uu.seUppsala universitets publikationer
Ändra sökning
Avgränsa sökresultatet
12345 151 - 200 av 219
RefereraExporteraLänk till träfflistan
Permanent länk
Referera
Referensformat
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Annat format
Fler format
Språk
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Annat språk
Fler språk
Utmatningsformat
  • html
  • text
  • asciidoc
  • rtf
Träffar per sida
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sortering
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
  • Standard (Relevans)
  • Författare A-Ö
  • Författare Ö-A
  • Titel A-Ö
  • Titel Ö-A
  • Publikationstyp A-Ö
  • Publikationstyp Ö-A
  • Äldst först
  • Nyast först
  • Skapad (Äldst först)
  • Skapad (Nyast först)
  • Senast uppdaterad (Äldst först)
  • Senast uppdaterad (Nyast först)
  • Disputationsdatum (tidigaste först)
  • Disputationsdatum (senaste först)
Markera
Maxantalet träffar du kan exportera från sökgränssnittet är 250. Vid större uttag använd dig av utsökningar.
  • 151.
    Narayana Reddy, Hemanth Kumar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Structural Studies of Large dsDNA Viruses using Single Particle Methods2019Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Structural studies of large biological assemblies pose a unique problem due to their size, complexity and heterogeneity. Conventional methods like x-ray crystallography, NMR, etc. are limited in their ability to address these issues. To overcome some of these limitations, single particle methods were used. In these methods, each particle image is manipulated individually to find the best possible set of images to reconstruct the 3D structure. The structural studies in this thesis, exploit the advantages of single particle methods. 

    The large data set generated by the SPI study of PR772 provides better statistics about the sample quality due to the use of GDVN, a container-free sample delivery method. By analyzing the diffusion map, we see that the use of GDVNs as a sample delivery method produces wide range of particle sizes owing to the large droplet that are created. 

    The high-resolution structure of bacteriophage PR772 confirmed the speculation about the heteropentameric nature of the penton and revealed the new architecture of the vertex complex consisting of a hetero-pentameric penton formed with three copies of P5 and two copies of P31. The beta propeller region of P2, formed by domains I and II is bound to the N-terminal domain of P5. The structure also reveals new conformations of N-terminal and C-terminal region of P3 which play an important role in particle assembly and structural stability. 

    The study of Melbournevirus revealed the protein composition in a packed particle. The CryoEM structure of Melbournevirus reveals a T=309 capsid with an inner lipid membrane. A dense body was found in the viral particle, a feature not observed in other viruses of the Marseilleviridae family. The density of this body is similar to a nucleic acid-protein complex. This observation, along with the histone-like protein identified during study, suggest genome organization in the viral particle, similar to higher organisms.

    The soft X-ray microscope operated in the water-window shows the progression of the Cedratvirus lurbo infection in the host cell without the use of chemical fixation, staining, sample dehydration or polymer embedding. The study revealed a significant bioconversion from the host cell to the viral particle at later stages of infection.

    Delarbeten
    1. Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source
    Öppna denna publikation i ny flik eller fönster >>Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source
    Visa övriga...
    2017 (Engelska)Ingår i: Scientific Data, E-ISSN 2052-4463, Vol. 4, artikel-id 170079Artikel i tidskrift (Refereegranskat) Published
    Nationell ämneskategori
    Biofysik
    Identifikatorer
    urn:nbn:se:uu:diva-328536 (URN)10.1038/sdata.2017.79 (DOI)000404232100001 ()28654088 (PubMedID)
    Projekt
    eSSENCE
    Tillgänglig från: 2017-06-27 Skapad: 2017-08-25 Senast uppdaterad: 2019-08-25Bibliografiskt granskad
    2. CryoEM of coliphage PR772 reveals the composition & structure of the elusive vertex complex and the capsid architecture.
    Öppna denna publikation i ny flik eller fönster >>CryoEM of coliphage PR772 reveals the composition & structure of the elusive vertex complex and the capsid architecture.
    (Engelska)Ingår i: eLIFE, E-ISSN 2050-084XArtikel i tidskrift (Refereegranskat) Submitted
    Abstract [en]

    Bacteriophage PR772, a member of the Tectiviridae family, has a 70-nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T=25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.

    Nyckelord
    PR772, Phage, Bacteriophage, PRD1, Vertex Complex, Penton, heteropentamer
    Nationell ämneskategori
    Strukturbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-391669 (URN)
    Forskningsfinansiär
    VetenskapsrådetKnut och Alice Wallenbergs StiftelseEU, Europeiska forskningsrådet
    Tillgänglig från: 2019-08-25 Skapad: 2019-08-25 Senast uppdaterad: 2019-08-25
    3. Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly
    Öppna denna publikation i ny flik eller fönster >>Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly
    Visa övriga...
    2018 (Engelska)Ingår i: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 516, s. 239-245, artikel-id S0042-6822(18)30028-XArtikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.

