| 1. |
- Canelas, A.B., et al.
(författare)
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Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains
- 2010
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 1:9
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Tidskriftsartikel (refereegranskat)abstract
- The field of systems biology is often held back by difficulties in obtaining comprehensive, high-quality, quantitative data sets. In this paper, we undertook an interlaboratory effort to generate such a data set for a very large number of cellular components in the yeast Saccharomyces cerevisiae, a widely used model organism that is also used in the production of fuels, chemicals, food ingredients and pharmaceuticals. With the current focus on biofuels and sustainability, there is much interest in harnessing this species as a general cell factory. In this study, we characterized two yeast strains, under two standard growth conditions. We ensured the high quality of the experimental data by evaluating a wide range of sampling and analytical techniques. Here we show significant differences in the maximum specific growth rate and biomass yield between the two strains. On the basis of the integrated analysis of the high-throughput data, we hypothesize that differences in phenotype are due to differences in protein metabolism.
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| 2. |
- Li, Juan, et al.
(författare)
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Ouabain protects against adverse developmental programming of the kidney
- 2010
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 1, s. 42-
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Tidskriftsartikel (refereegranskat)abstract
- The kidney is extraordinarily sensitive to adverse fetal programming. Malnutrition, the most common form of developmental challenge, retards the formation of functional units, the nephrons. The resulting low nephron endowment increases susceptibility to renal injury and disease. Using explanted rat embryonic kidneys, we found that ouabain, the Na, K-ATPase ligand, triggers a calcium-nuclear factor-kappa B signal, which protects kidney development from adverse effects of malnutrition. To mimic malnutrition, kidneys were serum deprived for 24 h. This resulted in severe retardation of nephron formation and a robust increase in apoptosis. In ouabain-exposed kidneys, no adverse effects of serum deprivation were observed. Proof of principle that ouabain rescues development of embryonic kidneys exposed to malnutrition was obtained from studies on pregnant rats given a low-protein diet and treated with ouabain or vehicle throughout pregnancy. Thus, we have identified a survival signal and a feasible therapeutic tool to prevent adverse programming of kidney development.
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| 3. |
- Olsson, Ulrika, et al.
(författare)
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Overlap between folding and functional energy landscapes for adenylate kinase conformational change
- 2010
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 1:8, s. 111-
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Tidskriftsartikel (refereegranskat)abstract
- Enzyme function is often dependent on fluctuations between inactive and active structural ensembles. Adenylate kinase isolated from Escherichia coli (AK(e)) is a small phosphotransfer enzyme in which interconversion between inactive (open) and active (closed) conformations is rate limiting for catalysis. AK(e) has a modular three-dimensional architecture with two flexible substrate-binding domains that interact with the substrates AMP, ADP and ATP. Here, we show by using a combination of biophysical and mutagenic approaches that the interconversion between open and closed states of the ATP-binding subdomain involves partial subdomain unfolding/refolding in an otherwise folded enzyme. These results provide a novel and, possibly general, molecular mechanism for the switch between open and closed conformations in AK(e).
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| 4. |
- Saline, Maria, et al.
(författare)
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The structure of superantigen complexed with TCR and MHC reveals novel insights into superantigenic T cell activation.
- 2010
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Ingår i: Nature communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 1:8
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Tidskriftsartikel (refereegranskat)abstract
- Superantigens (SAgs) are bacterial toxins that interact with immunoreceptors, T cell receptor (TCR) and major histocompatibility complex (MHC) class II, conventionally through the variable β-domain of TCR (TCRVβ). They induce a massive release of cytokines, which can lead to diseases such as food poisoning and toxic shock syndrome. In this study, we report the X-ray structure of the ternary complex between staphylococcal enterotoxin H (SEH) and its human receptors, MHC class II and TCR. The structure demonstrates that SEH predominantly interacts with the variable α-domain of TCR (TCRVα), which is supported by nuclear magnetic resonance (NMR) analyses. Furthermore, there is no contact between MHC and TCR upon complex formation. Structural analyses suggest that the major contact points to TCRVα are conserved among other bacterial SAgs. Consequently, a new dimension of SAg biology emerges, suggesting that in addition to the conventional interactions with the TCRVβ domain, SAgs can also activate T cells through the TCRVα domain.
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| 5. |
- Struyf, Eric, et al.
(författare)
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Historical land use change has lowered terrestrial silica mobilization
- 2010
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- Continental export of Si to the coastal zone is closely linked to the ocean carbon sink and to the dynamics of phytoplankton blooms in coastal ecosystems. Presently, however, the impact of human cultivation of the landscape on terrestrial Si fluxes remains unquantified and is not incorporated in models for terrestrial Si mobilization. In this paper, we show that land use is the most important controlling factor of Si mobilization in temperate European watersheds, with sustained cultivation (> 250 years) of formerly forested areas leading to a twofold to threefold decrease in baseflow delivery of Si. This is a breakthrough in our understanding of the biogeochemical Si cycle: it shows that human cultivation of the landscape should be recognized as an important controlling factor of terrestrial Si fluxes.
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| 6. |
- Utko, Pawel, et al.
(författare)
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Nanoelectromechanical coupling in fullerene peapods probed by resonant electrical transport experiments
- 2010
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 1
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Tidskriftsartikel (refereegranskat)abstract
- Fullerene peapods, which are carbon nanotubes encapsulating fullerene molecules, can offer enhanced functionality with respect to empty nanotubes. Their prospective applications include, for example, data storage devices, single-electron transistors and spin-qubit arrays for quantum computing. However, the present incomplete understanding of how a nanotube is affected by entrapped fullerenes is an obstacle for peapods to reach their full potential in nanoscale electronic applications. In this paper, we investigate the effect of C60 fullerenes on low-temperature electron transport through peapod quantum dots. Compared with empty nanotubes, we find an abnormal temperature dependence of Coulomb blockade oscillations, indicating the presence of a nanoelectromechanical coupling between electronic states of the nanotube and mechanical vibrations of fullerenes. This provides a method to detect the C60 presence and to probe the interplay between electrical and mechanical excitations in peapods, which thus emerge as a new class of nanoelectromechanical systems.
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