| 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. |
- Clark, Andrew G., et al.
(författare)
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Evolution of genes and genomes on the Drosophila phylogeny
- 2007
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 450:7167, s. 203-218
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Tidskriftsartikel (refereegranskat)abstract
- Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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| 3. |
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| 4. |
- Richards, Stephen, et al.
(författare)
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The genome of the model beetle and pest Tribolium castaneum.
- 2008
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Ingår i: Nature. - 1476-4687. ; 452:7190, s. 949-55
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Tidskriftsartikel (refereegranskat)abstract
- Tribolium castaneum is a representative of earth’s most numerous eukaryotic order, a powerful model organism for the study of generalized insect development, and also an important pest of stored agricultural products. We describe its genome sequence here. This omnivorous beetle has evolved an ability to interact with a diverse chemical environment as evidenced by large expansions in odorant and gustatory receptors, as well as p450 and other detoxification enzymes. Developmental patterns in Tribolium are more representative of other arthropods than those found in Drosophila, a fact represented in gene content and function. For one, Tribolium has retained more ancestral genes involved in cell-cell communication than Drosophila, and some are expressed in the growth zone crucial for axial elongation in short germ development. Systemic RNAi in T. castaneum appears to use mechanisms distinct from those found in C. elegans, but nevertheless offers similar power for the elucidation of gene function and identification of targets for selective insect control.
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| 5. |
- Burguière, Adeline, et al.
(författare)
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LosA, a key glycosyltransferase involved in the biosynthesis of a novel family of glycosylated acyltrehalose lipooligosaccharides from Mycobacterium marinum.
- 2005
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Ingår i: The Journal of biological chemistry. - 0021-9258. ; 280:51, s. 42124-33
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Tidskriftsartikel (refereegranskat)abstract
- Members of the genus Mycobacterium are characterized by cell envelopes rich in unusual free lipids, interacting with a covalently anchored mycolyl-arabinogalactan matrix. Previous studies have shown that Mycobacterium marinum produces large amounts of a diacylglycosylphenolphthiocerol, "phenolic" glycolipid. When cultivated on liquid Sauton medium, traces of a polar lipooligosaccharide (LOS) glycolipid antigen were also previously indicated. In this study, it was found that growth of the type strain of M. marinum on solid Sauton or Middlebrook 7H10 agar gave substantial, but different, amounts of a family of four major trehalose-based LOSs. The core pentasaccharide LOS-I was a rhamnosyl diglucosyl-acylated trehalose. The heptasaccharide, LOS-II, was derived from LOS-I by adding xylose accompanied by a novel sugar (X); repeated addition of this sugar unit X gave the octasaccharide LOS-III. LOS-IV has a decasaccharide component with two additional unusual sugar units, YZ. In a recent study (Alexander, D. C., Jones, J. R., Tan, T., Chen, J. M., and Liu, J. (2004) J. Biol. Chem. 279, 18824-18833), chromatographically similar glycolipids were assigned to the family of phosphatidylinositol mannosides (PIMs) and a "PimF" (Rv1500) glycosyltransferase implicated in the conversion of a supposed "PIM5" to a "PIM7." The present study indicates that these putative PIMs are in fact members of the phosphorus-free LOS family of glycolipids and that the protein product of Rv1500, which we have now termed LosA, is a glycosyltransferase involved in transferring sugars to LOS-III to form LOS-IV of M. marinum.
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| 6. |
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| 7. |
- Frith, Martin C., et al.
(författare)
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Pseudo-messenger RNA : Phantoms of the transcriptome
- 2006
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 2:4, s. 504-514
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Tidskriftsartikel (refereegranskat)abstract
- The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein- coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo - messenger RNAs ( approximately half of which are transposonassociated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein- coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense- mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non- standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level.
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| 8. |
- Grasselli, Robert K., et al.
(författare)
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Active centers, catalytic behavior, symbiosis and redox properties of MoV(Nb,Ta)TeO ammoxidation catalysts
- 2006
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Ingår i: Topics in Catalysis. - : Springer Science and Business Media LLC. - 1572-9028 .- 1022-5528. ; 38:1-3, s. 7-16
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Tidskriftsartikel (refereegranskat)abstract
- Selective as well as waste forming active centers were defined for MoVNbTeO and MoVTaTeO catalysts in the ammoxidation of propane to acrylonitrile and all catalytic functionalities were assigned to specific elements at the respective active centers. Symbiosis between M1 and M2 phases of these catalysts was observed, with phase cooperation being more extensive in the Nb than Ta containing compositions. The difference in catalytic effectiveness arises most likely because contact and surface area exposure of the two respective, cooperating phase pairs are not equal. The M1 phase of the catalysts is reducible by propane and ammonia in the absence of dioxygen and is regenerable to its original, fully oxidized state by dioxygen (air). No structural collapse is observed even after 120 C3H8 + NH3 reduction pulses. The so induced reduction of the catalyst extends up to 70 layers deep. The product distribution over the first few pulses is very similar to that under catalytic conditions, supporting the concept that lattice oxygen is involved in the catalytic ammoxidation process. Therefore, the ammoxidation of paraffins is a redox process, as is of course the well-known olefin ammoxidation process.
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| 9. |
- Liu, Jiurong, et al.
(författare)
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Generation of Oxide Nanopatterns by Combining Self-Assembly of S-Layer Proteins and Area-Selective Atomic Layer Deposition
- 2008
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 130:50, s. 16908-16913
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Tidskriftsartikel (refereegranskat)abstract
- We report an effective method to fabricate two-dimensional (2D) periodic oxide nanopatterns using S-layer proteins as a template. Specifically, S-layer proteins with a unit cell dimension of 20 nm were reassembled on silicon substrate to form 2D arrays with ordered pores of nearly identical sizes (9 nm). Octadecyltrichlorosilane (ODTS) was utilized to selectively react with the S-layer proteins, but not the Si surface exposed through the pores defined by the proteins. Because of the different surface functional groups on the ODTS-modified S-layer proteins and Si surface, area-selective atomic layer deposition of metal oxide-based high-k materials, such as hafnium oxide, in the pores was achieved. The periodic metal oxide nanopatterns were generated on Si substrate after selective removal of the ODTS-modified S-layer proteins. These nanopatterns of high-k materials are expected to facilitate further downscaling of logic and memory nanoelectronic devices.
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| 10. |
- Lu, Jun, et al.
(författare)
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A simple and effective method for calculating the bending loss and phase enhancement of a bent planar waveguide
- 2005
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Ingår i: Fiber and integrated optics (Print). - : Informa UK Limited. - 0146-8030 .- 1096-4681. ; 24:1, s. 25-36
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Tidskriftsartikel (refereegranskat)abstract
- A simple and effective method is introduced to calculate the bending loss and phase enhancement of a bent planar waveguide. The wave field is represented in terms of Airy functions and an eigenvalue equation is derived by matching the boundary conditions and the radiation condition in the outer cladding layer. The complex propagation constant is obtained by solving the eigenvalue equation with the Newton-Raphson method, and the imaginary part of the propagation constant gives directly the bending loss of the bent waveguide. The results are compared with the previous experimental and numerical results and are shown to be highly accurate and effective. The phase enhancement due to the bending is also studied.
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