    Nyckelord
    Amoeba, Capsid, Cryo-electron microscopy, Marseilleviridae, Melbournevirus, NCLDV, Protein complex, Structure, Tomography, Virus
    Nationell ämneskategori
    Biofysik
    Identifikatorer
    urn:nbn:se:uu:diva-370071 (URN)10.1016/j.virol.2018.01.021 (DOI)000428004800025 ()29407382 (PubMedID)
    Forskningsfinansiär
    Vetenskapsrådet, 628-20081109 822-2010-6157 822-2012-5260 828-2012-108Knut och Alice Wallenbergs Stiftelse, KAW-2011.081EU, Europeiska forskningsrådet, ERC-291602Stiftelsen för internationalisering av högre utbildning och forskning (STINT), JA2014-5721
    Tillgänglig från: 2018-12-18 Skapad: 2018-12-18 Senast uppdaterad: 2019-08-25Bibliografiskt granskad
    4. Giant DNA virus infection reveals high bioconversion from amoeba to virus
    Öppna denna publikation i ny flik eller fönster >>Giant DNA virus infection reveals high bioconversion from amoeba to virus
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    During the last couple of decades, new discoveries of giant DNA viruses visible under a light microscope and with genome larger than 500 kbp are becoming more and more frequent. Interestingly, about two-thirds of their predicted genes correspond to open reading frames without recognizable database homologs. Herein, we quantitatively investigate viral replication of the newly discovered Lurbovirus to understand what cellular function is retained through the unknown open reading frames. We apply high-resolution soft x-ray microscopy to intact cell systems in their near-native state with high carbon-to-water contrast. New virions produced inside the cell are visible from 12 hours post infection and increase to several hundreds after 48 hours post infection. Due to the large size of the virion, this corresponds to a high bioconversion of 6-12 % from amoebal host to virus. We associate the high bioconversion of large DNA viruses with their large genome that enables complex functionality. The vacuolated structure of the amoebal host disappears when virions are starting to be produced at 12 hours post infection, whereas large circular x-ray-lucent cytoplasmic areas persist that are attributed to viral factories. The nucleus and nucleolus appear unaffected throughout the whole replication cycle, which suggests that nuclear functions are needed for viral replication to occur, whereas other functions are retained in the viral factories in the cytoplasm of the host cell.

    Nyckelord
    dsDNA, lurbo, Cedratvirus, x-ray, microscope
    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-391670 (URN)
    Tillgänglig från: 2019-08-25 Skapad: 2019-08-25 Senast uppdaterad: 2019-08-25
  • 152.
    Naumova, Maria
    et al.
    Paderborn Univ, Dept Chem, D-33098 Paderborn, Germany;Hamburg Univ, Inst Nanaostruktur & Festkorperphys, D-20355 Hamburg, Germany.
    Khakhulin, Dmitry
    Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany;European XFEL GmbH, D-22869 Schenefeld, Germany.
    Rebarz, Mateusz
    Acad Sci Czech Republ, ELI Beamlines, Inst Phys, Prague 18221, Czech Republic.
    Rohrmueller, Martin
    Paderborn Univ, Dept Phys, D-33098 Paderborn, Germany.
    Dicke, Benjamin
    Hamburg Univ, Inst Nanaostruktur & Festkorperphys, D-20355 Hamburg, Germany.
    Biednov, Mykola
    Hamburg Univ, Inst Nanaostruktur & Festkorperphys, D-20355 Hamburg, Germany.
    Britz, Alexander
    Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany;European XFEL GmbH, D-22869 Schenefeld, Germany.
    Espinoza, Shirly
    Acad Sci Czech Republ, ELI Beamlines, Inst Phys, Prague 18221, Czech Republic.
    Grimm-Lebsanft, Benjamin
    Hamburg Univ, Inst Nanaostruktur & Festkorperphys, D-20355 Hamburg, Germany.
    Kloz, Miroslav
    Acad Sci Czech Republ, ELI Beamlines, Inst Phys, Prague 18221, Czech Republic.
    Kretzschmar, Norman
    European Synchrotron Radiat Facil, F-38000 Grenoble, France.
    Neuba, Adam
    Paderborn Univ, Dept Chem, D-33098 Paderborn, Germany.
    Ortmeyer, Jochen
    Paderborn Univ, Dept Chem, D-33098 Paderborn, Germany.
    Schoch, Roland
    Paderborn Univ, Dept Chem, D-33098 Paderborn, Germany.
    Andreasson, Jakob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Acad Sci Czech Republ, ELI Beamlines, Inst Phys, Prague 18221, Czech Republic;Chalmers Univ Technol, Condensed Matter Phys, Dept Phys, Gothenburg, Sweden;DESY, Ctr Free Elect Laser Sci, D-22607 Hamburg, Germany.
    Bauer, Matthias
    Paderborn Univ, Dept Chem, D-33098 Paderborn, Germany.
    Bressler, Christian
    Hamburg Ctr Ultrafast Imaging, D-22761 Hamburg, Germany;European XFEL GmbH, D-22869 Schenefeld, Germany.
    Schmidt, Wolf Gero
    Paderborn Univ, Dept Phys, D-33098 Paderborn, Germany.
    Henkel, Gerald
    Paderborn Univ, Dept Chem, D-33098 Paderborn, Germany.
    Ruebhausen, Michael
    Hamburg Univ, Inst Nanaostruktur & Festkorperphys, D-20355 Hamburg, Germany.
    Structural dynamics upon photoexcitation-induced charge transfer in a dicopper(I)-disulfide complex2018Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, nr 9, s. 6274-6286Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The structural dynamics of charge-transfer states of nitrogen-ligated copper complexes has been extensively investigated in recent years following the development of pump-probe X-ray techniques. In this study we extend this approach towards copper complexes with sulfur coordination and investigate the influence of charge transfer states on the structure of a dicopper(I) complex with coordination by bridging disulfide ligands and additionally tetramethylguanidine units [CuI2(NSSN)(2)](2+). In order to directly observe and refine the photoinduced structural changes in the solvated complex we applied picosecond pump-probe X-ray absorption spectroscopy (XAS) and wide-angle X-ray scattering (WAXS). Additionally, the ultrafast evolution of the electronic excited states was monitored by femtosecond transient absorption spectroscopy in the UV-Vis probe range. DFT calculations were used to predict molecular geometries and electronic structures of the ground and metal-to-ligand charge transfer states with singlet and triplet spin multiplicities, i.e. S-0, (MLCT)-M-1 and (MLCT)-M-3, respectively. Combining these techniques we elucidate the electronic and structural dynamics of the solvated complex upon photoexcitation to the MLCT states. In particular, femtosecond optical transient spectroscopy reveals three distinct timescales of 650 fs, 10 ps and 4100 ps, which were assigned as internal conversion to the ground state (Sn -> S-0), intersystem crossing (MLCT)-M-1 -> (MLCT)-M-3, and subsequent relaxation of the triplet to the ground state, respectively. Experimental data collected using both X-ray techniques are in agreement with the DFT-predicted structure for the triplet state, where coordination bond lengths change and one of the S-S bridges is cleaved, causing the movement of two halves of the molecule relative to each other. Extended X-ray absorption fine structure spectroscopy resolves changes in Cu-ligand bond lengths with precision on the order of 0.01 angstrom, whereas WAXS is sensitive to changes in the global shape related to relative movement of parts of the molecule. The results presented herein widen the knowledge on the electronic and structural dynamics of photoexcited copper-sulfur complexes and demonstrate the potential of combining the pump-probe X-ray absorption and scattering for studies on photoinduced structural dynamics in copper-based coordination complexes.

