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Seibert, Marvin
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Publications (10 of 60) Show all publications
Reddy, H. K. N., Yoon, C. H., Aquila, A., Awel, S., Ayyer, K., Barty, A., . . . Xavier Paulraj, L. (2017). Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source. Scientific Data, 4, Article ID 170079.
Open this publication in new window or tab >>Coherent soft X-ray diffraction imaging of Coliphage PR772 at the Linac coherent light source
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2017 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 4, 170079Article in journal (Refereed) Published
Abstract [en]

Single-particle diffraction from X-ray Free Electron Lasers offers the potential for molecular structure determination without the need for crystallization. In an effort to further develop the technique, we present a dataset of coherent soft X-ray diffraction images of Coliphage PR772 virus, collected at the Atomic Molecular Optics (AMO) beamline with pnCCD detectors in the LAMP instrument at the Linac Coherent Light Source. The diameter of PR772 ranges from 65-70 nm, which is considerably smaller than the previously reported similar to 600 nm diameter Mimivirus. This reflects continued progress in XFEL-based single-particle imaging towards the single molecular imaging regime. The data set contains significantly more single particle hits than collected in previous experiments, enabling the development of improved statistical analysis, reconstruction algorithms, and quantitative metrics to determine resolution and self-consistency.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-328536 (URN)10.1038/sdata.2017.79 (DOI)000404232100001 ()28654088 (PubMedID)
Projects
eSSENCE
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilThe Swedish Foundation for International Cooperation in Research and Higher Education (STINT)
Available from: 2017-06-27 Created: 2017-08-25 Last updated: 2017-11-29Bibliographically approved
Daurer, B. J., Okamoto, K., Bielecki, J., Maia, F. R. .., Mühlig, K., Seibert, M. M., . . . Larsson, D. S. D. (2017). Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses. IUCrJ, 4(3), 251-262.
Open this publication in new window or tab >>Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
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2017 (English)In: IUCrJ, ISSN 0972-6918, E-ISSN 2052-2525, Vol. 4, no 3, 251-262 p.Article in journal (Refereed) Published
Abstract [en]

This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of similar to 40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from similar to 35 to similar to 300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 * 10(12) photons per mu m(2) per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.

Keyword
X-ray diffraction, free-electron laser, flash X-ray imaging, diffraction before destruction, virus, Omono River virus, OmRV
National Category
Chemical Sciences Biophysics
Identifiers
urn:nbn:se:uu:diva-323439 (URN)10.1107/S2052252517003591 (DOI)000400460500008 ()28512572 (PubMedID)
Projects
eSSENCE
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilSwedish Foundation for Strategic Research The Swedish Foundation for International Cooperation in Research and Higher Education (STINT)Helge Ax:son Johnsons stiftelse
Available from: 2017-11-14 Created: 2017-11-14 Last updated: 2018-01-02Bibliographically approved
Hantke, M. F., Hasse, D., Ekeberg, T., John, K., Svenda, M., Loh, D., . . . Maia, F. R. .. (2016). A data set from flash X-ray imaging of carboxysomes. Scientific Data, 3, Article ID 160061.
Open this publication in new window or tab >>A data set from flash X-ray imaging of carboxysomes
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, 160061Article in journal (Refereed) Published
Abstract [en]

