| 1. |
- Kanchana, V., et al.
(författare)
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Lattice dynamics and elastic properties of the 4 f electron system : CeN
- 2011
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 84:20, s. 205135-
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Tidskriftsartikel (refereegranskat)abstract
- The electronic structure, structural stability, and lattice dynamics of cerium mononitride are investigated using ab initio density-functional methods involving an effective potential derived from the generalized gradient approximation and without special treatment for the 4 f states. The 4 f states are hence allowed to hop from site to site, without an on-site Hubbard U, and contribute to the bonding, in a picture often referred to as itinerant. It is argued that this picture is appropriate for CeN at low temperatures, while the anomalous thermal expansion observed at elevated temperatures indicates entropy-driven localization of the Ce f electrons, similar to the behavior of elemental cerium. The elastic constants are predicted from the total energy variation of strained crystals and are found to be large, typical for nitrides. The phonon dispersions are calculated showing no soft modes, and the Gruneisen parameter behaves smoothly. The electronic structure is also calculated using the quasiparticle self-consistent GW approximation (where G denotes the Green's function and W denotes the screened interaction). The Fermi surface of CeN is dominated by large egg-shaped electron sheets centered on the X points, which stem from the p-f mixing around the X point. In contrast, assuming localized f electrons leads to a semimetallic picture with small band overlaps around X.
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| 2. |
- Liu, Shuyu, et al.
(författare)
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Demographic History and Natural Selection Shape Patterns of Deleterious Mutation Load and Barriers to Introgression across Populus Genome
- 2022
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Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 39:2
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole-genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.
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| 3. |
- Liu, Yanna, et al.
(författare)
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Nontarget Mass Spectrometry Reveals New Perfluoroalkyl Substances in Fish from the Yangtze River and Tangxun Lake, China
- 2018
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 52:10, s. 5830-5840
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Tidskriftsartikel (refereegranskat)abstract
- Nontarget high-resolution mass spectrometry (Nt-HRMS) has been proven useful for the identification of unknown poly- and perfluoroalkyl substances (PFASs) in commercial products and water, but applications to biological samples are limited. China is the major PFAS-manufacturing nation; thus, here, we adapted our Nt-HRMS methods to fish collected from the Yangtze River and Tangxun Lake to discover potentially bioaccumulative PFASs in aquatic organisms destined for human consumption. In addition to traditional PFASs, over 330 other fluorinated analytes belonging to 10 classes of PFASs were detected among the pooled fish livers, including 6 sulfonate classes, 2 amine classes, 1 carboxylate class, and 1 N-heterocycle class. One class was detected in samples from both locations, 8 classes were detected exclusively in Tangxun Lake fish, and 1 class was detected exclusively in Yangtze River fish, 10 km downstream of a fluorochemical manufacturing site where we first reported these substances in wastewater 3 years ago. Overall, 4 of the PFAS classes (>165 analytes) are reported for the first time here. Wider monitoring and toxicological testing should be a priority for understanding the health risks posed to people and wildlife exposed to these substances.
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| 4. |
- Shi, Tingting, et al.
(författare)
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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees
- 2024
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Ingår i: Molecular Plant. - : Elsevier. - 1674-2052 .- 1752-9867. ; 17:5, s. 725-746
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.
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