  • 153. Nelson, A. J.
    et al.
    Toleikis, S.
    Chapman, H.
    Bajt, S.
    Krzywinski, J.
    Chalupsky, J.
    Juha, L.
    Cihelka, J.
    Hajkova, V.
    Vysin, L.
    Burian, T.
    Kozlova, M.
    Fäustlin, R. R.
    Nagler, B.
    Vinko, S. M.
    Whitcher, T.
    Dzelzainis, T.
    Renner, O.
    Saksl, K.
    Khorsand, A. R.
    Heimann, P. A.
    Sobierajski, R.
    Klinger, D.
    Jurek, M.
    Pelka, J.
    Iwan, Bianca
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Andreasson, Jakob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Timneanu, Nicusor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Fajardo, M.
    Wark, J. S.
    Riley, D.
    Tschentscher, T.
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Lee, R. W.
    Soft x-ray free electron laser microfocus for exploring matter under extreme conditions2009Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 17, nr 20, s. 18271-18278Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have focused a beam (BL3) of FLASH (Free-electron LASer in Hamburg: lambda = 13.5 nm, pulse length 15 fs, pulse energy 10-40 mu J, 5Hz) using a fine polished off-axis parabola having a focal length of 270 mm and coated with a Mo/Si multilayer with an initial reflectivity of 67% at 13.5 nm. The OAP was mounted and aligned with a picomotor controlled six-axis gimbal. Beam imprints on poly(methyl methacrylate) -PMMA were used to measure focus and the focused beam was used to create isochoric heating of various slab targets. Results show the focal spot has a diameter of <= 1 mu m. Observations were correlated with simulations of best focus to provide further relevant information.

  • 154.
    Okamoto, Kenta
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Miyazaki, Naoyuki
    Natl Inst Physiol Sci, Okazaki, Aichi, Japan..
    Larsson, Daniel S. D.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Kobayashi, Daisuke
    Natl Inst Infect Dis, Dept Med Entomol, Tokyo, Japan..
    Svenda, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Mühlig, Kerstin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Gunn, Laura H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Isawa, Haruhiko
    Natl Inst Infect Dis, Dept Med Entomol, Tokyo, Japan..
    Kobayashi, Mutsuo
    Natl Inst Infect Dis, Dept Med Entomol, Tokyo, Japan..
    Sawabe, Kyoko
    Natl Inst Infect Dis, Dept Med Entomol, Tokyo, Japan..
    Murata, Kazuyoshi
    Natl Inst Physiol Sci, Okazaki, Aichi, Japan..
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes2016Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, artikel-id 33170Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 angstrom resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 angstrom resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps. Both viruses have an elevated plateau around their icosahedral 5-fold axes, surrounded by a deep canyon. Sequence and structural analysis suggests that this plateau region is mainly composed of the extended C-terminal region of the capsid proteins. In contrast to IMNV, the infectious form of OmRV lacks extensive fibre complexes at its 5-fold axes as directly confirmed by a contrast-enhancement technique, using Zernike phase-contrast cryo-EM. Instead, these fibre complexes are replaced by a short "plug" structure at the five-fold axes of OmRV. OmRV and IMNV have acquired an extracellular phase, and the structures at the five-fold axes may be significant in adaptation to cell-to-cell transmission in metazoan hosts.

  • 155.
    Okamoto, Kenta
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Miyazaki, Naoyuki
    National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585 Japan.
    Reddy, Hemanth K.N.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hantke, Max F
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Maia, Filipe R.N.C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Larsson, Daniel S D
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Abergel, Chantal
    Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille 13288, France.
    Claverie, Jean-Michel
    Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479) Centre National de la Recherche Scientifique & Aix-Marseille University, Marseille 13288, France; Assistance Publique des Hôpitaux de Marseille, La Timone, 13005 Marseille, France.
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Institute of Physics AS CR, v.v.i., Na Slovance 2, 18221 Prague 8, Czech Republic.
    Murata, Kazuyoshi
    National Institute for Physiological Sciences (NIPS), Okazaki, Aichi, 444-8585 Japan.
    Svenda, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly2018Ingår i: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 516, s. 239-245, artikel-id S0042-6822(18)30028-XArtikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.

