| 1. |
- 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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| 2. |
- Li, Jie, et al.
(författare)
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Sphenostylisins A-K : bioactive modified isoflavonoid constituents of the root bark of Sphenostylis marginata ssp. erecta
- 2013
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Ingår i: Journal of Organic Chemistry. - : American Chemical Society (ACS). - 0022-3263 .- 1520-6904. ; 78:20, s. 10166-10177
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Tidskriftsartikel (refereegranskat)abstract
- Sphenostylisins A-C (1-3), three complex dimeric compounds representing two novel carbon skeletons, along with an additional eight new compounds, sphenostylisins D-K (4-11), were isolated from the active chloroform-soluble extract of the root bark of Sphenostylis marginata ssp. erecta using a bioactivity-guided isolation approach. The structures were elucidated by means of detailed spectroscopic analysis, including NMR and HRESIMS analysis, and tandem MS fragmentation was utilized to further support the structures of 1-3. The absolute configuration of sphenostylisin C (3) was established by electronic circular dichroism analysis. Plausible biogenetic relationships between the modified isoflavonoids 1-11 are proposed, and a cyclization reaction of 9 was conducted to support one of the biogenetic proposals made. All of these pure isolates were evaluated against a panel of in vitro bioassays, and among the results obtained, sphenostylisin A (1) was found to be a very potent NF-κB inhibitor (IC50 = 6 nM).
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| 3. |
- Bueno Pérez, Lynette, et al.
(författare)
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Caeruleanone A, a rotenoid with a new arrangement of the D-ring from the fruits of Millettia caerulea.
- 2014
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Ingår i: Organic Letters. - : American Chemical Society (ACS). - 1523-7060 .- 1523-7052. ; 16:5, s. 1462-1465
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Tidskriftsartikel (refereegranskat)abstract
- Caeruleanone A (1), a novel rotenoid with an unprecedented arrangement of the D-ring, was isolated with another two new analogues, caeruleanones B (2) and C (3), together with 11 known rotenoids from the fruits of Millettia caerulea. The structures of the new compounds were determined by spectroscopic data analysis, with that of 1 being confirmed by single-crystal X-ray diffraction. Compounds 2 and 3 displayed potent mitochondrial transmembrane potential inhibitory and quinone reductase induction activities.
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| 4. |
- Chasman, Daniel I., et al.
(författare)
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Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function
- 2012
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 21:24, s. 5329-5343
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Tidskriftsartikel (refereegranskat)abstract
- In conducting genome-wide association studies (GWAS), analytical approaches leveraging biological information may further understanding of the pathophysiology of clinical traits. To discover novel associations with estimated glomerular filtration rate (eGFR), a measure of kidney function, we developed a strategy for integrating prior biological knowledge into the existing GWAS data for eGFR from the CKDGen Consortium. Our strategy focuses on single nucleotide polymorphism (SNPs) in genes that are connected by functional evidence, determined by literature mining and gene ontology (GO) hierarchies, to genes near previously validated eGFR associations. It then requires association thresholds consistent with multiple testing, and finally evaluates novel candidates by independent replication. Among the samples of European ancestry, we identified a genome-wide significant SNP in FBXL20 (P 5.6 10(9)) in meta-analysis of all available data, and additional SNPs at the INHBC, LRP2, PLEKHA1, SLC3A2 and SLC7A6 genes meeting multiple-testing corrected significance for replication and overall P-values of 4.5 10(4)2.2 10(7). Neither the novel PLEKHA1 nor FBXL20 associations, both further supported by association with eGFR among African Americans and with transcript abundance, would have been implicated by eGFR candidate gene approaches. LRP2, encoding the megalin receptor, was identified through connection with the previously known eGFR gene DAB2 and extends understanding of the megalin system in kidney function. These findings highlight integration of existing genome-wide association data with independent biological knowledge to uncover novel candidate eGFR associations, including candidates lacking known connections to kidney-specific pathways. The strategy may also be applicable to other clinical phenotypes, although more testing will be needed to assess its potential for discovery in general.
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| 5. |
- Chen, Guanying, et al.
(författare)
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(alpha-NaYbF4:Tm3+)/CaF2 Core/Shell Nanoparticles with Efficient Near-Infrared to Near-Infrared Upconversion for High-Contrast Deep Tissue Bioimaging
- 2012
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 6:9, s. 8280-8287
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Tidskriftsartikel (refereegranskat)abstract
- We describe the development of novel and biocompatible core/shell (alpha-NaYbF4:Tm3+)/CaF2 nanoparticles that exhibit highly efficient NIRin-NIROut upconversion (UC) for high contrast and deep bioimaging. When excited at similar to 980 nm, these nanoparticles emit photoluminescence (PL) peaked at similar to 800 nm. The quantum yield of this UC PL under low power density excitation (similar to 0.3 W/cm(2)) is 0.6 +/- 0.1%. This high UC PL efficiency is realized by suppressing surface quenching effects via heteroepitaxial growth of a biocompatible CaF2 shell, which results in a 35-fold increase in the intensity of UC PL from the core. Small-animal whole-body UC PL imaging with exceptional contrast (signal-to-background ratio of 310) is shown using BALB/c mice intravenously injected with aqueously dispersed nanoparticles (700 pmol/kg). High-contrast UC PL imaging of deep tissues is also demonstrated, using a nanoparticle-loaded synthetic fibrous mesh wrapped around rat femoral bone and a cuvette with nanoparticle aqueous dispersion covered with a 3.2 cm thick animal tissue (pork).
