| 1. |
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| 2. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 3. |
- Wang, Bo-Yao, et al.
(författare)
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Nonlinear bandgap opening behavior of BN co-doped graphene
- 2016
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Ingår i: Carbon. - : Elsevier. - 0008-6223 .- 1873-3891. ; 107, s. 857-864
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Tidskriftsartikel (refereegranskat)abstract
- We have demonstrated a nonlinear behavior for the bandgap opening of doped graphene by controlling the concentration of B and N co-dopants. X-ray absorption and emission spectra reveal that the bandgap increases from 0 to 0.6 eV as the concentration of BN dopants is increased from 0 to 6%, while the bandgap closes when the doping concentration becomes 56%. This nonlinear behavior of bandgap opening of the BN-doped graphene depending on the BN concentrations is consistent with the valenceband photoemission spectroscopic measurements. The spatially resolved B, N and C K-edge scanning transmission x-ray microscopy and their x-ray absorption near- edge structure spectra all support the scenario of the development of h-BN-like domains at high concentrations of BN. Ab initio calculation, by taking into account of the strong correlation between the bandgap and the geometry/concentration of the dopant, has been performed with various BN-dopant nano-domains embedded in the graphene monolayer to verify the unique bandgap behavior. Based on the experimental measurements and ab initio calculation, we propose the progressive formation of a phase-separated zigzag-edged BN domain from BN quantum dots with increasing BN-dopant concentration to explain the extraordinary nonlinear behavior of bandgap opening of BN-doped graphene sheets. This study reveals a new way to engineer the bandgap of low-dimensional systems.
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| 4. |
- Liu, Lihui, et al.
(författare)
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Ablation of ERO1A induces lethal endoplasmic reticulum stress responses and immunogenic cell death to activate anti-tumor immunity
- 2023
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Ingår i: Cell Reports Medicine. - : Cell Press. - 2666-3791. ; 4:10
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Tidskriftsartikel (refereegranskat)abstract
- Immunophenotyping of the tumor microenvironment (TME) is essential for enhancing immunotherapy effi-cacy. However, strategies for characterizing the TME exhibit significant heterogeneity. Here, we show that endoplasmic reticular oxidoreductase-1a (ERO1A) mediates an immune-suppressive TME and attenuates the response to PD-1 blockade. Ablation of ERO1A in tumor cells substantially incites anti-tumor T cell im-munity and promotes the efficacy of aPD-1 in therapeutic models. Single-cell RNA-sequencing analyses confirm that ERO1A correlates with immunosuppression and dysfunction of CD8+ T cells along anti-PD-1 treatment. In human lung cancer, high ERO1A expression is associated with a higher risk of recurrence following neoadjuvant immunotherapy. Mechanistically, ERO1A ablation impairs the balance between IRE1a and PERK signaling activities and induces lethal unfolded protein responses in tumor cells undergoing endoplasmic reticulum stress, thereby enhancing anti-tumor immunity via immunogenic cell death. These findings reveal how tumor ERO1A induces immunosuppression, highlighting its potential as a therapeutic target for cancer immunotherapy.
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| 5. |
- An, Junghwa, et al.
(författare)
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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 2009
- 2010
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 10:2, s. 404-408
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Tidskriftsartikel (refereegranskat)abstract
- This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.
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| 6. |
- Feng, Shaohong, et al.
(författare)
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Dense sampling of bird diversity increases power of comparative genomics
- 2020
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
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Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
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| 7. |
- He, Lei, et al.
(författare)
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Non-symmetric responses of leaf onset date to natural warming and cooling in northern ecosystems
- 2023
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Ingår i: PNAS Nexus. - 2752-6542. ; 2:9
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Tidskriftsartikel (refereegranskat)abstract
- The northern hemisphere has experienced regional cooling, especially during the global warming hiatus (1998-2012) due to ocean energy redistribution. However, the lack of studies about the natural cooling effects hampers our understanding of vegetation responses to climate change. Using 15,125 ground phenological time series at 3,620 sites since the 1950s and 31-year satellite greenness observations (1982-2012) covering the warming hiatus period, we show a stronger response of leaf onset date (LOD) to natural cooling than to warming, i.e. the delay of LOD caused by 1°C cooling is larger than the advance of LOD with 1°C warming. This might be because cooling leads to larger chilling accumulation and heating requirements for leaf onset, but this non-symmetric LOD response is partially offset by warming-related drying. Moreover, spring greening magnitude, in terms of satellite-based greenness and productivity, is more sensitive to LOD changes in the warming area than in the cooling. These results highlight the importance of considering non-symmetric responses of spring greening to warming and cooling when predicting vegetation-climate feedbacks.
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| 8. |
- Richards, Stephen, et al.
(författare)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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Ingår i: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Tidskriftsartikel (refereegranskat)abstract
- Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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| 9. |
- Turenne, Diego, et al.
(författare)
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Nonequilibrium sub–10 nm spin-wave soliton formation in FePt nanoparticles
- 2022
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:13
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Tidskriftsartikel (refereegranskat)abstract
- Magnetic nanoparticles such as FePt in the L10 phase are the bedrock of our current data storage technology. As the grains become smaller to keep up with technological demands, the superparamagnetic limit calls for materials with higher magnetocrystalline anisotropy. This, in turn, reduces the magnetic exchange length to just a few nanometers, enabling magnetic structures to be induced within the nanoparticles. Here, we describe the existence of spin-wave solitons, dynamic localized bound states of spin-wave excitations, in FePt nanoparticles. We show with time-resolved x-ray diffraction and micromagnetic modeling that spin-wave solitons of sub–10 nm sizes form out of the demagnetized state following femtosecond laser excitation. The measured soliton spin precession frequency of 0.1 THz positions this system as a platform to develop novel miniature devices.
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| 10. |
- Yu, Shujun, et al.
(författare)
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Macroscopic, Spectroscopic, and Theoretical Investigation for the Interaction of Phenol and Naphthol on Reduced Graphene Oxide
- 2017
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Ingår i: Environmental Science and Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 51:6, s. 3278-3286
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Tidskriftsartikel (refereegranskat)abstract
- Interaction of phenol and naphthol with reduced graphene oxide (rGO), and their competitive behavior on rGO were examined by batch experiments, spectroscopic analysis and theoretical calculations. The batch sorption showed that the removal percentage of phenol or naphthol on rGO in bisolute systems was significantly lower than those of phenol or naphthol in single-solute systems. However, the overall sorption capacity of rGO in bisolute system was higher than single-solute system, indicating that the rGO was a very suitable material for the simultaneous elimination of organic pollutants from aqueous solutions. The interaction mechanism was mainly pi-pi interactions and hydrogen bonds, which was evidenced by FTIR, Raman and theoretical calculation. FTIR and Raman showed that a blue shift of C=C and -OH stretching modes and the enhanced intensity ratios of I-D/I-G after phenols sorption. The theoretical calculation indicated that the total hydrogen bond numbers, diffusion constant and solvent accessible surface area of naphthol were higher than those of phenol, indicating higher sorption affinity of rGO for naphthol as compared to phenol. These findings were valuable for elucidating the interaction mechanisms between phenols and graphene-based materials, and provided an essential start in simultaneous removal of organics from wastewater.
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