| 1. |
- Birney, Ewan, et al.
(författare)
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
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Tidskriftsartikel (refereegranskat)abstract
- We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.
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| 2. |
- Jiang, Q. H., et al.
(författare)
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High-temperature ferroelectric phase transition observed in multiferroic Bi0.91La0.05Tb0.04FeO3
- 2009
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 95:1, s. 12909-
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Tidskriftsartikel (refereegranskat)abstract
- A single-phase Bi0.91La0.05Tb0.04FeO3 polycrystalline ceramic was fabricated by spark-plasma-sintering the precursor powder prepared by a sol-gel method. Temperature-dependent properties of polycrystalline Bi0.91La0.05Tb0.04FeO3 were characterized by x-ray diffraction, dielectric, and piezoelectric measurement. The x-ray diffraction results revealed a phase transition near 700 degrees C. Especially, temperature-dependent dielectric behavior demonstrated that there was a dielectric abnormal peak at about 697 degrees C, in addition to those two well-known dielectric abnormal peaks at 337 degrees C (Neel temperature) and 831 degrees C (Curie temperature). The observations, together with thermal depoled behavior, suggest a ferroelectric-ferroelectric phase transition from R(3)c to Pbnm at around 700 degrees C.
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| 3. |
- Li, Gui-Lan, et al.
(författare)
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Open-closed conformational change revealed by the crystal structures of 3-keto-L-gulonate 6-phosphate decarboxylase from Streptococcus mutans
- 2009
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Ingår i: Biochemical and Biophysical Research Communications. - : Elsevier BV. - 1090-2104 .- 0006-291X. ; 381:3, s. 33-429
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Tidskriftsartikel (refereegranskat)abstract
- The 3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC) catalyses the decarboxylation of 3-keto-L-gulonate 6-phosphate to L-xylulose in the presence of magnesium ions. The enzyme is involved in L-ascorbate metabolism and plays an essential role in the pathway of glucuronate interconversion. Crystal structures of Streptococcus mutans KGPDC were determined in the absence and presence of the product analog D-ribulose 5-phosphate. We have observed an 8 A alphaB-helix movement and other structural rearrangements around the active site between the apo-structures and product analog bound structure. These drastic conformational changes upon ligand binding are the first observation of this kind for the KGPDC family. The flexibilities of both the alpha-helix lid and the side chains of Arg144 and Arg197 are associated with substrate binding and product releasing. The open-closed conformational changes of the active site, through the movements of the alpha-helix lid and the arginine residues are important for substrate binding and catalysis.
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| 4. |
- Lin, Yuan-Hua, et al.
(författare)
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Electrical transport properties of La2CuO4 ceramics processed by the spark plasma sintering
- 2007
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Ingår i: Journal of The American Ceramic Society. - : Wiley. - 0002-7820 .- 1551-2916. ; 90:12, s. 4005-4008
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Tidskriftsartikel (refereegranskat)abstract
- Highly dense La2CuO4 ceramics have been prepared by the spark plasma sintering technique. Temperature dependence of electrical conductivity indicates that La2CuO4 ceramics sintered at over 875 degrees C exhibit a metal-like behavior, which should be ascribed to the special La2CuO4 crystal structure and its correlation splitting of the half-filled d(x2-y2) band. Our experimental data indicate that all of the La2CuO4 samples exhibit positive thermoelectric power in the whole measuring temperature range, indicating that the majority of charge carriers are holes. It is desirable to obtain good thermoelectric performance for this system by optimizing the electrical properties and reducing the thermal conductivity.
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| 5. |
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| 6. |
- Liu, Wen-Chun, et al.