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| 6. |
- Li, Lanfen, et al.
(författare)
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Structural genomics studies of human caries pathogen Streptococcus mutans
- 2014
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Ingår i: Journal of Structural and Functional Genomics. - : Springer Science and Business Media LLC. - 1345-711X .- 1570-0267. ; 15:3, s. 9-91
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Tidskriftsartikel (refereegranskat)abstract
- Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice.
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| 7. |
- Lu, Lu, et al.
(författare)
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Crystal structure of tubulin folding cofactor A from Arabidopsis thaliana and its beta-tubulin binding characterization
- 2010
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Ingår i: FEBS Letters. - : Wiley. - 1873-3468 .- 0014-5793. ; 584:16, s. 9-3533
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Tidskriftsartikel (refereegranskat)abstract
- Microtubules are composed of polymerized alpha/beta-tubulin heterodimers. Biogenesis of assembly-competent tubulin dimers is a complex multistep process that requires sequential actions of distinct molecular chaperones and cofactors. Tubulin folding cofactor A (TFCA), which captures beta-tubulin during the folding pathway, has been identified in many organisms. Here, we report the crystal structure of Arabidopsis thaliana TFC A (KIESEL, KIS), which forms a monomeric three-helix bundle. The functional binding analysis demonstrated that KIS interacts with beta-tubulin in plant. Furthermore, mutagenesis studies indicated that the alpha-helical regions of KIS participate in beta-tubulin binding. Unlike the budding yeast TFC A, the two loop regions of KIS are not required for this interaction suggesting a distinct binding mechanism of TFC A to beta-tubulin in plants.
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| 8. |
- Lu, Lu, et al.
(författare)
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Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thaliana
- 2010
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Ingår i: Acta Crystallographica. Section F: Structural Biology and Crystallization Communications. - 2053-230X. ; 66:Pt 8, s. 6-954
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Tidskriftsartikel (refereegranskat)abstract
- Tubulin-folding cofactor A (TFC A) is a molecular post-chaperonin that is involved in the beta-tubulin-folding pathway. It has been identified in many organisms including yeasts, humans and plants. In this work, Arabidopsis thaliana TFC A was expressed in Escherichia coli and purified to homogeneity. After thrombin cleavage, a well diffracting crystal was obtained by the sitting-drop vapour-diffusion method at 289 K. The crystal diffracted to 1.6 A resolution using synchrotron radiation and belonged to space group I4(1), with unit-cell parameters a=55.0, b=55.0, c=67.4 A.
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| 9. |
- Ma, Ming-Guo, et al.
(författare)
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Fabrication and characterization of Ag/calcium silicate core-shell nanocomposites
- 2011
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Ingår i: Materials letters (General ed.). - : Elsevier BV. - 0167-577X .- 1873-4979. ; 65:19-20, s. 3069-3071
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Tidskriftsartikel (refereegranskat)abstract
- The Ag/calcium silicate nanocomposite with core-shell nanostructure has been successfully synthesized using Ag solution, Ca(NO(3))(2)center dot 4H(2)O and Na(2)SiO(3)center dot 9H(2)O in ethanol/water mixed solvents at room temperature for 48 h. Ag solution was previously prepared by microwave-assisted method in ethylene glycol (EG) at 150 degrees C for 10 min. The nanocomposites consisted of Ag core and an amorphous calcium silicate shell. The XRD and EDS results confirmed that the product was the Ag/calcium silicate nanocomposite. The TEM micrographs indicated that the Ag/calcium silicate nanocomposite was core-shell nanoparticles. The effects of Ca (NO(3))(2)center dot 4H(2)O and Na(2)SiO(3)center dot 9H(2)O concentration on the shells of Ag/calcium silicate nanocomposite were investigated. The products were characterized by X-ray powder diffraction (XRD), transmission electron microscopy (TEM), and energy-dispersive X-ray spectra (EDS). This method is simple, fast and may be extended to the synthesis of the other kinds of core-shell nanocomposites.
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| 10. |
- Pan, Liang, et al.
(författare)
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a A Resistance-Switchable and Ferroelectric Metal Organic Framework
- 2014
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 136:50, s. 17477-17483
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Tidskriftsartikel (refereegranskat)abstract
- The ever-emerging demands on miniaturization of electronic devices have pushed the development of innovative materials with desired properties. One major endeavor is the development of organic- or organic-inorganic hybrid-based electronics as alternatives or supplements to silicon-based devices. Herein we report the first observation of the coexistence of resistance switching and ferroelectricity in a metal-organic framework (MOF) material, [InC16H11N2O8]center dot 1.5H(2)O, denoted as RSMOF-1. The electrical resistance of RSMOF-1 can be turned on and off repeatedly with a current ratio of 30. A first-principles molecular dynamics simulation suggests that the resistive switching effect is related to the ferroelectric transition of N center dot center dot center dot H-O center dot center dot center dot H-N bridge-structured dipoles of the guest water molecules and the amino-tethered MOF nanochannel. The discovery of the resistive switching effect and ferroelectricity in MOFs offers great potential for the physical implementation of novel electronics for next-generation digital processing and communication.
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