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- Schoenrock, A., et al.
(författare)
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Efficient prediction of human protein-protein interactions at a global scale
- 2014
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Ingår i: Bmc Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 15
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Tidskriftsartikel (refereegranskat)abstract
- Background: Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. Results: On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments. Conclusions: The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.
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| 2. |
- Englert, Hanna, et al.
(författare)
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Targeting NETs using dual-active DNase1 variants
- 2023
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Ingår i: Frontiers in Immunology. - : Frontiers Media SA. - 1664-3224. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundNeutrophil Extracellular Traps (NETs) are key mediators of immunothrombotic mechanisms and defective clearance of NETs from the circulation underlies an array of thrombotic, inflammatory, infectious, and autoimmune diseases. Efficient NET degradation depends on the combined activity of two distinct DNases, DNase1 and DNase1-like 3 (DNase1L3) that preferentially digest double-stranded DNA (dsDNA) and chromatin, respectively.MethodsHere, we engineered a dual-active DNase with combined DNase1 and DNase1L3 activities and characterized the enzyme for its NET degrading potential in vitro. Furthermore, we produced a mouse model with transgenic expression of the dual-active DNase and analyzed body fluids of these animals for DNase1 and DNase 1L3 activities. We systematically substituted 20 amino acid stretches in DNase1 that were not conserved among DNase1 and DNase1L3 with homologous DNase1L3 sequences.ResultsWe found that the ability of DNase1L3 to degrade chromatin is embedded into three discrete areas of the enzyme's core body, not the C-terminal domain as suggested by the state-of-the-art. Further, combined transfer of the aforementioned areas of DNase1L3 to DNase1 generated a dual-active DNase1 enzyme with additional chromatin degrading activity. The dual-active DNase1 mutant was superior to native DNase1 and DNase1L3 in degrading dsDNA and chromatin, respectively. Transgenic expression of the dual-active DNase1 mutant in hepatocytes of mice lacking endogenous DNases revealed that the engineered enzyme was stable in the circulation, released into serum and filtered to the bile but not into the urine.ConclusionTherefore, the dual-active DNase1 mutant is a promising tool for neutralization of DNA and NETs with potential therapeutic applications for interference with thromboinflammatory disease states.
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| 4. |
- Omidi, N., et al.
(författare)
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A Single Deformed Bow Shock for Titan-Saturn System
- 2017
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Ingår i: Journal of Geophysical Research - Space Physics. - : American Geophysical Union (AGU). - 2169-9380 .- 2169-9402. ; 122:11, s. 11058-11075
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Tidskriftsartikel (refereegranskat)abstract
- During periods of high solar wind pressure, Saturn's bow shock is pushed inside Titan's orbit exposing the moon and its ionosphere to the solar wind. The Cassini spacecraft's T96 encounter with Titan occurred during such a period and showed evidence for shocks associated with Saturn and Titan. It also revealed the presence of two foreshocks: one prior to the closest approach (foreshock 1) and one after (foreshock 2). Using electromagnetic hybrid (kinetic ions and fluid electrons) simulations and Cassini observations, we show that the origin of foreshock 1 is tied to the formation of a single deformed bow shock for the Titan-Saturn system. We also report the observations of a structure in foreshock 1 with properties consistent with those of spontaneous hot flow anomalies formed in the simulations and previously observed at Earth, Venus, and Mars. The results of hybrid simulations also show the generation of oblique fast magnetosonic waves upstream of the outbound Titan bow shock in agreement with the observations of large-amplitude magnetosonic pulsations in foreshock 2. We also discuss the implications of a single deformed bow shock for new particle acceleration mechanisms and also Saturn's magnetopause and magnetosphere.
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