| 1. |
- Birney, Ewan, et al.
(författare)
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
- 2007
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 447:7146, s. 799-816
-
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.
|
|
| 2. |
- Graham, Nicholas A. J., et al.
(författare)
-
Climate Warming, Marine Protected Areas and the Ocean-Scale Integrity of Coral Reef Ecosystems
- 2008
-
Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 3:8, s. e3039-
-
Tidskriftsartikel (refereegranskat)abstract
- Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure, diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales, with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance. This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should be integrated into existing management frameworks and combined with policies to improve system-wide resilience to climate variation and change.
|
|
| 3. |
- Norberg, Daniel, 1977-
(författare)
-
Quantum Chemical Studies of Radical Cation Rearrangement, Radical Carbonylation, and Homolytic Substitution Reactions
- 2007
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Quantum chemical calculations have been performed to investigate radical cation rearrangement, radical carbonylation, and homolytic substitution reactions of organic molecules. The rearrangement of the bicyclopropylidiene radical cation to the tetramethyleneethane radical cation is predicted to proceed with stepwise disrotatory opening of the two rings. Each ring opening is found to be combined with a striking pyramidalization of a carbon atom in the central bond. The isomerization of the norbornadiene radical cation to the cycloheptatriene radical cation (CHT.+), initialized by opening of a bridgehead–methylene bond, is investigated. The most favorable path involves concerted rearrangement to the norcaradiene radical cation followed by ring opening to CHT.+. The barrier of this channel is found to be significantly reduced upon substitution of the methylene group with C(CH3)2. Stepwise mechanisms are predicted to be favored over concerted isomerization for the McLafferty rearrangement of the radical cations of butanal and 3-fluorobutanal. The barrier for the concerted rearrangement is found to be lowered by 17.2 kcal/mol upon substitution, a result which is rationalized by the calculated dipole moments and atomic charges. Recent experiments showed that photoinitiated carbonylation of alkyl iodides with [11C]carbon monoxide may be significantly enhanced by using small amounts of ketones that have nπ* character of their excited triplet state. DFT calculations show the feasibility of an atom transfer type mechanism, proposed to explain these observations. Moreover, the computational results rationalize the observed differences in yield when using various alcohol solvents. Finally, following photolysis of methyliodide, recent electron spin resonance spectroscopy experiments demonstrated that the SH2 reaction •CD3 + SiD3CH3 → CD3SiD3 + •CH3 proceeds with high selectivity over the energetically more favorable D abstraction. The role of geometrical effects, especially the formation of prereactive complexes between methylsilane and methyliodide is studied, and a plausible explanation for the experimentally observed paradox is presented.
|
|
| 4. |
- Pelmenschikov, Vladimir, 1978-
(författare)
-
Theoretical Modeling of Enzyme Catalysis with Focus on Radical Chemistry
- 2005
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Hybrid density functional theory (DFT) B3LYP method is applied to study the four diverse enzyme systems: zinc-containing peptidases (thermolysin and stromelysin), methyl-coenzyme M reductase, ribonucleotide reductases (classes I and III), and superoxide dismutases (Cu,Zn- and Ni-dependent enzymes). Powerfull tools of modern quantum chemistry are used to address the questions of biological pathways at their molecular level, proposing a novel mechanism for methane production by methyl-coenzyme M reductase and providing additional insights into hydrolysis by zinc peptidases, substrate conversion by ribonucleotide reductases, and biological superoxide dismutation. Catalysis by these enzymes, with the exception of zinc peptidases, involves radical chemistry.
|
|
