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| 2. |
- Adolfsson, J., et al.
(författare)
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QCD challenges from pp to A–A collisions
- 2020
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Ingår i: European Physical Journal A. - : Springer Science and Business Media LLC. - 1434-6001 .- 1434-601X. ; 56:11
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Forskningsöversikt (refereegranskat)abstract
- This paper is a write-up of the ideas that were presented, developed and discussed at the third International Workshop on QCD Challenges from pp to A–A, which took place in August 2019 in Lund, Sweden (Workshop link: https://indico.lucas.lu.se/event/1214/). The goal of the workshop was to focus on some of the open questions in the field and try to come up with concrete suggestions for how to make progress on both the experimental and theoretical sides. The paper gives a brief introduction to each topic and then summarizes the primary results.
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| 3. |
- Hakkaart, C, et al.
(författare)
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Copy number variants as modifiers of breast cancer risk for BRCA1/BRCA2 pathogenic variant carriers
- 2022
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Ingår i: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 5:1, s. 1061-
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Tidskriftsartikel (refereegranskat)abstract
- The contribution of germline copy number variants (CNVs) to risk of developing cancer in individuals with pathogenic BRCA1 or BRCA2 variants remains relatively unknown. We conducted the largest genome-wide analysis of CNVs in 15,342 BRCA1 and 10,740 BRCA2 pathogenic variant carriers. We used these results to prioritise a candidate breast cancer risk-modifier gene for laboratory analysis and biological validation. Notably, the HR for deletions in BRCA1 suggested an elevated breast cancer risk estimate (hazard ratio (HR) = 1.21), 95% confidence interval (95% CI = 1.09–1.35) compared with non-CNV pathogenic variants. In contrast, deletions overlapping SULT1A1 suggested a decreased breast cancer risk (HR = 0.73, 95% CI 0.59-0.91) in BRCA1 pathogenic variant carriers. Functional analyses of SULT1A1 showed that reduced mRNA expression in pathogenic BRCA1 variant cells was associated with reduced cellular proliferation and reduced DNA damage after treatment with DNA damaging agents. These data provide evidence that deleterious variants in BRCA1 plus SULT1A1 deletions contribute to variable breast cancer risk in BRCA1 carriers.
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| 4. |
- B. Brant Carvalho, Paulo H., et al.
(författare)
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Exploring High-Pressure Transformations in Low-Z (H2, Ne) Hydrates at Low Temperatures
- 2022
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Ingår i: Crystals. - : MDPI AG. - 2073-4352. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- The high pressure structural behavior of H-2 and Ne clathrate hydrates with approximate composition H-2/Ne center dot~4H(2)O and featuring cubic structure II (CS-II) was investigated by neutron powder diffraction using the deuterated analogues at ~95 K. CS-II hydrogen hydrate transforms gradually to isocompositional C-1 phase (filled ice II) at around 1.1 GPa but may be metastably retained up to 2.2 GPa. Above 3 GPa a gradual decomposition into C-2 phase (H-2 center dot H2O, filled ice I-c) and ice VIII' takes place. Upon heating to 200 K the CS-II to C-1 transition completes instantly whereas C-1 decomposition appears sluggish also at 200 K. C-1 was observed metastably up to 8 GPa. At 95 K C-1 and C-2 hydrogen hydrate can be retained below 1 GPa and yield ice II and ice I-c, respectively, upon complete release of pressure. In contrast, CS-II neon hydrate undergoes pressure-induced amorphization at 1.9 GPa, thus following the general trend for noble gas clathrate hydrates. Upon heating to 200 K amorphous Ne hydrate crystallizes as a mixture of previously unreported C-2 hydrate and ice VIII'.
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| 5. |
- B. Brant Carvalho, Paulo H., et al.
