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- Carrillo, M., et al.
(författare)
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High-resolution crystal structures of transient intermediates in the phytochrome photocycle
- 2021
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Ingår i: Structure. - : Elsevier BV. - 0969-2126. ; 29:7
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes are red/far-red light photoreceptors in bacteria to plants, which elicit a variety of important physiological responses. They display a reversible photocycle between the resting Pr state and the light-activated Pfr state. Light signals are transduced as structural change through the entire protein to modulate its activity. It is unknown how the Pr-to-Pfr interconversion occurs, as the structure of intermediates remains notoriously elusive. Here, we present short-lived crystal structures of the photosensory core modules of the bacteriophytochrome from myxobacterium Stigmatella aurantiaca captured by an X-ray free electron laser 5 ns and 33 ms after light illumination of the Pr state. We observe large structural displacements of the covalently bound bilin chromophore, which trigger a bifurcated signaling pathway that extends through the entire protein. The snapshots show with atomic precision how the signal progresses from the chromophore, explaining how plants, bacteria, and fungi sense red light.
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| 2. |
- Claesson, Elin, 1989, et al.
(författare)
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The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser
- 2020
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Ingår i: eLife. - 2050-084X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light.
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| 3. |
- Xia, CY, et al.
(författare)
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Hodgkin Lymphoma Monozygotic Triplets Reveal Divergences in DNA Methylation Signatures
- 2020
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Ingår i: Frontiers in oncology. - : Frontiers Media SA. - 2234-943X. ; 10, s. 598872-
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Tidskriftsartikel (refereegranskat)abstract
- We studied DNA methylation profiles in four different cell populations from a unique constellation of monozygotic triplets in whom two had developed Hodgkin Lymphoma (HL). We detected shared differences in DNA methylation signatures when comparing the two HL-affected triplets with the non-affected triplet. The differences were observed in naïve B-cells and marginal zone-like B-cells. DNA methylation differences were also detected when comparing each of the HL-affected triplets against each other. Even though we cannot determine whether treatment and/or disease triggered the observed differences, we believe our data are important on behalf of forthcoming studies, and that it might provide important clues for a better understanding of HL pathogenesis.
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| 5. |
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| 6. |
- Yang, H., et al.
(författare)
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Numerical investigations of Re-independence and influence of wall heating on flow characteristics and ventilation in full-scale 2D street canyons
- 2021
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Ingår i: Building and Environment. - : IEEE. - 0360-1323 .- 1873-684X. ; 189
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Tidskriftsartikel (refereegranskat)abstract
- Validated by wind tunnel data, this study numerically investigates the integrated impacts of wind and thermal buoyancy on urban turbulence, ventilation and pollutant dispersion in full-scale 2D deep street canyons (aspect ratio AR = H/W = 3 and 5, W = 24 m). Isothermal urban airflows for such deep street canyons can be Reynolds-number-independent when reference Reynolds number (Re) exceeds the critical Re (Rec~106,107 when AR = 3, 5), i.e. AR = 5 experiences two main vortices and one-order smaller NEV* (~10−3, the normalized net escape velocity) than AR = 3 with a single main vortex (NEV*~10−2). With sufficiently large Re (Re > Rec) and the same air-wall temperature difference (Ri = 2.62, 4.36 when AR = 3, 5), four uniform wall heating patterns were considered, including leeward-wall heating (L-H), windward-wall heating (W–H), ground heating (G-H), and all-wall heating (A-H). Various indicators were adopted to evaluate street ventilation and pollutant dilution capacity (e.g. age of air (τ,s), NEV*, pollutant transport rates (PTR)). Full-scale wall heating produces a strong upward near-wall buoyancy force, which significantly influences flow patterns and improves street ventilation for most cases. When AR = 3, L-H strengthens the single-vortex airflow. When AR = 5, L-H converts the isothermal double vortices into a single-clockwise vortex. For both ARs, W–H reverses the main clockwise vortex to an enhanced counterclockwise one, moreover G-H and A-H cause a more complicated multi-vortex pattern than isothermal cases. Overall, when AR = 3, L-H and W–H increase NEV* by 68% and 40% than the isothermal case. When AR = 5, four wall heating patterns all raise NEV* considerably (by 150%–556%). For both ARs, the L-H, W–H and A-H amplify the contribution of mean flows on removing pollutants but reduce that by turbulent diffusion compared with isothermal cases.
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