  • 156.
    Okamoto, Kenta
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Miyazaki, Naoyuki
    NIPS, Okazaki, Aichi 4448585, Japan..
    Song, Chihong
    NIPS, Okazaki, Aichi 4448585, Japan..
    Maia, Filipe
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Reddy, Hemanth K.N.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Abergel, Chantal
    CNRS, UMR 7256, IMM FR 3479, Struct & Genom Informat Lab, F-13288 Marseille, France..
    Claverie, Jean-Michel
    CNRS, UMR 7256, IMM FR 3479, Struct & Genom Informat Lab, F-13288 Marseille, France.;Aix Marseille Univ, F-13288 Marseille, France.;AP HM, F-13005 Marseille, France..
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Inst Phys AS CR, Vvi, Na Slovance 2, Prague 18221 8, Czech Republic..
    Svenda, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Murata, Kazuyoshi
    NIPS, Okazaki, Aichi 4448585, Japan..
    Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy2017Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikel-id 13291Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Pithoviridae giant virus family exhibits the largest viral particle known so far, a prolate spheroid up to 2.5 mu m in length and 0.9 mu m in diameter. These particles show significant variations in size. Little is known about the structure of the intact virion due to technical limitations with conventional electron cryo-microscopy (cryo-EM) when imaging thick specimens. Here we present the intact structure of the giant Pithovirus sibericum particle at near native conditions using high-voltage electron cryo-tomography (cryo-ET) and energy-filtered cryo-EM. We detected a previously undescribed low-density outer layer covering the tegument and a periodical structuring of the fibres in the striated apical cork. Energy-filtered Zernike phase-contrast cryo-EM images show distinct substructures inside the particles, implicating an internal compartmentalisation. The density of the interior volume of Pithovirus particles is three quarters lower than that of the Mimivirus. However, it is remarkably high given that the 600 kbp Pithovirus genome is only half the size of the Mimivirus genome and is packaged in a volume up to 100 times larger. These observations suggest that the interior is densely packed with macromolecules in addition to the genomic nucleic acid.

  • 157.
    Pabis, Anna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Risso, Valeria A.
    Univ Granada, Fac Ciencias, Dept Quim Fis, E-18071 Granada, Spain..
    Sanchez-Ruiz, Jose M.
    Univ Granada, Fac Ciencias, Dept Quim Fis, E-18071 Granada, Spain..
    Kamerlin, Shina C. Lynn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Strukturbiologi.
    Cooperativity and flexibility in enzyme evolution2018Ingår i: Current opinion in structural biology, ISSN 0959-440X, E-ISSN 1879-033X, Vol. 48, s. 83-92Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Enzymes are flexible catalysts, and there has been substantial discussion about the extent to which this flexibility contributes to their catalytic efficiency. What has been significantly less discussed is the extent to which this flexibility contributes to their evolvability. Despite this, recent years have seen an increasing number of both experimental and computational studies that demonstrate that cooperativity and flexibility play significant roles in enzyme innovation. This review covers key developments in the field that emphasize the importance of enzyme dynamics not just to the evolution of new enzyme function(s), but also as a property that can be harnessed in the design of new artificial enzymes.

  • 158. Park, Hyung Joo
    et al.
    Loh, N. Duane
    Sierra, Raymond G.
    Hampton, Christina Y.
    Starodub, Dmitri
    Martin, Andrew V.
    Barty, Anton
    Aquila, Andrew
    Schulz, Joachim
    Steinbrener, Jan
    Shoeman, Robert L.
    Lomb, Lukas
    Kassemeyer, Stephan
    Bostedt, Christoph
    Bozek, John
    Epp, Sascha W.
    Erk, Benjamin
    Hartmann, Robert
    Rolles, Daniel
    Rudenko, Artem
    Rudek, Benedikt
    Foucar, Lutz
    Kimmel, Nils
    Weidenspointner, Georg
    Hauser, Guenter
    Holl, Peter
    Pedersoli, Emanuele
    Liang, Mengning
    Hunter, Mark S.
    Gumprecht, Lars
    Coppola, Nicola
    Wunderer, Cornelia
    Graafsma, Heinz
    Maia, Filipe R. N. C.
    Ekeberg, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hantke, Max Felix
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Fleckenstein, Holger
    Hirsemann, Helmut
    Nass, Karol
    Tobias, Herbert J.
    Farquar, George R.
    Benner, W. Henry
    Hau-Riege, Stefan
    Reich, Christian
    Hartmann, Andreas
    Soltau, Heike
    Marchesini, Stefano
    Bajt, Sasa
    Barthelmess, Miriam
    Strueder, Lothar
    Ullrich, Joachim
    Bucksbaum, Philip
    Frank, Matthias
    Schlichting, Ilme
    Chapman, Henry N.
    Bogan, Michael J.
    Elser, Veit
    Toward unsupervised single-shot diffractive imaging of heterogeneous particles using X-ray free-electron lasers2013Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 21, nr 23, s. 28729-28742Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Single shot diffraction imaging experiments via X-ray free-electron lasers can generate as many as hundreds of thousands of diffraction patterns of scattering objects. Recovering the real space contrast of a scattering object from these patterns currently requires a reconstruction process with user guidance in a number of steps, introducing severe bottlenecks in data processing. We present a series of measures that replace user guidance with algorithms that reconstruct contrasts in an unsupervised fashion. We demonstrate the feasibility of automating the reconstruction process by generating hundreds of contrasts obtained from soot particle diffraction experiments.

