| 1. |
- Ignatov, Dmitriy, et al.
(författare)
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Generation of Sequencing Libraries for Structural Analysis of Bacterial 5′ UTRs
- 2020
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Ingår i: STAR Protocols. - : Elsevier BV. - 2666-1667. ; 1:2
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Tidskriftsartikel (refereegranskat)abstract
- The structure of 5′ untranslated regions (5′ UTRs) of bacterial mRNAs often determines the fate of the transcripts. Using a dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) approach, we developed a protocol to generate sequence libraries to determine the base-pairing status of adenines and cytosines in the 5′ UTRs of bacterial mRNAs. Our method increases the sequencing depth of the 5′ UTRs and allows detection of changes in their structures by sequencing libraries of moderate sizes. For complete details on the use and execution of this protocol, please refer to Ignatov et al. (2020).
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| 2. |
- Kitchen, Philip, et al.
(författare)
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Calcein Fluorescence Quenching to Measure Plasma Membrane Water Flux in Live Mammalian Cells
- 2020
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Ingår i: STAR Protocols. - : Elsevier BV. - 2666-1667. ; 1:3
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Tidskriftsartikel (refereegranskat)abstract
- Aquaporins (AQPs) are membrane channel proteins that facilitate the movement of water down osmotic gradients across biological membranes. This protocol allows measurements of AQP-mediated water transport across the plasma membrane of live mammalian cells. Calcein is a fluorescent dye that is quenched in a concentration-dependent manner. Therefore, on short timescales, its concentration-dependent fluorescence can be used as a probe of cell volume, and therefore a probe of water transport into or out of cells. For complete details on the use and execution of this protocol, please refer to Kitchen et al. (2020) and Kitchen and Conner (2015). For the underlying methodology development, please refer to Fenton et al. (2010) and Solenov et al. (2004).
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| 3. |
- Salvatori, Roger, 1988, et al.
(författare)
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Mapping protein networks in yeast mitochondria using proximity-dependent biotin identification coupled to proteomics
- 2020
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Ingår i: STAR PROTOCOLS. - : Elsevier BV. - 2666-1667. ; 1:3
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Tidskriftsartikel (refereegranskat)abstract
- Proximity-dependent biotin identification (BioID) permits biotinylation of proteins interacting directly, indirectly, or just localized in proximity of a protein of interest (bait). Here, we describe how BioID coupled to proteomics and network biology can be used to map protein proximities in yeast mitochondria, aiding in visualization of complex protein-protein interaction landscapes. For complete information on the use and execution of this protocol, please refer to Singh et al., 2020.
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