source of markers for our mapping.
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| 4. |
- Kawabe, Akira, et al.
(author)
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Comparative gene mapping in Arabidopsis lyrata chromosomes 6 and 7 and A. thaliana chromosome IV : Evolutionary history, rearrangements and local recombination rates
- 2006
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In: Genetical Research. - 0016-6723 .- 1469-5073. ; 88:1, s. 45-56
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Journal article (peer-reviewed)abstract
- We have increased the density of genetic markers on the Arabidopsis lyrata chromosomes AL6 and AL7 corresponding to the A. thaliana chromosome IV, in order to determine chromosome rearrangements between these two species, and to compare recombination fractions across the same intervals. We confirm the two rearrangements previously inferred (a reciprocal translocation and a large inversion, which we infer to be pericentric). By including markers around the centromere regions of A. thaliana chromosomes IV and V, we localize the AL6 centromere, and can localize the breakpoints of these chromosome rearrangements more precisely than previously. One translocation breakpoint was close to the centromere, and the other coincided with one end of the inversion, suggesting that a single event caused both rearrangements. At the resolution of our mapping, apart from these rearrangements, all other markers are in the same order in A. lyrata and A. thaliana. We could thus compare recombination rates in the two species. We found slightly higher values in A. thaliana, and a minimum estimate for regions not close to a centromere in A. lyrata is 4-5 centimorgans per megabase. The mapped region of AL7 includes the self-incompatibility loci (S-loci), and this region has been predicted to have lower recombination than elsewhere in the genome. We mapped 17 markers in a region of 1·23 Mb surrounding these loci, and compared the approximately 600 kb closest to the S-loci with the surrounding region of approximately the same size. There were significantly fewer recombination events in the closer than the more distant region, supporting the above prediction, but showing that the low recombination region is very limited in size. © 2006 Cambridge University Press.
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| 5. |
- Luo, Yiqi, et al.
(author)
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Transient dynamics of terrestrial carbon storage : Mathematical foundation and its applications
- 2017
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In: Biogeosciences. - : Copernicus GmbH. - 1726-4170 .- 1726-4189. ; 14:1, s. 145-161
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Journal article (peer-reviewed)abstract
- Terrestrial ecosystems have absorbed roughly 30 % of anthropogenic CO2 emissions over the past decades, but it is unclear whether this carbon (C) sink will endure into the future. Despite extensive modeling and experimental and observational studies, what fundamentally determines transient dynamics of terrestrial C storage under global change is still not very clear. Here we develop a new framework for understanding transient dynamics of terrestrial C storage through mathematical analysis and numerical experiments. Our analysis indicates that the ultimate force driving ecosystem C storage change is the C storage capacity, which is jointly determined by ecosystem C input (e.g., net primary production, NPP) and residence time. Since both C input and residence time vary with time, the C storage capacity is time-dependent and acts as a moving attractor that actual C storage chases. The rate of change in C storage is proportional to the C storage potential, which is the difference between the current storage and the storage capacity. The C storage capacity represents instantaneous responses of the land C cycle to external forcing, whereas the C storage potential represents the internal capability of the land C cycle to influence the C change trajectory in the next time step. The influence happens through redistribution of net C pool changes in a network of pools with different residence times. Moreover, this and our other studies have demonstrated that one matrix equation can replicate simulations of most land C cycle models (i.e., physical emulators). As a result, simulation outputs of those models can be placed into a three-dimensional (3-D) parameter space to measure their differences. The latter can be decomposed into traceable components to track the origins of model uncertainty. In addition, the physical emulators make data assimilation computationally feasible so that both C flux-and pool-related datasets can be used to better constrain model predictions of land C sequestration. Overall, this new mathematical framework offers new approaches to understanding, evaluating, diagnosing, and improving land C cycle models.
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| 6. |
- Nielsen, Elisabet I, 1973-
(author)
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Pharmacometric Models for Antibacterial Agents to Improve Dosing Strategies
- 2011
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Doctoral thesis (other academic/artistic)abstract
- Antibiotics are among the most commonly prescribed drugs. Although the majority of these drugs were developed several decades ago, optimal dosage (dose, dosing interval and treatment duration) have still not been well defined. This thesis focuses on the development and evaluation of pharmacometric models that can be used as tools in the establishment of improved dosing strategies for novel and already clinically available antibacterial drugs. Infectious diseases are common causes of death in preterm and term newborn infants. A population pharmacokinetic (PK) model for gentamicin was developed based on data from a prospective study. Body-weight and age (gestational and post-natal age) were found to be major factors contributing to variability in gentamicin clearance and therefore important patient characteristics to consider for improved dosing regimens. A semi-mechanistic pharmacokinetic-pharmacodynamic (PKPD) model was also developed, to characterize in vitro bacterial growth and killing kinetics following exposure to six antibacterial drugs, representing a broad selection of mechanisms of action and PK as well as PD characteristics. The model performed well in describing a wide range of static and dynamic drug exposures and was easily applied to other bacterial strains and antibiotics. It is, therefore, likely to find application in early drug development programs. Dosing of antibiotics is usually based on summary endpoints such as the PK/PD indices. Predictions based on the PKPD model showed that the commonly used PK/PD indices were well identified for all investigated drugs, supporting that models based on in vitro data can be predictive of antibacterial effects observed in vivo. However, the PK/PD indices were sensitive to the study conditions and were not always consistent between patient populations. The PK/PD indices may therefore extrapolate poorly across sub-populations. A semi-mechanistic modeling approach, utilizing the type of models described here, may thus have higher predictive value in a dose optimization tailored to specific patient populations.
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