Ultra-intense femtosecond X-ray pulses from X-ray lasers permit structural studies on single particles and biomolecules without crystals. We present a large data set on inherently heterogeneous, polyhedral carboxysome particles. Carboxysomes are cell organelles that vary in size and facilitate up to 40% of Earth’s carbon fixation by cyanobacteria and certain proteobacteria. Variation in size hinders crystallization. Carboxysomes appear icosahedral in the electron microscope. A protein shell encapsulates a large number of Rubisco molecules in paracrystalline arrays inside the organelle. We used carboxysomes with a mean diameter of 115±26 nm from Halothiobacillus neapolitanus. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min. Every diffraction pattern is a unique structure measurement and high-throughput imaging allows sampling the space of structural variability. The different structures can be separated and phased directly from the diffraction data and open a way for accurate, high-throughput studies on structures and structural heterogeneity in biology and elsewhere.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300202 (URN)10.1038/sdata.2016.61 (DOI)000390225400006 ()
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
Munke, A., Andreasson, J., Aquila, A., Awel, S., Ayyer, K., Barty, A., . . . Zook, J. (2016). Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source. Scientific Data, 3, 160064:1-12, Article ID 160064.
Open this publication in new window or tab >>Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, 160064:1-12 p., 160064Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300203 (URN)10.1038/sdata.2016.64 (DOI)000390225700001 ()
Projects
eSSENCE
Available from: 2016-08-01 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
van der Schot, G., Svenda, M., Maia, F. R. .., Hantke, M. F., DePonte, D. P., Seibert, M. M., . . . Ekeberg, T. (2016). Open data set of live cyanobacterial cells imaged using an X-ray laser. Scientific Data, 3, Article ID 160058.
Open this publication in new window or tab >>Open data set of live cyanobacterial cells imaged using an X-ray laser
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, 160058Article in journal (Refereed) Published
Abstract [en]

Structural studies on living cells by conventional methods are limited to low resolution because radiation damage kills cells long before the necessary dose for high resolution can be delivered. X-ray free-electron lasers circumvent this problem by outrunning key damage processes with an ultra-short and extremely bright coherent X-ray pulse. Diffraction-before-destruction experiments provide high-resolution data from cells that are alive when the femtosecond X-ray pulse traverses the sample. This paper presents two data sets from micron-sized cyanobacteria obtained at the Linac Coherent Light Source, containing a total of 199,000 diffraction patterns. Utilizing this type of diffraction data will require the development of new analysis methods and algorithms for studying structure and structural variability in large populations of cells and to create abstract models. Such studies will allow us to understand living cells and populations of cells in new ways. New X-ray lasers, like the European XFEL, will produce billions of pulses per day, and could open new areas in structural sciences.

National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-300201 (URN)10.1038/sdata.2016.58 (DOI)000390225400003 ()
Note

Data Descriptor

Available from: 2016-08-05 Created: 2016-08-05 Last updated: 2017-11-28Bibliographically approved
Ekeberg, T., Svenda, M., Seibert, M. M., Abergel, C., Maia, F. R. .., Seltzer, V., . . . Hajdu, J. (2016). Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser. Scientific Data, 3, Article ID UNSP 160060.
Open this publication in new window or tab >>Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
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2016 (English)In: Scientific Data, E-ISSN 2052-4463, Vol. 3, UNSP 160060Article in journal (Refereed) Published
Abstract [en]

Free-electron lasers (FEL) hold the potential to revolutionize structural biology by producing X-ray pules short enough to outrun radiation damage, thus allowing imaging of biological samples without the limitation from radiation damage. Thus, a major part of the scientific case for the first FELs was three-dimensional (3D) reconstruction of non-crystalline biological objects. In a recent publication we demonstrated the first 3D reconstruction of a biological object from an X-ray FEL using this technique. The sample was the giant Mimivirus, which is one of the largest known viruses with a diameter of 450 nm. Here we present the dataset used for this successful reconstruction. Data-analysis methods for single-particle imaging at FELs are undergoing heavy development but data collection relies on very limited time available through a highly competitive proposal process. This dataset provides experimental data to the entire community and could boost algorithm development and provide a benchmark dataset for new algorithms.

National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-314814 (URN)10.1038/sdata.2016.60 (DOI)000390225400005 ()
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationEU, European Research CouncilStiftelsen Olle Engkvist Byggmästare
Available from: 2017-02-07 Created: 2017-02-06 Last updated: 2017-11-29Bibliographically approved
van der Schot, G., Svenda, M., Maia, F. R. N., Hantke, M., DePonte, D. P., Seibert, M. M., . . . Ekeberg, T. (2015). Imaging single cells in a beam of live cyanobacteria with an X-ray laser. Nature Communications, 6, Article ID 5704.
Open this publication in new window or tab >>Imaging single cells in a beam of live cyanobacteria with an X-ray laser
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2015 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, 5704Article in journal (Refereed) Published
Abstract [en]

