| 1. |
- Gao, Jie, et al.
(author)
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Demography and speciation history of the homoploid hybrid pine Pinus densata on the Tibetan Plateau
- 2012
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In: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 21:19, s. 4811-4827
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Journal article (peer-reviewed)abstract
- Pinus densata is an ecologically successful homoploid hybrid that inhabits vast areas of heterogeneous terrain on the south-eastern Tibetan Plateau as a result of multiple waves of colonization. Its region of origin, route of colonization onto the plateau and the directions of introgression with its parental species have previously been defined, but little is known about the isolation and divergence history of its populations. In this study, we surveyed nucleotide polymorphism over eight nuclear loci in 19 representative populations of P. densata and its parental species. Using this information and coalescence simulations, we assessed the historical changes in its population size, gene flow and divergence in time and space. The results indicate a late Miocene origin for P. densata associated with the recent uplift of south-eastern Tibet. The subsequent differentiation between geographical regions of this species began in the late Pliocene and was induced by regional topographical changes and Pleistocene glaciations. The ancestral P. densata population had a large effective population size but the central and western populations were established by limited founders, suggesting that there were severe bottlenecks during the westward migration out of the ancestral hybrid zone. After separating from their ancestral populations, population expansion occurred in all geographical regions especially in the western range. Gene flow in P. densata was restricted to geographically neighbouring populations, resulting in significant differentiation between regional groups. The new information on the divergence and demographic history of P. densata reported herein enhances our understanding of its speciation process on the Tibetan Plateau.
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| 2. |
- Gu, Bobo, et al.
(author)
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Fiber-optic metal ion sensor based on thin-core fiber modal interferometer with nanocoating self-assembled via hydrogen bonding
- 2011
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In: Sensors and actuators. B, Chemical. - : Elsevier BV. - 0925-4005 .- 1873-3077. ; 160:1, s. 1174-1179
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Journal article (peer-reviewed)abstract
- A new fiber-optic metal ion sensor based on a thin-core fiber modal interferometer (TCFMI) is presented. Poly(4-vinylpyridine) (P4VP) and poly(acrylic acid) (PAA) are layer-by-layer deposited on the side surface of the TCFMI via hydrogen bonding for the detection of metal ion in aqueous solutions. Ultraviolet-visible (UV-vis) absorption spectroscopy is employed to monitor the self-assembly process, and the thickness and morphology of the nanocoating are characterized by scanning electron microscopy (SEM). When the sensor is immersed into the aqueous solutions containing metal ions, the refractive index (RI) of the nanocoating is changed because of the association of metal ions with the nanocoating, which was verified by energy dispersive X-ray (EDX). Based on the RI sensing capability of TCFMI, one can detect the concentration of metal ions through the measurement of the dip wavelength of the sensor's transmission spectrum. The experiment results exhibit that the sensor is reusable and with a fast response in a wide metal ion concentration range (10 nM-0.1 M). The limit of detection (LOD) of the sensor is around 9.6 nM experimentally.
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| 3. |
- Wang, Zhaoming, et al.
(author)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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