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- 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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- Margulies, Elliott H, et al.
(författare)
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 17:6, s. 760-774
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Tidskriftsartikel (refereegranskat)abstract
- A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation, alignment, and evolutionary constraint analyses of 23 mammalian species for all ENCODE targets. Alignments were generated using four different methods; comparisons of these methods reveal large-scale consistency but substantial differences in terms of small genomic rearrangements, sensitivity (sequence coverage), and specificity (alignment accuracy). We describe the quantitative and qualitative trade-offs concomitant with alignment method choice and the levels of technical error that need to be accounted for in applications that require multisequence alignments. Using the generated alignments, we identified constrained regions using three different methods. While the different constraint-detecting methods are in general agreement, there are important discrepancies relating to both the underlying alignments and the specific algorithms. However, by integrating the results across the alignments and constraint-detecting methods, we produced constraint annotations that were found to be robust based on multiple independent measures. Analyses of these annotations illustrate that most classes of experimentally annotated functional elements are enriched for constrained sequences; however, large portions of each class (with the exception of protein-coding sequences) do not overlap constrained regions. The latter elements might not be under primary sequence constraint, might not be constrained across all mammals, or might have expendable molecular functions. Conversely, 40% of the constrained sequences do not overlap any of the functional elements that have been experimentally identified. Together, these findings demonstrate and quantify how many genomic functional elements await basic molecular characterization.
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- Pifferi, A, et al.
(författare)
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Performance assessment of photon migration instruments: the MEDPHOT protocol
- 2005
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Ingår i: Applied Optics. - 2155-3165. ; 44:11, s. 2104-2114
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Tidskriftsartikel (refereegranskat)abstract
- We propose a comprehensive protocol for the performance assessment of photon migration instruments. The protocol has been developed within the European Thematic Network MEDPHOT (optical methods for medical diagnosis and monitoring of diseases) and is based on five criteria: accuracy, linearity, noise, stability, and reproducibility. This protocol was applied to a total of 8 instruments with a set of 32 phantoms, covering a wide range of optical properties.
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- Ujvari, Beata, et al.
(författare)
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Experimental studies of blowfly (Calliphora stygia) longevity: A little dietary fat is beneficial but too much is detrimental
- 2009
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Ingår i: Comparative Biochemistry and Physiology A. - : Elsevier BV. - 1531-4332. ; 154:3, s. 383-388
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Tidskriftsartikel (refereegranskat)abstract
- This paper is one in a series of experimental studies on the effects of food composition on aging and longevity, using the golden-haired blowfly Calliphora stygia as the animal model Here we examine how diet. fat content affects blowfly life history traits such as longevity, reproduction, feeding rate, body mass, total fat content and membrane fatty acid composition. The highest median and maximum longevity was observed in blowflies fed on low fat diets, while high-fat diets caused more rapid death of the blowflies. A major result was that blowflies feeding on the lowest fat diet had the highest maximal lifespan demonstrating that low levels of diet fat enhanced blowfly lifespan. Diet also influenced gender-specific mortality rates; females lived longer on a high-fat diet, while males lived longer on a low fat diet. Furthermore, we provide data for and explain how blowfly feeding rates, egg production and male harassment affected blowfly longevity. Our results highlight the need for further studies to understand how dietary fats are metabolised and utilised in the golden-haired blowfly. (C) 2009 Elsevier Inc. All rights reserved.
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