There exists a conspicuous gap of knowledge about the organization of life at mesoscopic levels. Ultra-fast coherent diffractive imaging with X-ray free-electron lasers can probe structures at the relevant length scales and may reach sub-nanometer resolution on micron-sized living cells. Here we show that we can introduce a beam of aerosolised cyanobacteria into the focus of the Linac Coherent Light Source and record diffraction patterns from individual living cells at very low noise levels and at high hit ratios. We obtain two-dimensional projection images directly from the diffraction patterns, and present the results as synthetic X-ray Nomarski images calculated from the complex-valued reconstructions. We further demonstrate that it is possible to record diffraction data to nanometer resolution on live cells with X-ray lasers. Extension to sub-nanometer resolution is within reach, although improvements in pulse parameters and X-ray area detectors will be necessary to unlock this potential.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-245040 (URN)10.1038/ncomms6704 (DOI)000350034400002 ()25669616 (PubMedID)
Available from: 2015-02-24 Created: 2015-02-24 Last updated: 2017-12-04Bibliographically approved
Ekeberg, T., Svenda, M., Abergel, C., Maia, F. R. N., Seltzer, V., Claverie, J.-M., . . . Hajdu, J. (2015). Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser. Physical Review Letters, 114(9), 098102:1-6, Article ID 098102.
Open this publication in new window or tab >>Three-dimensional reconstruction of the giant mimivirus particle with an X-ray free-electron laser
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2015 (English)In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 114, no 9, 098102:1-6 p., 098102Article in journal (Refereed) Published
National Category
Biophysics
Identifiers
urn:nbn:se:uu:diva-246129 (URN)10.1103/PhysRevLett.114.098102 (DOI)000351000300010 ()25793853 (PubMedID)
Available from: 2015-03-02 Created: 2015-03-02 Last updated: 2017-08-28Bibliographically approved
Hattne, J., Echols, N., Tran, R., Kern, J., Gildea, R. J., Brewster, A. S., . . . Sauter, N. K. (2014). Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers. Nature Methods, 11(5), 545-548.
Open this publication in new window or tab >>Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers
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2014 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 5, 545-548 p.Article in journal (Refereed) Published
Abstract [en]

X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

National Category
Structural Biology
Identifiers
urn:nbn:se:uu:diva-232835 (URN)10.1038/nmeth.2887 (DOI)24633409 (PubMedID)
Available from: 2014-09-25 Created: 2014-09-25 Last updated: 2017-12-05Bibliographically approved
Rath, A. D., Timneanu, N., Maia, F. R. N., Bielecki, J., Fleckenstein, H., Iwan, B., . . . Andreasson, J. (2014). Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser. Optics Express, 22(23), 28914-28925.
Open this publication in new window or tab >>Explosion dynamics of sucrose nanospheres monitored by time of flight spectrometry and coherent diffractive imaging at the split-and-delay beam line of the FLASH soft X-ray laser
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2014 (English)In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 22, no 23, 28914-28925 p.Article in journal (Refereed) Published
Abstract [en]

We use a Mach-Zehnder type autocorrelator to split and delay XUV pulses from the FLASH soft X-ray laser for triggering and subsequently probing the explosion of aerosolised sugar balls. FLASH was running at 182 eV photon energy with pulses of 70 fs duration. The delay between the pump-probe pulses was varied between zero and 5 ps, and the pulses were focused to reach peak intensities above 1016 W/cm2 with an off-axis parabola. The direct pulse triggered the explosion of single aerosolised sucrose nano-particles, while the delayed pulse probed the exploding structure. The ejected ions were measured by ion time of flight spectrometry, and the particle sizes were measured by coherent diffractive imaging. The results show that sucrose particles of 560-1000 nm diameter retain their size for about 500 fs following the first exposure. Significant sample expansion happens between 500 fs and 1 ps. We present simulations to support these observations.

Keyword
UV, EUV, and X-ray lasers, Coherence imaging, Spectroscopy, ionization
National Category
Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-237616 (URN)10.1364/OE.22.028914 (DOI)000345268500111 ()25402130 (PubMedID)
Available from: 2014-12-03 Created: 2014-12-03 Last updated: 2017-12-05Bibliographically approved
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