| 1. |
- Kawakatsu, Taiji, et al.
(författare)
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Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
- 2016
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Ingår i: Cell. - : Elsevier. - 0092-8674 .- 1097-4172. ; 166:2, s. 492-505
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Tidskriftsartikel (refereegranskat)abstract
- The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.
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| 2. |
- Lu, Longyu, et al.
(författare)
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Tunable Magnetism in Atomically Thin Itinerant Antiferromagnet with Room-Temperature Ferromagnetic Order
- 2024
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Ingår i: Nano Letters. - 1530-6984. ; 24:20, s. 5984-5992
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Tidskriftsartikel (refereegranskat)abstract
- Addressing the need for modulated spin configurations is crucial, as they serve as the foundational building blocks for next-generation spintronics, particularly in atomically thin structures and at room temperature. In this work, we realize intrinsic ferromagnetism in monolayer flakes and tunable ferro-/antiferromagnetism in (Fe0.56Co0.44)5GeTe2 antiferromagnets. Remarkably, the ferromagnetic ordering (≥1 L) and antiferromagnetic ordering (≥4 L) remain discernible up to room temperature. The TC (∼310 K) of the monolayer flakes sets a record high for known exfoliated monolayer van der Waals magnets. Within the framework of A-type antiferromagnetism, a notable odd-even layer-number effect at elevated temperatures (T = 150 K) is observed. Of particular interest is the strong ferromagnetic order in even-layer flakes at low temperatures. The intricate interplay among magnetic field strength, layer number, and temperature gives rise to a diverse array of phenomena, holding promise not only for new physics but also for practical applications.
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| 3. |
- Song, Guohe, et al.
(författare)
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TIMP1 is a prognostic marker for the progression and metastasis of colon cancer through FAK-PI3K/AKT and MAPK pathway
- 2016
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Ingår i: Journal of Experimental & Clinical Cancer Research. - London, United Kingdom : BioMed Central (BMC). - 1756-9966. ; 35:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Tissue inhibitor matrix metalloproteinase 1 (TIMP1) plays a vital role in carcinogenesis, yet its precise functional roles and regulation remain unclear. In this study, we aim to investigate its biological function and clinical significance in human colon cancer.Methods: We analyzed the expression of TIMP1 in both public database (Oncomine and TCGA) and 94 cases of primary colon cancer and matched normal colon tissue specimens. The underlying mechanisms of altered TIMP1 expression on cell tumorigenesis, proliferation, and metastasis were explored in vitro and in vivo.Results: TIMP1 was overexpressed in colon tumorous tissues and lymph node metastasis specimens than in normal tissues. The aberrant expression of TIMP1 was significantly associated with the regional lymph node metastasis (p = 0.033), distant metastasis (p = 0.039), vascular invasion (p = 0.024) and the American Joint Committee on Cancer (AJCC) stage (p = 0.026). Cox proportional hazards model showed that TIMP1 was an independent prognostic indicator of disease-free survival (HR = 2.603, 95 % CI: 1.115-6.077, p = 0.027) and overall survival (HR = 2.907, 95 % CI: 1.254-6.737, p = 0.013) for patients with colon cancer. Consistent with this, our findings highlight that suppression of TIMP1 expression decreased proliferation, and metastasis but increased apoptosis by inducing TIMP1 specific regulated FAK-PI3K/AKT and MAPK pathway.Conclusion: TIMP1 might play an important role in promoting tumorigenesis and metastasis of human colon cancer and function as a potential prognostic indicator for colon cancer.
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| 4. |
- Xiao, Chao, et al.
(författare)
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RBBP6 increases radioresistance and serves as a therapeutic target for preoperative radiotherapy in colorectal cancer
- 2018
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Ingår i: Cancer Science. - : Blackwell Publishing. - 1347-9032 .- 1349-7006. ; 109:4, s. 1075-1087
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Tidskriftsartikel (refereegranskat)abstract
- Radiotherapy (RT) can be used as preoperative treatment to downstage initially unresectable locally rectal carcinoma, but the radioresistance and recurrence remain significant problems. Retinoblastoma binding protein 6 (RBBP6) has been implicated in the regulation of cell cycle, apoptosis and chemoresistance both in vitro and in vivo. This study investigated whether the inhibition of RBBP6 expression would improve radiosensitivity in human colorectal cancer cells. After SW620 and HT29 cells were exposed to radiation, the levels of RBBP6 mRNA and protein increased over time in both two cells. Moreover, a significant reduction in clonogenic survival and a decrease in cell viability in parallel with an obvious increase in cell apoptosis were demonstrated in irradiated RBBP6-knockdown cells. Besides, transfection with RBBP6 shRNA improved levels of G2-M phase arrest which blocked the cells in a more radiosensitive period of the cell cycle. These observations indicated that cell cycle and apoptosis mechanisms may be connected with tumor cell survival following radiotherapy. In vivo, tumor growth rate of nude mice in RBBP6-knockdown group was significantly slower than that in other groups. These results indicated that RBBP6 overexpression could resist colorectal cancer cells against radiation by regulating cell cycle and apoptosis pathways, and inhibition of RBBP6 could enhance radiosensitivity of human colorectal cancer.
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| 5. |
- Gao, Zhaoju, et al.
