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  • 1. Alonso-Mori, R.
    et al.
    Asa, K.
    Bergmann, U.
    Brewster, A. S.
    Chatterjee, R.
    Cooper, J. K.
    Frei, H. M.
    Fuller, F. D.
    Goggins, E.
    Gul, S.
    Fukuzawa, H.
    Iablonskyi, D.
    Ibrahim, M.
    Katayama, T.
    Kroll, T.
    Kumagai, Y.
    McClure, B. A.
    Messinger, Johannes
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Motomura, K.
    Nagaya, K.
    Nishiyama, T.
    Saracini, C.
    Sato, Y.
    Sauter, N. K.
    Sokaras, D.
    Takanashi, T.
    Togashi, T.
    Ueda, K.
    Weare, W. W.
    Weng, T-C
    Yabashi, M.
    Yachandra, V. K.
    Young, I. D.
    Zouni, A.
    Kern, J. F.
    Yano, J.
    Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs2016In: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 194, p. 621-638Article in journal (Refereed)
    Abstract [en]

    The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.

  • 2.
    Surowiec, Izabella
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Sartorius Stedim Data Analytics, Tvistevägen 48, 907 36 Umeå, Sweden.
    Skotare, Tomas
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Sjögren, Rickard
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Sartorius Stedim Data Analytics, Tvistevägen 48, 907 36 Umeå, Sweden.
    Gouveia-Figueira, Sandra C.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Orikiiriza, Judy Tatwan
    Bergström, Sven
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Normark, Johan
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry. Sartorius Stedim Data Analytics, Tvistevägen 48, 907 36 Umeå, Sweden.
    Joint and unique multiblock analysis of biological data: multiomics malaria study2019In: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 218, p. 268-283Article in journal (Refereed)
    Abstract [en]

    Modern profiling technologies enable obtaining large amounts of data which can be later used for comprehensive understanding of the studied system. Proper evaluation of such data is challenging, and cannot be faced by bare analysis of separate datasets. Integrated approaches are necessary, because only data integration allows finding correlation trends common for all studied data sets and revealing hidden structures not known a priori. This improves understanding and interpretation of the complex systems. Joint and Unique MultiBlock Analysis (JUMBA) is an analysis method based on the OnPLS-algorithm that decomposes a set of matrices into joint parts containing variation shared with other connected matrices and variation that is unique for each single matrix. Mapping unique variation is important from a data integration perspective, since it certainly cannot be expected that all variation co-varies. In this work we used JUMBA for integrated analysis of lipidomic, metabolomic and oxylipin datasets obtained from profiling of plasma samples from children infected with P. falciparum malaria. P. falciparum is one of the primary contributors to childhood mortality and obstetric complications in the developing world, what makes development of the new diagnostic and prognostic tools, as well as better understanding of the disease, of utmost importance. In presented work JUMBA made it possible to detect already known trends related to disease progression, but also to discover new structures in the data connected to food intake and personal differences in metabolism. By separating the variation in each data set into joint and unique, JUMBA reduced complexity of the analysis, facilitated detection of samples and variables corresponding to specific structures across multiple datasets and by doing this enabled fast interpretation of the studied system. All this makes JUMBA a perfect choice for multiblock analysis of systems biology data.

  • 3.
    Wallgren, Marcus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Beranova, Lenka
    J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
    Pham, Quoc Dat
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Khanh, Linh
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Lidman, Martin
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Procek, Jan
    Institute of Biomedical Engineering and Instrumentation, Wrocław University of Technology, Wrocław, Poland.
    Cyprych, Konrad
    Institute of Biomedical Engineering and Instrumentation, Wrocław University of Technology, Wrocław, Poland.
    Kinnunen, Paavo
    Helsinki Biophysics and Biomembrane Group, Department of Biomedical Engineering and Computational Science, Aalto University, Espoo, Finland.
    Hof, Martin
    J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
    Gröbner, Gerhard
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Impact of oxidized phospholipids on the structural and dynamic organization of phospholipid membranes: a combined DSC and solid state NMR study2013In: Faraday discussions (Online), ISSN 1359-6640, E-ISSN 1364-5498, Vol. 161, p. 499-513Article in journal (Refereed)
    Abstract [en]

    Membranes undergo severe changes under oxidative stress conditions due to the creation of oxidized phospholipid (OxPls) species which possess molecular properties quite different from their parental lipid components. These OxPls play crucial roles in various pathological disorders and their occurrence is involved in the onset of intrinsic apoptosis, a fundamental pathway in programmed mammalian cell death. However, the molecular mechanisms by which these lipids can exert their apoptotic action via their host membranes (e.g. altering membrane protein function) are poorly understood. Therefore, we studied the impact of OxPls on the organization and biophysical properties of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) based lipid membranes by differential scanning calorimetry (DSC) and solid state nuclear magnetic resonance (NMR) spectroscopy. Incorporation of defined OxPls with either a carboxyl group (1-Palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC)) or aldehyde (1-Palmitoyl-(9´oxononanoyl)-sn-glycero-3-phosphocholine (PoxnoPC)) at their truncated sn-2-chain ends enabled us to reveal OxPls species dependent differences. The calorimetric studies revealed significant effects of OxPls on the thermotropic phase behavior of DMPC bilayers, especially at elevated levels where PazePC induced more pronounced effects than PoxnoPC. Temperature dependent changes in the solid state 31P NMR spectra which provided information of the of lipid headgroup region in these mixed membrane system, reflected this complex phase behavior. In the temperature region between 293 K (onset of L-phase) and 298 K two overlapping NMR spectra were visible which reflect the co-existence of two liquid-crystalline lamellar phases with presumably one reflecting OxPls-poor domains and the other OxPls-rich domains. Deconvolution of the DSC profiles also revealed these two partially overlapping thermal events. In addition, also a third thermal, non NMR-visible, event occurred at low temperatures, which mostly likely can be associated with a solid-phase mixing/demixing process of the OxPl-containing membranes. The observed phase transitions were moved to higher temperatures in the presence of heavy water due its condensing effect, where additional wideline 2H NMR studies revealed a complex hydration pattern in the presence of OxPls.

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