| 1. |
- Kattge, Jens, et al.
(författare)
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TRY plant trait database - enhanced coverage and open access
- 2020
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Ingår i: Global Change Biology. - : Wiley-Blackwell. - 1354-1013 .- 1365-2486. ; 26:1, s. 119-188
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Tidskriftsartikel (refereegranskat)abstract
- Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.
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| 2. |
- Conn, Charlotte E, et al.
(författare)
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Membrane Protein Structures in Lipid Bilayers; Small-Angle Neutron Scattering With Contrast-Matched Bicontinuous Cubic Phases
- 2020
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Ingår i: Frontiers in chemistry. - : Frontiers Media S.A.. - 2296-2646. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- . Deuterated vesicles can be used to obtain the radius of gyration of membrane proteins, but protein-protein interference effects within the vesicles severely limits this method such that the protein structure cannot be modeled. We show herein that different membrane protein conformations can be distinguished within the lipid bilayer of the bicontinuous cubic phase using contrast-matching. Time-resolved studies performed using SANS illustrate the complex phase behavior in lyotropic liquid crystalline systems and emphasize the importance of this development. We believe that studying membrane protein structures and phase behavior in contrast-matched lipid bilayers will advance both biological and pharmaceutical applications of membrane-associated proteins, biosensors and food science.
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| 3. |
- Cotrim, Camila A., et al.
(författare)
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Heterologous Expression and Biochemical Characterization of the Human Zinc Transporter 1 (ZnT1) and Its Soluble C-Terminal Domain
- 2021
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Ingår i: Frontiers in Chemistry. - : Frontiers Media SA. - 2296-2646. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Human zinc transporter 1 (hZnT1) belongs to the cation diffusion facilitator (CDF) family. It plays a major role in transporting zinc (Zn2+) from the cytoplasm across the plasma membrane and into the extracellular space thereby protecting cells from Zn2+ toxicity. Through homology with other CDF family members, ZnT1 is predicted to contain a transmembrane region and a soluble C-terminal domain though little is known about its biochemistry. Here, we demonstrate that human ZnT1 and a variant can be produced by heterologous expression in Saccharomyces cerevisiae cells and purified in the presence of detergent and cholesteryl hemisuccinate. We show that the purified hZnT1 variant has Zn2+/H+ antiporter activity. Furthermore, we expressed, purified and characterized the soluble C-terminal domain of hZnT1 (hZnT1-CTD) in a bacterial expression system. We found that the hZnT1-CTD melting temperature increases at acidic pH, thus, we used an acetate buffer at pH 4.5 for purifications and concentration of the protein up to 12 mg/mL. Small-angle X-ray scattering analysis of hZnT1-CTD is consistent with the formation of a dimer in solution with a V-shaped core.
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| 4. |
- Pietras, Zuzanna, 1993-, et al.
(författare)
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Technical considerations for small-angle neutron scattering from biological macromolecules in solution : Cross sections, contrasts, instrument setup and measurement
- 2022
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Ingår i: Methods in Enzymology. - : Elsevier. ; , s. 157-189
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Bokkapitel (refereegranskat)abstract
- Small angle scattering affords an approach to evaluate the structure of dilute populations of macromolecules in solution where the measured scattering intensities relate to the distribution of scattering-pair distances within each macromolecule. When small angle neutron scattering (SANS) with contrast variation is employed, additional structural information can be obtained regarding the internal organization of biomacromolecule complexes and assemblies. The technique allows for the components of assemblies to be selectively ‘matched in’ and ‘matched out’ of the scattering profiles due to the different ways the isotopes of hydrogen—protium 1H, and deuterium 2H (or D)—scatter neutrons. The isotopic substitution of 1H for D in the sample enables the controlled variation of the scattering contrasts. A contrast variation experiment requires trade-offs between neutron beam intensity, q-range, wavelength and q-resolution, isotopic labelling levels, sample concentration and path-length, and measurement times. Navigating these competing aspects to find an optimal combination is a daunting task. Here we provide an overview of how to calculate the neutron scattering contrasts of dilute biological macromolecule samples prior to an experiment and how this then informs the approach to configuring SANS instruments and the measurement of a contrast variation series dataset.
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| 5. |
- Shou, Keyun, et al.
(författare)
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Effect of red blood cell shape changes on haemoglobin interactions and dynamics : a neutron scattering study
- 2020
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Ingår i: Royal Society Open Science. - : ROYAL SOC. - 2054-5703. ; 7:10
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Tidskriftsartikel (refereegranskat)abstract
- By using a combination of experimental neutron scattering techniques, it is possible to obtain a statistical perspective on red blood cell (RBC) shape in suspensions, and the inter-relationship with protein interactions and dynamics inside the confinement of the cell membrane. In this study, we examined the ultrastructure of RBC and protein-protein interactions of haemoglobin (Hb) in them using ultra-small-angle neutron scattering and small-angle neutron scattering (SANS). In addition, we used the neutron backscattering method to access Hb motion on the ns time scale and angstrom length scale. Quasi-elastic neutron scattering (QENS) experiments were performed to measure diffusive motion of Hb in RBCs and in an RBC lysate. By using QENS, we probed both internal Hb dynamics and global protein diffusion, on the accessible time scale and length scale by QENS. Shape changes of RBCs and variation of intracellular Hb concentration were induced by addition of the Na+-selective ionophore monensin and the K+-selective one, valinomycin. The experimental SANS and QENS results are discussed within the framework of crowded protein solutions, where free motion of Hb is obstructed by mutual interactions.
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