  • 159.
    Parkinson, Dilworth Y.
    et al.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Beattie, Keith
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Chen, Xian
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Correa, Joaquin
    Natl Energy Res Sci Comp Ctr, Berkeley, CA 94720 USA..
    Dart, Eli
    Energy Sci Network, Berkeley, CA 94720 USA..
    Daurer, Benedikt J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Deslippe, Jack R.
    Natl Energy Res Sci Comp Ctr, Berkeley, CA 94720 USA..
    Hexemer, Alexander
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Krishnan, Harinarayan
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    MacDowell, Alastair A.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Marchesini, Stefano
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Padmore, Howard A.
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Patton, Simon J.
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Perciano, Talita
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Sethian, James A.
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Math, Berkeley, CA 94720 USA..
    Shapiro, David
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Stromsness, Rune
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Tamura, Nobumichi
    Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA..
    Tierney, Brian L.
    Energy Sci Network, Berkeley, CA 94720 USA..
    Tull, Craig E.
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Ushizima, Daniela
    Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA 94720 USA..
    Real-Time Data-Intensive Computing2016Ingår i: Proceedings Of The 12Th International Conference On Synchrotron Radiation Instrumentation (SRI2015), 2016, artikel-id 050001Konferensbidrag (Refereegranskat)
    Abstract [en]

    Today users visit synchrotrons as sources of understanding and discovery-not as sources of just light, and not as sources of data. To achieve this, the synchrotron facilities frequently provide not just light but often the entire end station and increasingly, advanced computational facilities that can reduce terabytes of data into a form that can reveal a new key insight. The Advanced Light Source (ALS) has partnered with high performance computing, fast networking, and applied mathematics groups to create a "super-facility", giving users simultaneous access to the experimental, computational, and algorithmic resources to make this possible. This combination forms an efficient closed loop, where data-despite its high rate and volume-is transferred and processed immediately and automatically on appropriate computing resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beamtime. We will describe our work at the ALS ptychography, scattering, micro-diffraction, and micro-tomography beamlines.

  • 160.
    Passoni, Matteo
    et al.
    Politecnico di Milano.
    Zani, Alessandro
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik. Politecnico di Milano.
    Sgattoni, Andrea
    Politecnico di Milano.
    Dellasega, David
    Politecnico di Milano.
    Macchi, Andrea
    Università di Pisa.
    Prencipe, Irene
    Politecnico di Milano.
    Floquet, Vincent
    CEA Saclay.
    Martin, Philippe
    CEA Saclay.
    Liseykina, Tatiana
    Universität Rostock.
    Ceccotti, Tiberio
    CEA Saclay.
    Energetic ions at moderate laser intensities using foam-based multi-layered targets2014Ingår i: Plasma Physics and Controlled Fusion, ISSN 0741-3335, E-ISSN 1361-6587, Vol. 56, nr 4, s. 045001-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The experimental feasibility of the laser-driven ion acceleration concept with multi-layered,foam-based targets has been investigated. Targets with the required features have beenproduced and characterized, exploiting the potential of the pulsed laser deposition technique.In the intensity range 1016–1017 Wcm−2, they allow us to obtain maximum proton energies2–3 times higher compared to bare solid targets, able to reach and surpass the MeV range withboth low and ultrahigh contrast pulses. The results of two-dimensional particle-in-cellsimulations, supporting the interpretation of the experimental results, and directions to exploitthe concept also at ultrahigh intensities, are presented.

  • 161.
    Patriksson, Alexandra
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    van der Spoel, David
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    A temperature predictor for parallel tempering simulations2008Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, nr 15, s. 2073-2077Artikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
    Abstract [en]

    An algorithm is proposed that generates a set of temperatures for use in parallel tempering simulations ( also known as temperature- replica exchange molecular dynamics simulations) of proteins to obtain a desired exchange probability P-des. The input consists of the number of protein atoms and water molecules in the system, information about the use of constraints and virtual sites and the lower temperature limits. The temperatures generated yield probabilities which are very close to Pdes ( correlation 97%), independent of force. field and over a wide temperature range.

  • 162. Pedersoli, E.
    et al.
    Loh, N. D.
    Capotondi, F.
    Hampton, C. Y.
    Sierra, R. G.
    Starodub, D.
    Bostedt, C.
    Bozek, J.
    Nelson, A. J.
    Aslam, M.
    Li, S.
    Dravid, V. P.
    Martin, A. V.
    Aquila, A.
    Barty, A.
    Fleckenstein, H.
    Gumprecht, L.
    Liang, M.
    Nass, K.
    Schulz, J.
    White, T. A.
    Coppola, N.
    Bajt, S.
    Barthelmess, M.
    Graafsma, H.
    Hirsemann, H.
    Wunderer, C.
    Epp, S. W.
    Erk, B.
    Rudek, B.
    Rudenko, A.
    Foucar, L.
    Kassemeyer, S.
    Lomb, L.
    Rolles, D.
    Shoeman, R. L.
    Steinbrener, J.
    Hartmann, R.
    Hartmann, A.
    Hauser, G.
    Holl, P.
    Kimmel, N.
    Reich, C.
    Soltau, H.
    Weidenspointner, G.
    Benner, W. H.
    Farquar, G. R.
    Hau-Riege, S. P.
    Hunter, M. S.
    Ekeberg, Tomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Hantke, Max
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Tobias, H. J.
    Marchesini, S.
    Frank, M.
    Strueder, L.
    Schlichting, I.
    Ullrich, J.
    Chapman, H. N.
    Bucksbaum, P. H.
    Kiskinova, M.
    Bogan, M. J.
    Mesoscale morphology of airborne core-shell nanoparticle clusters: x-ray laser coherent diffraction imaging2013Ingår i: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 46, nr 16 SI, s. 164033-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Unraveling the complex morphology of functional materials like core-shell nanoparticles and its evolution in different environments is still a challenge. Only recently has the single-particle coherent diffraction imaging (CDI), enabled by the ultrabright femtosecond free-electron laser pulses, provided breakthroughs in understanding mesoscopic morphology of nanoparticulate matter. Here, we report the first CDI results for Co@SiO2 core-shell nanoparticles randomly clustered in large airborne aggregates, obtained using the x-ray free-electron laser at the Linac Coherent Light Source. Our experimental results compare favourably with simulated diffraction patterns for clustered Co@SiO2 nanoparticles with similar to 10 nm core diameter and similar to 30 nm shell outer diameter, which confirms the ability to resolve the mesoscale morphology of complex metastable structures. The findings in this first morphological study of core-shell nanomaterials are a solid base for future time-resolved studies of dynamic phenomena in complex nanoparticulate matter using x-ray lasers.