(författare)
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Pressure-induced amorphization of noble gas clathrate hydrates
- 2021
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 103:6
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Tidskriftsartikel (refereegranskat)abstract
- The high-pressure structural behavior of the noble gas (Ng) clathrate hydrates Ar center dot 6.5 H2O and Xe center dot 7.2 H2O featuring cubic structures II and I, respectively, was investigated by neutron powder diffraction (using the deuterated analogues) at 95 K. Both hydrates undergo pressure-induced amorphization (PIA), indicated by the disappearance of Bragg diffraction peaks, but at rather different pressures, at 1.4 and above 4.0 GPa, respectively. Amorphous Ar hydrate can be recovered to ambient pressure when annealed at >1.5 GPa and 170 K and is thermally stable up to 120 K. In contrast, it was impossible to retain amorphous Xe hydrate at pressures below 3 GPa. Molecular dynamics (MD) simulations were used to obtain general insight into PIA of Ng hydrates, from Ne to Xe. Without a guest species, both cubic clathrate structures amorphize at 1.2 GPa, which is very similar to hexagonal ice. Filling of large-sized H cages does not provide stability toward amorphization for structure II, whereas filled small-sized dodecahedral D cages shift PIA successively to higher pressures with increasing size of the Ng guest. For structure I, filling of both kinds of cages, large-sized T and small-sized D, acts to stabilize in a cooperative fashion. Xe hydrate represents a special case. In MD, disordering of the guest hydration structure is already seen at around 2.5 GPa. However, the different coordination numbers of the two types of guests in the crystalline cage structure are preserved, and the state is shown to produce a Bragg diffraction pattern. The experimentally observed diffraction up to 4 GPa is attributed to this semicrystalline state.
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| 6. |
- Davies, James S., et al.
(författare)
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Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter
- 2023
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a “transport” domain and a “scaffold” domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na+ and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an ‘elevator-with-an-operator’ mechanism.
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| 7. |
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| 8. |
- B. Brant Carvalho, Paulo H., et al.
(författare)
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Elucidating the guest disorder in structure II argon hydrate : A neutron diffraction isotopic substitution study
- 2020
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Ingår i: Journal of Solid State Chemistry. - : Elsevier. - 0022-4596 .- 1095-726X. ; 285
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Tidskriftsartikel (refereegranskat)abstract
- Clathrate hydrates with the cubic structure II (CS-II) form typically with large guest molecules, such as tetrahydrofuran, trimethylamine oxide, or propane. However, CS-II is also realized for argon hydrate despite the comparatively small van der Waals diameter of the guest (around 3.8 angstrom). Here, the structure of deuterated argon hydrate was studied at ambient pressure in the temperature range 20-95 K using neutron diffraction and comparing natural Ar with Ar-36, which scatters neutrons more than 13 times more efficiently. The procedure allowed to unambiguously establish the positional disorder within the large cages of CS-H, while simultaneously refining host and guest structures. These cages are singly occupied and off-centered argon atoms distribute on two tetrahedron-shaped split positions with a ratio 3:1. Molecular dynamics (MD) simulations revealed that the crystallographic positional disorder structure is due to mobile argon atoms even at 20 K. The MD potential energy distribution confirmed the diffraction model. It is noted that the unit cell volumes of argon hydrate in the investigated temperature range are virtually identical to N-2 hydrate, which has a similar composition at ambient pressure, indicating a very similar (slightly attractive) host-guest interaction.
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| 9. |
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| 10. |
- Currie, Michael J., et al.
(författare)
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Structural and biophysical analysis of a Haemophilus influenzae tripartite ATP-independent periplasmic (TRAP) transporter
- 2024
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Ingår i: ELIFE. - 2050-084X. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Tripartite ATP-independent periplasmic (TRAP) transporters are secondary-active transporters that receive their substrates via a soluble-binding protein to move bioorganic acids across bacterial or archaeal cell membranes. Recent cryo-electron microscopy (cryo-EM) structures of TRAP transporters provide a broad framework to understand how they work, but the mechanistic details of transport are not yet defined. Here we report the cryo-EM structure of the Haemophilus influenzae N-acetylneuraminate TRAP transporter (HiSiaQM) at 2.99 & Aring; resolution (extending to 2.2 & Aring; at the core), revealing new features. The improved resolution (the previous HiSiaQM structure is 4.7 & Aring; resolution) permits accurate assignment of two Na+ sites and the architecture of the substrate-binding site, consistent with mutagenic and functional data. Moreover, rather than a monomer, the HiSiaQM structure is a homodimer. We observe lipids at the dimer interface, as well as a lipid trapped within the fusion that links the SiaQ and SiaM subunits. We show that the affinity (K-D) for the complex between the soluble HiSiaP protein and HiSiaQM is in the micromolar range and that a related SiaP can bind HiSiaQM. This work provides key data that enhances our understanding of the 'elevator-with-an-operator' mechanism of TRAP transporters.
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