(författare)
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Short-chain ligand achieves ultra-stable CsPbX3 perovskite quantum dots for white light-emitting diodes
- 2024
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Ingår i: Applied Physics Letters. - : American Institute of Physics (AIP). - 0003-6951 .- 1077-3118. ; 124:4
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Tidskriftsartikel (refereegranskat)abstract
- All-inorganic perovskite quantum dots (PeQDs) have aroused great research interest in white light-emitting diodes (WLED) due to their excellent optoelectronic properties, but the poor stability, caused by dynamically binding long-chain capping ligands, hinders their future practical applications. To address this issue, here, we exploit short-chain butyric acid (BA) to replace long-chain oleic acid (OA) as capping ligand of CsPbX3 PeQDs by a hot-injection method. The addition of BA not only makes the morphology of CsPbBr3 PeQDs uniform and improves the crystallinity but also effectively suppresses nonradiative recombination, achieving a near unit photoluminescence quantum yield of 96%. The BA capped CsPbBr3 PeQDs exhibit high stability up to 180 d stored in ambient environment and also significantly improved resistance against polar solvent, ultra-violet lamp irradiation, and heat, which is rationalized by the strong binding capacity and shortened distance of BA to the PeQDs through ab initio calculations. Furthermore, by combining green-emission CsPbBr3 and red-emission CsPbBr0.8I2.2 PeQDs with blue GaN chip, we achieved WLEDs with excellent luminous properties, showing their great potential in practical application of wide-color-gamut display and lighting.
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| 6. |
- George, Julie, et al.
(författare)
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Comprehensive genomic profiles of small cell lung cancer
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 524:7563, s. 47-U73
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Tidskriftsartikel (refereegranskat)abstract
- We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Dex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
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| 7. |
- Hu, Zhang-Jun, et al.
(författare)
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A TPA-caged precursor of (imino)coumarin for "turn-on" fluorogenic detection of Cu
- 2016
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Ingår i: Analytica Chimica Acta. - : ELSEVIER SCIENCE BV. - 0003-2670 .- 1873-4324. ; 933, s. 189-195
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Tidskriftsartikel (refereegranskat)abstract
- We strategize to utilize the precursors of (imino) coumarin fluorophores to deliver novel reactive Cu+ probes, where tris[(2-pyridyl)-methyl] amine (TPA) works as a reactive receptor towards Cu+. To verify this strategy, CP1, a representative probe and relevant sensing behaviors towards Cu+ are presented here. CP1 features good solubility and fast response for monitoring labile copper in aqueous solution and live cells. The sensing mechanism of CP1 is determined by HPLC titration and mass spectrometric analysis. The probe CP1 exhibits a 60-fold fluorescence enhancement and a detection limitation of 10.8 nM upon the detection of Cu+. CP1 is further applied for imaging labile copper in live cells. This work provides a starting point for future development of Cu+ probes, based on in situ formation of (imino) coumarin scaffolds, as well as their further investigations of copper signaling and biological events. (C) 2016 Elsevier B.V. All rights reserved.
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| 8. |
- Ju, Minhua, et al.
(författare)
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Preparation of size-controllable monodispersed carbon@silica core-shell microspheres and hollow silica microspheres
- 2017
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Ingår i: Microporous and Mesoporous Materials. - : Elsevier. - 1387-1811 .- 1873-3093. ; 247, s. 75-85
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Tidskriftsartikel (refereegranskat)abstract
- Size-controllable monodispersed carbon@silica core-shell microspheres and hollow silica microspheres were prepared in a simple homemade T-type mixer by polymerization of furfuryl alcohol (FA) and hydrolysis of TEOS in H2SO4 water phase microdroplets to obtain polyfurfuryl alcohol (PFA)@silica microspheres, followed by carbonization and calcination. The FA and TEOS diffuse into the water phase from an oil phase. The flow rates of oil and water phase were 4 and 2 ml h−1, respectively. It was found that the concentration of FA has a more significant effect on the diameter of carbon@silica core-shell microspheres than TEOS due to the template effect of the PFA core. However, the diameter of the hollow silica microspheres was influenced by the concentration of TEOS more significantly. The obtained core-shell microspheres and hollow silica microspheres have large surface area of 555 and 769 m2 g−1, respectively. The hollow silica microspheres have both microporous and mesoporous structure, and the percentage of mesoporous volume was as high as 89%. In addition, based on the study results, a rational formation process of the carbon@silica core-shell microsphere and hollow silica microspheres was assumed.
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| 9. |
- Ju, Minhua, et al.
(författare)
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Two-Phase Diffusion Technique for the Preparation of Ultramacroporous/Mesoporous Silica Microspheres via Interface Hydrolysis, Diffusion, and Gelation of TEOS
- 2018
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 34:5, s. 2046-2056
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Tidskriftsartikel (refereegranskat)abstract
- Honeycombed hierarchical ultramacroporous/mesoporous silica microspheres were prepared via the hydrolysis of TEOS in the oil-water interface, with subsequent diffusion and gelation in the acidic water-phase microdroplets with the assistance of a simple homemade microdevice. The diffusion of furfuryl alcohol (FA) also happened at a relatively high rate during the hydrolysis and diffusion of TEOS. Therefore, plenty of FA will be inside of the water microdroplets and form a decent number of polyfurfuryl alcohol (PFA) microparticles, thereby obtaining honeycombed hierarchical porosity silica microspheres with abundant ultramacroporous cavities and mesopores after calcination. It was found that the concentration of FA, residence time, and reaction temperature have significant effects on the porosity and pore size due to the influence on the diffusion rate and amount of FA in water-phase microdroplets. The honeycombed silica microspheres have obvious microscopic visible ultramacroporous cavities with the submicrometer cavity diameter as high as 85% porosity based on the rough overall volume of microsphere. N2 adsorption-desorption isotherms show that the honeycombed hierarchical porosity silica microspheres have a high surface area of 602 m2 g-1, a mesopore volume of 0.77 cm3/g, and a mesopore porosity of 99.6% based on the total pore volume of N2 adsorption-desorption. On the basis of the experiment results, a rational formation process of the honeycombed hierarchical porosity silica microspheres was deduced.
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| 10. |
- 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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