  • 163. Pedersoli, Emanuele
    et al.
    Capotondi, Flavio
    Cocco, Daniele
    Zangrando, Marco
    Kaulich, Burkhard
    Menk, Ralf H.
    Locatelli, Andrea
    Mentes, Tevfik O.
    Spezzani, Carlo
    Sandrin, Gilio
    Bacescu, Daniel M.
    Kiskinova, Maya
    Bajt, Sasa
    Barthelmess, Miriam
    Barty, Anton
    Schulz, Joachim
    Gumprecht, Lars
    Chapman, Henry N.
    Nelson, A. J.
    Frank, Matthias
    Pivovaroff, Michael J.
    Woods, Bruce W.
    Bogan, Michael J.
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Multipurpose modular experimental station for the DiProI beamline of Fermi@Elettra free electron laser2011Ingår i: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 82, nr 4, s. 043711-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a compact modular apparatus with a flexible design that will be operated at the DiProI beamline of the Fermi@Elettra free electron laser (FEL) for performing static and time-resolved coherent diffraction imaging experiments, taking advantage of the full coherence and variable polarization of the short seeded FEL pulses. The apparatus has been assembled and the potential of the experimental setup is demonstrated by commissioning tests with coherent synchrotron radiation. This multipurpose experimental station will be open to general users after installation at the Fermi@Elettra free electron laser in 2011.

  • 164.
    Philippe, Nadege
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Legendre, Matthieu
    Doutre, Gabriel
    Coute, Yohann
    Poirot, Olivier
    Lescot, Magali
    Arslan, Defne
    Seltzer, Virginie
    Bertaux, Lionel
    Bruley, Christophe
    Garin, Jerome
    Claverie, Jean-Michel
    Abergel, Chantal
    Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes2013Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 341, nr 6143, s. 281-286Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated a reappraisal of the upper limits of the viral world, both in terms of particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions typical of parasitic bacteria. The diversity of these giant viruses (the Megaviridae) was assessed by sampling a variety of aquatic environments and their associated sediments worldwide. We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the first members of the proposed "Pandoravirus" genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study.

  • 165.
    Pietrini, Alberto
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Statistical processing of Flash X-ray Imaging of protein complexes2019Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Flash X-ray Imaging (FXI) at X-ray Free Electron Lasers (XFELs) is a promising technique that permits the investigation of the 3D structure of molecules without the need for crystallization, by diffracting on single individual sample particles.

    In the past few years, some success has been achieved by using FXI on quite large biological complexes (40 nm-1 μm in diameter size). Still, the desired dream-goal of imaging a single individual of a molecule or a protein complex (<15 nm in diameter size) has not been reached yet. The main issue that prevented us from a complete success has been the low signal strength, almost comparable to background noise. That is particularly true for experiments performed at the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS).

    In this thesis, we provide a brief review of the CXI instrument (focusing on experiments there performed) and present a statistical method to deal with low signal-to-noise ratios. We take into account a variety of biological particles, showing the benefits of estimating a background model from sample data and using that for processing said data. Moreover, we present the results of some computer simulations in order to explore the limits and potentials of the proposed approach.

    Last, we show another method (named COACS) that, being fed with the previous findings from the background model, helps obtaining clearer results in the phase retrieval problem.