(författare)
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Genotyping of Hepatitis B Virus - Genotypes A to G by Multiplex Polymerase Chain Reaction
- 2008
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Ingår i: Intervirology. - : S. Karger AG. - 0300-5526 .- 1423-0100. ; 51:4, s. 247-252
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Tidskriftsartikel (refereegranskat)abstract
- <i>Objectives:</i> Eight genotypes (A–H) of hepatitis B virus (HBV) are known with variations in nucleotide sequences greater than 8%. Several recent publications found that the clinical course and outcome of antiviral therapy depended on the genotype of the infecting HBV strain. Large epidemiological studies will require the availability of a system which is rapid, reliable and can be performed on a large number of samples. <i>Methods:</i> To establish a simple and accurate genotyping method, the study collected 369 HBV complete genomic sequences from the GenBank database. Type-specific primers were also designed that separated HBV genotypes A to G by multiplex polymerase chain reaction. <i>Results:</i> By comparison with the traditional restriction fragment length polymorphism method, over 93% of 441 samples were accurately genotyped by current assay, with a higher detection rate and sensitivity to detect mixed HBV infections. <i>Conclusions:</i> This methodology can be applied only to areas prevalent with HBV genotypes A to G. However, it provides an efficient alternative for clinical diagnosis and large-scale studies.
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| 7. |
- Nan, Jie, et al.
(författare)
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Bioinformatics and structural characterization of a hypothetical protein from Streptococcus mutans : implication of antibiotic resistance
- 2009
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 4:10, s. 7245-7245
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Tidskriftsartikel (refereegranskat)abstract
- As an oral bacterial pathogen, Streptococcus mutans has been known as the aetiologic agent of human dental caries. Among a total of 1960 identified proteins within the genome of this organism, there are about 500 without any known functions. One of these proteins, SMU.440, has very few homologs in the current protein databases and it does not fall into any protein functional families. Phylogenetic studies showed that SMU.440 is related to a particular ecological niche and conserved specifically in some oral pathogens, due to lateral gene transfer. The co-occurrence of a MarR protein within the same operon among these oral pathogens suggests that SMU.440 may be associated with antibiotic resistance. The structure determination of SMU.440 revealed that it shares the same fold and a similar pocket as polyketide cyclases, which indicated that it is very likely to bind some polyketide-like molecules. From the interlinking structural and bioinformatics studies, we have concluded that SMU.440 could be involved in polyketide-like antibiotic resistance, providing a better understanding of this hypothetical protein. Besides, the combination of multiple methods in this study can be used as a general approach for functional studies of a protein with unknown function.
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| 8. |
- Su, Xiao Dong, et al.
(författare)
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A large-scale, high-efficiency and low-cost platform for structural genomics studies
- 2006
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Ingår i: Acta Crystallographica. Section D: Biological Crystallography. - 0907-4449. ; 62:Pt 8, s. 51-843
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Tidskriftsartikel (refereegranskat)abstract
- A large-scale, high-efficiency and low-cost platform based on a Beckman Coulter Biomek FX and custom-made automation systems for structural genomics has been set up at Peking University, Beijing, People's Republic of China. This platform has the capacity to process up to 2000 genes per year for structural and functional analyses. Bacillus subtilis, a model organism for Gram-positive bacteria, and Streptococcus mutans, a major pathogen of dental caries, were selected as the main targets. To date, more than 470 B. subtilis and 1200 S. mutans proteins and hundreds of proteins from other sources, including human liver proteins, have been selected as targets for this platform. The selected genes are mainly related to important metabolism pathways and/or have potential relevance for drug design. To date, 40 independent structures have been determined; of these 11 are in the category of novel structures by the criterion of having less than 30% sequence identity to known structures. More than 13 structures were determined by SAD/MAD phasing. The macromolecular crystallography beamline at the Beijing Synchrotron Radiation Facility and modern phasing programs have been crucial components of the operation of the platform. The idea and practice of the genomic approach have been successfully adopted in a moderately funded structural biology program and it is believed this adaptation will greatly improve the production of protein structures. The goal is to be able to solve a protein structure of moderate difficulty at a cost about US 10,000 dollars.
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