| 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. |
- Chow, Wah Soon, et al.
(författare)
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Quantifying and monitoring functional photosystem II and the stoichiometry of the two photosystems in leaf segments : approaches and approximations
- 2012
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Ingår i: Photosynthesis Research. - Dordrecht : Springer. - 0166-8595 .- 1573-5079. ; 113:1-3, s. 63-74
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Forskningsöversikt (refereegranskat)abstract
- Given its unique function in light-induced water oxidation and its susceptibility to photoinactivation during photosynthesis, photosystem II (PS II) is often the focus of studies of photosynthetic structure and function, particularly in environmental stress conditions. Here we review four approaches for quantifying or monitoring PS II functionality or the stoichiometry of the two photosystems in leaf segments, scrutinizing the approximations in each approach. (1) Chlorophyll fluorescence parameters are convenient to derive, but the information-rich signal suffers from the localized nature of its detection in leaf tissue. (2) The gross O-2 yield per single-turnover flash in CO2-enriched air is a more direct measurement of the functional content, assuming that each functional PS II evolves one O-2 molecule after four flashes. However, the gross O-2 yield per single-turnover flash (multiplied by four) could over-estimate the content of functional PS II if mitochondrial respiration is lower in flash illumination than in darkness. (3) The cumulative delivery of electrons from PS II to P700(+) (oxidized primary donor in PS I) after a flash is added to steady background far-red light is a whole-tissue measurement, such that a single linear correlation with functional PS II applies to leaves of all plant species investigated so far. However, the magnitude obtained in a simple analysis (with the signal normalized to the maximum photo-oxidizable P700 signal), which should equal the ratio of PS II to PS I centers, was too small to match the independently-obtained photosystem stoichiometry. Further, an under-estimation of functional PS II content could occur if some electrons were intercepted before reaching PS I. (4) The electrochromic signal from leaf segments appears to reliably quantify the photosystem stoichiometry, either by progressively photoinactivating PS II or suppressing PS I via photo-oxidation of a known fraction of the P700 with steady far-red light. Together, these approaches have the potential for quantitatively probing PS II in vivo in leaf segments, with prospects for application of the latter two approaches in the field.
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| 3. |
- Fan, Hongchao, et al.
(författare)
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Shell model representation as a substitute of LOD3 for 3D modeling in CityGML
- 2011
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Ingår i: Geo-spatial Information Science. - : Informa UK Limited. - 1009-5020 .- 1993-5153. ; 14:2, s. 78-84
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Tidskriftsartikel (refereegranskat)abstract
- The OGC standard for 3D city modeling is widely used in an increasing number of applications. It defines five consecutive Levels of Detail (LoD0 to LoD4 with increasing accuracy and structural complexity), in which LoD3 includes all exterior appearances and geometrical details and subsequently requires much storage space. A new LoD is introduced as shell model with the exterior shell of the LoD3 model and the opening objects like windows, doors as well as smaller façade objects are projected onto walls. In this paper, a user survey is presented. The results of this survey show that the shell model can give users almost the same visual impression as the LoD3 model. Furthermroe, algorithms are developed to extract the shell model from LoD3 model. Experiments show that this shell model can reduce up to 90% storage of the original LoD3 model. Therefore, on one hand it can be used as a substitute for a LoD3 model for the visualization on small displays. On the other hand, it can be treated as a sub-level of detail (SLoD3) in CityGML, since it retains almost the same amount of information but requires much less storage space.
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| 4. |
- Hu, Liangbing, et al.
(författare)
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Transparent and conductive paper from nanocellulose fibers
- 2013
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Ingår i: Energy & Environmental Science. - 1754-5692 .- 1754-5706. ; 6:2, s. 513-518
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Tidskriftsartikel (refereegranskat)abstract
- Here we report on a novel substrate, nanopaper, made of cellulose nanofibrils, an earth abundant material. Compared with regular paper substrates, nanopaper shows superior optical properties. We have carried out the first study on the optical properties of nanopaper substrates. Since the size of the nanofibrils is much less than the wavelength of visible light, nanopaper is highly transparent with large light scattering in the forward direction. Successful depositions of transparent and conductive materials including tin-doped indium oxide, carbon nanotubes and silver nanowires have been achieved on nanopaper substrates, opening up a wide range of applications in optoelectronics such as displays, touch screens and interactive paper. We have also successfully demonstrated an organic solar cell on the novel substrate.
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| 5. |
- 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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| 6. |
- Na, Manli, et al.
(författare)
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Adenovirus assembly is impaired by BMI1-related histone deacetylase activity.
- 2014
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Ingår i: Virology. - : Elsevier BV. - 1096-0341 .- 0042-6822. ; 456:Apr 17, s. 227-237
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Tidskriftsartikel (refereegranskat)abstract
- Polycomb ring finger oncogene BMI1 (B cell-specific Moloney murine leukemia virus integration site 1) plays a critical role in development of several types of cancers. Here, we report an inverse relationship between levels of BMI1 expression and adenovirus (Ad) progeny production. Enforced BMI1 expression in A549 cells impaired Ad progeny production. In contrast, knocking-down of endogenous BMI1 expression enhanced progeny production of a conditionally replicating Ad and wild-type Ad5 and Ad11p. Ad vectors overexpressing BMI1 were not impaired in the replication of progeny genomes and in the expression of E1A and Ad structural proteins. However, 293 cells infected by Ad vector overexpressing BMI1 contained a large proportion of morphologically irregular Ad particles. This effect was reversed in 293 cells pre-treated with the histone deacetylase (HDAC) inhibitor trichostatin A (TSA) in parallel with the production of infectious Ad particles. Our findings suggest an inhibitory role of BMI1 in Ad morphogenesis that can be implied in Ad tropism and Ad-mediated cancer therapy.
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| 7. |
- Wang, Zhaoming, et al.
(författare)
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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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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)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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