    Delarbeten
    1. Artifact reduction in the CSPAD detectors used for LCLS experiments
    Öppna denna publikation i ny flik eller fönster >>Artifact reduction in the CSPAD detectors used for LCLS experiments
    2017 (Engelska)Ingår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, s. 1092-1097Artikel i tidskrift (Refereegranskat) Published
    Nationell ämneskategori
    Biofysik
    Identifikatorer
    urn:nbn:se:uu:diva-328543 (URN)10.1107/S160057751701058X (DOI)000408902800025 ()28862634 (PubMedID)
    Projekt
    eSSENCE
    Tillgänglig från: 2017-07-18 Skapad: 2017-08-25 Senast uppdaterad: 2019-01-14Bibliografiskt granskad
    2. A statistical approach to detect protein complexes at X-ray free electron laser facilities
    Öppna denna publikation i ny flik eller fönster >>A statistical approach to detect protein complexes at X-ray free electron laser facilities
    Visa övriga...
    2018 (Engelska)Ingår i: Communications Physics, E-ISSN 2399-3650, Vol. 1, s. 92:1-11, artikel-id 92Artikel i tidskrift (Refereegranskat) Published
    Nationell ämneskategori
    Biofysik
    Identifikatorer
    urn:nbn:se:uu:diva-369876 (URN)10.1038/s42005-018-0092-6 (DOI)000452676300003 ()
    Projekt
    eSSENCE
    Tillgänglig från: 2018-12-07 Skapad: 2018-12-17 Senast uppdaterad: 2019-05-06Bibliografiskt granskad
    3. Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy
    Öppna denna publikation i ny flik eller fönster >>Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy
    2018 (Engelska)Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 26, s. 24422-24443Artikel i tidskrift (Refereegranskat) Published
    Nationell ämneskategori
    Beräkningsmatematik Biofysik
    Identifikatorer
    urn:nbn:se:uu:diva-360037 (URN)10.1364/OE.26.024422 (DOI)000444705000012 ()30469561 (PubMedID)
    Projekt
    eSSENCE
    Tillgänglig från: 2018-09-05 Skapad: 2018-09-09 Senast uppdaterad: 2019-01-14Bibliografiskt granskad
  • 166.
    Pietrini, Alberto
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Bielecki, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Timneanu, Nicusor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Hantke, Max F.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Andreasson, Jakob
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Loh, N. Duane
    Larsson, Daniel S. D.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Boutet, Sébastien
    Hajdu, Janos
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Maia, Filipe R. N. C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Nettelblad, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    A statistical approach to detect protein complexes at X-ray free electron laser facilities2018Ingår i: Communications Physics, E-ISSN 2399-3650, Vol. 1, s. 92:1-11, artikel-id 92Artikel i tidskrift (Refereegranskat)
  • 167.
    Pietrini, Alberto
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Nettelblad, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Artifact reduction in the CSPAD detectors used for LCLS experiments2017Ingår i: Journal of Synchrotron Radiation, ISSN 0909-0495, E-ISSN 1600-5775, Vol. 24, s. 1092-1097Artikel i tidskrift (Refereegranskat)
  • 168.
    Pietrini, Alberto
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Nettelblad, Carl
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Using convex optimization of autocorrelation with constrained support and windowing for improved phase retrieval accuracy2018Ingår i: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 26, s. 24422-24443Artikel i tidskrift (Refereegranskat)
  • 169.
    Popp, David
    et al.
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Loh, N. Duane
    Natl Univ Singapore, Dept Phys, Singapore 117557, Singapore.;Natl Univ Singapore, Ctr BioImaging Sci, Singapore 117546, Singapore..
    Zorgati, Habiba
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.;Natl Univ Singapore, Dept Biochem, Singapore 117597, Singapore..
    Ghoshdastider, Umesh
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Liow, Lu Ting
    Natl Univ Singapore, Dept Med, Singapore 119074, Singapore..
    Ivanova, Magdalena I.
    Univ Michigan, Dept Neurol, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA..
    Larsson, Mårten
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.
    DePonte, Daniel P.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Bean, Richard
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;European XFEL GmbH, D-22761 Hamburg, Germany..
    Beyerlein, Kenneth R.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Gati, Cornelius
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Oberthuer, Dominik
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Inst Biochem & Mol Biol, D-22607 Hamburg, Germany..
    Arnlund, David
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Branden, Gisela
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Berntsen, Peter
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Cascio, Duilio
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Chavas, Leonard M. G.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chen, Joe P. J.
    Univ Canterbury, Computat Imaging Grp, Dept Elect & Comp Engn, Christchurch, New Zealand.;Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA..
    Ding, Ke
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore..
    Fleckenstein, Holger
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Gumprecht, Lars
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Harimoorthy, Rajiv
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Mossou, Estelle
    Inst Laue Langevin, F-38000 Grenoble, France.;Keele Univ, EPSAM ISTM, Keele ST5 5BG, Staffs, England..
    Sawaya, Michael R.
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Brewster, Aaron S.
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA..
    Hattne, Johan
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA.;Howard Hughes Med Inst, Janelia Res Campus,19700 Helix Dr, Ashburn, VA 20147 USA..
    Sauter, Nicholas K.
    Lawrence Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA 94720 USA..
    Seibert, Marvin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Seuring, Carolin
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Stellato, Francesco
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Tilp, Thomas
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Eisenberg, David S.
    Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA..
    Messerschmidt, Marc
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Williams, Garth J.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Koglin, Jason E.
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Makowski, Lee
    Northeastern Univ, Dept Bioengn, 360 Huntington Ave, Boston, MA 02115 USA..
    Millane, Rick P.
    Univ Canterbury, Computat Imaging Grp, Dept Elect & Comp Engn, Christchurch, New Zealand..
    Forsyth, Trevor
    Inst Laue Langevin, F-38000 Grenoble, France.;Keele Univ, EPSAM ISTM, Keele ST5 5BG, Staffs, England..
    Boutet, Sebastien
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    White, Thomas A.
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Barty, Anton
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Chapman, Henry
    DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany.;Univ Hamburg, Dept Phys, Luruper Chaussee 149, D-22607 Hamburg, Germany..
    Chen, Swaine L.
    Natl Univ Singapore, Dept Med, Singapore 119074, Singapore.;ASTAR, Biopolis, Genome Inst Singapore, Singapore 138672, Singapore..
    Liang, Mengning
    SLAC Natl Accelerator Lab, Linac Coherent Light Source, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA.;DESY, Ctr Free Electron Laser Sci, Notkestr 85, D-22607 Hamburg, Germany..
    Neutze, Richard
    Univ Gothenburg, Dept Chem & Mol Biol, S-40530 Gothenburg, Sweden..
    Robinson, Robert C.
    ASTAR, Inst Mol & Cell Biol, Biopolis, Singapore 138673, Singapore.;Natl Univ Singapore, Dept Biochem, Singapore 117597, Singapore.;Okayama Univ, Res Inst Interdisciplinary Sci, Okayama 7008530, Japan..
    Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser2017Ingår i: CYTOSKELETON, ISSN 1949-3584, Vol. 74, nr 12, s. 472-481Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked -strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual -synuclein amyloids.

