| 1. |
- 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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| 2. |
- 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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| 3. |
- Frank, Ari M., et al.
(författare)
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De novo peptide sequencing and identification with precision mass spectrometry
- 2007
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 6:1, s. 114-123
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Tidskriftsartikel (refereegranskat)abstract
- The recent proliferation of novel mass spectrometers such as Fourier transform, QTOF, and OrbiTrap marks a transition into the era of precision mass spectrometry, providing a 2 orders of magnitude boost to the mass resolution, as compared to low-precision ion-trap detectors. We investigate peptide de novo sequencing by precision mass spectrometry and explore some of the differences when compared to analysis of low-precision data. We demonstrate how the dramatically improved performance of de novo sequencing with precision mass spectrometry paves the way for novel approaches to peptide identification that are based on direct sequence lookups, rather than comparisons of spectra to a database. With the direct sequence lookup, it is not only possible to search a database very efficiently, but also to use the database in novel ways, such as searching for products of alternative splicing or products of fusion proteins in cancer. Our de novo sequencing software is available for download at http://peptide.ucsd.edu/.
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| 4. |
- 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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| 5. |
- Juhlin, Christopher, et al.
(författare)
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Seismic imaging of reflectors in the SG4 borehole, Middle Urals, Russia
- 1997
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Ingår i: Tectonophysics. - : Elsevier. - 0040-1951 .- 1879-3266. ; 276:1-4, s. 1-18
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The upper crust in the Middle Urals is known to be highly reflective. However, it is not clear whether the observed reflections originate from lithological boundaries or from fault zones. The SG4 borehole located in the Tagil Synform of the Middle Urals, drilled to 5354 m as of August 1995, presents one opportunity to study the source of this reflectivity. The hole has penetrated several different lithologies as well as numerous tectonic or fracture zones. The upper 5070 m consist of island arc rocks which have presumably been thrust on top of basalts. To allow correlations between available surface seismic studies and the borehole observations vertical and offset seismic profile data were acquired in the borehole over the interval 520 m to 3940 m. Two shot points were used, a near offset one at 135 m from the wellhead and a far offset one at 1845 m from the wellhead. After processing, the borehole seismic data show numerous reflecting horizons. Many reflections correlate with major fracture zones, while others have no clear correlation with fracture zones nor lithological contrasts. The interval between approximately 4450 m and 5100 m, which is imaged below the bottom of the survey, shows a layered reflective pattern that correlates with the lower part of a flysch unit which ends at 5070 m. The basalts below appear to be relatively transparent. A prominent east-dipping reflector on a W-E CDP line about 700 m north of the wellhead is not clearly imaged on the borehole seismic. However, in a pilot hole which deviates a few hundred metres in the northerly direction from the main hole, a marked low-velocity zone is observed at the corresponding depth for this reflector, indicating its source to be from a fault zone. That the fault zone is not clearly observed on the borehole seismic data is attributed to 3D effects.
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