| 1. |
- Hillier, Ladeana W, et al.
(författare)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Tidskriftsartikel (refereegranskat)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 2. |
- Ayarza, P, et al.
(författare)
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Integrated geological and geophysical studies in the SG4 borehole area, Tagil Volcanic Arc, Middle Urals: Location of seismic reflectors and source of the reflectivity
- 2000
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Ingår i: Journal of Geophysical Research. - : AMER GEOPHYSICAL UNION. - 0148-0227 .- 2156-2202. ; 105:B9, s. 21333-21352
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Tidskriftsartikel (refereegranskat)abstract
- Near-vertical incidence reflection seismic data acquired in the Tagil Volcanic Arc (Middle Urals) show the upper crust to be highly reflective. Two intersecting seismic lines located near the ongoing ∼5400 m deep SG4 borehole show that the main reflectivity strikes approximately N-S and dips ∼35°–55° to the east. Prominent reflections intercept the borehole at ∼1000, ∼1500, 2800–2900, ∼3400, and between ∼4000 and 5400 m, which correspond to intervals of low velocity/low density/low resistivity. The surface projections of these reflections lie parallel to the strike of magnetic anomaly trends. Multioffset vertical seismic profile (VSP) data acquired in the SG4 borehole show a seismic response dominated by P to S reflected converted waves from the moderately east dipping reflectivity and from a set of very steep east dipping reflectors not imaged by the surface data. Modeling of the VSP data constrains the depth at which reflectors intercept the borehole and suggests that the P to S conversions are best explained by low-velocity porous intervals rather than higher-velocity mafic material. The most prominent east dipping reflection on the surface seismic data is only imaged on VSP shots that sample the crust closer to the E-W seismic line. This discrepancy between the VSP and the surface seismic data is attributed to rapid lateral changes in the physical properties of the reflector. Surface and borehole data suggest that the low-velocity/low-density/low-resistivity intervals are the most important source of reflectivity in the SG4 borehole area, although lithological contrasts may also play a role. Drill cores from the these zones contain hydrothermal alteration minerals indicating interaction with fluids. Tectonic criteria suggest that they might represent imbricated fracture zones often bounding different lithologies and/or intrusions. Some of them might also represent high-porosity lava flows or pyroclastic units, common in island arc environments.
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| 3. |
- Burnum-Johnson, Kristin E., et al.
(författare)
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New Views of Old Proteins : Clarifying the Enigmatic Proteome
- 2022
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Ingår i: Molecular & Cellular Proteomics. - : Elsevier BV. - 1535-9476 .- 1535-9484. ; 21:7
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Tidskriftsartikel (refereegranskat)abstract
- All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide a >10 years of projection for technologies to meet the challenges that protein biology presents. With a broad perspective, we discuss grand opportunities to transition the science of proteomics into a more propulsive enterprise. Extrapolating recent trends, we describe a next generation of approaches to define, quantify, and visualize the multiple dimensions of the proteome, thereby transforming our understanding and interactions with human disease in the coming decade.
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| 4. |
- Yang, Xinping, et al.
(författare)
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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing
- 2016
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Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 164:4, s. 805-817
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Tidskriftsartikel (refereegranskat)abstract
- While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms'' are functionally divergent (i.e., "functional alloforms'').
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