  • 170.
    R. N. C. Maia, Filipe
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Ultrafast Coherent X-ray Diffractive Nanoimaging2010Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    X-ray lasers are creating unprecedented research opportunities in physics,chemistry and biology. The peak brightness of these lasers exceeds presentsynchrotrons by 1010, the coherence degeneracy parameters exceedsynchrotrons by 109, and the time resolution is 105 times better. In theduration of a single flash, the beam focused to a micron-sized spot has the samepower density as all the sunlight hitting the Earth, focused to a millimetresquare. Ultrafast coherent X-ray diffractive imaging (CXDI) with X-ray lasers exploitsthese unique properties of X-ray lasers to obtain high-resolution structures fornon-crystalline biological (and other) objects. In such an experiment, thesample is quickly vaporised, but not before sufficient scattered light can berecorded. The continuous diffraction pattern can then be phased and thestructure of a more or less undamaged sample recovered% (speed of light vs. speed of a shock wave).This thesis presents results from the first ultrafast X-ray diffractive imagingexperiments with linear accelerator-driven free-electron lasers and fromoptically-driven table-top X-ray lasers. It also explores the possibility ofinvestigating phase transitions in crystals by X-ray lasers. An important problem with ultrafast CXDI of small samples such as single proteinmolecules is that the signal from a single measurement will be small, requiringsignal enhancement by averaging over multiple equivalent samples. We present anumerical investigation of the problems, including the case where samplemolecules are not exactly identical, and propose tentative solutions. A new software package (Hawk) has been developed for data processing and imagereconstruction. Hawk is the first publicly available software package in thisarea, and it is released as an open source software with the aspiration offostering the development of this field.

    Delarbeten
    1. Femtosecond diffractive imaging with a soft-X-ray free-electron laser
    Öppna denna publikation i ny flik eller fönster >>Femtosecond diffractive imaging with a soft-X-ray free-electron laser
    Visa övriga...
    2006 (Engelska)Ingår i: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 2, nr 12, s. 839-843Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Theory predicts(1-4) that, with an ultrashort and extremely bright coherent X-ray pulse, a single diffraction pattern may be recorded from a large macromolecule, a virus or a cell before the sample explodes and turns into a plasma. Here we report the first experimental demonstration of this principle using the FLASH soft-X-ray free-electron laser. An intense 25 fs, 4 x 10(13) W cm(-2) pulse, containing 10(12) photons at 32 nm wavelength, produced a coherent diffraction pattern from a nanostructured non-periodic object, before destroying it at 60,000 K. A novel X-ray camera assured single-photon detection sensitivity by filtering out parasitic scattering and plasma radiation. The reconstructed image, obtained directly from the coherent pattern by phase retrieval through oversampling(5-9), shows no measurable damage, and is reconstructed at the diffraction-limited resolution. A three-dimensional data set may be assembled from such images when copies of a reproducible sample are exposed to the beam one by one(10).

    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-24416 (URN)10.1038/nphys461 (DOI)000242478000021 ()
    Tillgänglig från: 2007-02-05 Skapad: 2007-02-05 Senast uppdaterad: 2017-12-07Bibliografiskt granskad
    2. Structural studies of melting on the picosecond time scale
    Öppna denna publikation i ny flik eller fönster >>Structural studies of melting on the picosecond time scale
    2008 (Engelska)Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, nr 42, s. 6344-6349Artikel, forskningsöversikt (Refereegranskat) Published
    Abstract [en]

    Ultrafast structural studies of laser-induced melting have demonstrated that the solid-liquid phase transition can take place on a picosecond time scale in a variety of materials. Experimental studies using ångström wavelength X-rays from the sub-picosecond pulse source at Stanford (now retired) on non-thermal melting of semi-conductors, such as indium antimonide, employed the decay of a single Bragg-peak to measure the time component of the phase transition. These materials were found to start melting within one picosecond after the laser pulse. Recent computer simulations have described the thermal melting of ice induced by an infrared laser pulse. Here it was shown that melting can happen within a few picoseconds, somewhat slower than non-thermal melting in semi-conductors. These computer simulations are compatible with spectroscopy experiments on ice-melting, demonstrating that simulations form a very powerful complement to experiments targeting the process of phase-transitions. Here we present an overview of recent experimental and theoretical studies of melting, as well as new simulations of ice-melting where the effect of the size of the crystal on scattering is studied. Based on simulations of a near-macroscopic crystal, we predict the decay of the most intense Bragg peaks of ice following heating by laser pulse, by modeling the scattering from the melting sample in the simulations.

    Nationell ämneskategori
    Fysik Kemi Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-121924 (URN)10.1039/b807550f (DOI)000260485600001 ()18972022 (PubMedID)
    Tillgänglig från: 2010-03-31 Skapad: 2010-03-31 Senast uppdaterad: 2017-12-12Bibliografiskt granskad
    3. Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source
    Öppna denna publikation i ny flik eller fönster >>Single-Shot Diffractive Imaging with a Table-Top Femtosecond Soft X-Ray Laser-Harmonics Source
    Visa övriga...
    2009 (Engelska)Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 103, nr 2, s. 028104-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Coherent x-ray diffractive imaging is a powerful method for studies on   nonperiodic structures on the nanoscale. Access to femtosecond dynamics   in major physical, chemical, and biological processes requires   single-shot diffraction data. Up to now, this has been limited to   intense coherent pulses from a free electron laser. Here we show that   laser-driven ultrashort x-ray sources offer a comparatively inexpensive  alternative. We present measurements of single-shot diffraction patterns from isolated nano-objects with a single 20 fs pulse from a   table-top high-harmonic x-ray laser. Images were reconstructed with a   resolution of 119 nm from the single shot and 62 nm from multiple shots.

    Nationell ämneskategori
    Fysik
    Identifikatorer
    urn:nbn:se:uu:diva-121910 (URN)10.1103/PhysRevLett.103.028104 (DOI)000267887800065 ()
    Tillgänglig från: 2010-03-31 Skapad: 2010-03-31 Senast uppdaterad: 2017-12-12Bibliografiskt granskad
    4. Structural variability and the incoherent addition of scattered intensities in single-particle diffraction
    Öppna denna publikation i ny flik eller fönster >>Structural variability and the incoherent addition of scattered intensities in single-particle diffraction