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1.
  • Andreasson, Jakob, et al. (author)
  • Automated identification and classification of single particle serial femtosecond X-ray diffraction data
  • 2014
  • In: Optics Express. - 1094-4087. ; 22:3, s. 2497-2510
  • Journal article (peer-reviewed)abstract
    • The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e. g. for the European XFEL, which is expected to produce 100 million pulses per hour. (C)2014 Optical Society of America
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2.
  • Chapman, Henry N, et al. (author)
  • Femtosecond X-ray protein nanocrystallography.
  • 2011
  • In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 470:7332, s. 73-7
  • Journal article (peer-reviewed)abstract
    • X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200nm to 2μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.
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3.
  • Ekeberg, Tomas, et al. (author)
  • Single-shot diffraction data from the Mimivirus particle using an X-ray free-electron laser
  • 2016
  • In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
  • Journal article (peer-reviewed)abstract
    • 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.
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4.
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5.
  • Ekeberg, Tomas, 1983-, et al. (author)
  • Three-dimensional structure determination with an X-ray laser
  • Other publication (other academic/artistic)abstract
    • Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus. 
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6.
  • Hantke, Max F., et al. (author)
  • A data set from flash X-ray imaging of carboxysomes
  • 2016
  • In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
  • Journal article (peer-reviewed)abstract
    • 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.
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7.
  • Hantke, Max F., et al. (author)
  • High-throughput imaging of heterogeneous cell organelles with an X-ray laser
  • 2014
  • In: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 8:12, s. 943-949
  • Journal article (peer-reviewed)abstract
    • We overcome two of the most daunting challenges in single-particle diffractive imaging: collecting many high-quality diffraction patterns on a small amount of sample and separating components from mixed samples. We demonstrate this on carboxysomes, which are polyhedral cell organelles that vary in size and facilitate up to 40% of Earth's carbon fixation. A new aerosol sample-injector allowed us to record 70,000 low-noise diffraction patterns in 12 min with the Linac Coherent Light Source running at 120 Hz. We separate different structures directly from the diffraction data and show that the size distribution is preserved during sample delivery. We automate phase retrieval and avoid reconstruction artefacts caused by missing modes. We attain the highest-resolution reconstructions on the smallest single biological objects imaged with an X-ray laser to date. These advances lay the foundations for accurate, high-throughput structure determination by flash-diffractive imaging and offer a means to study structure and structural heterogeneity in biology and elsewhere.
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8.
  • Kassemeyer, Stephan, et al. (author)
  • Femtosecond free-electron laser x-ray diffraction data sets for algorithm development
  • 2012
  • In: Optics Express. - 1094-4087. ; 20:4, s. 4149-4158
  • Journal article (peer-reviewed)abstract
    • We describe femtosecond X-ray diffraction data sets of viruses and nanoparticles collected at the Linac Coherent Light Source. The data establish the first large benchmark data sets for coherent diffraction methods freely available to the public, to bolster the development of algorithms that are essential for developing this novel approach as a useful imaging technique. Applications are 2D reconstructions, orientation classification and finally 3D imaging by assembling 2D patterns into a 3D diffraction volume.
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9.
  • Seibert, M. Marvin, et al. (author)
  • Single mimivirus particles intercepted and imaged with an X-ray laser
  • 2011
  • In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 470:7332, s. 78-81
  • Journal article (peer-reviewed)abstract
    • X-ray lasers offer new capabilities in understanding the structure of biological systems, complex materials and matter under extreme conditions(1-4). Very short and extremely bright, coherent X-ray pulses can be used to outrun key damage processes and obtain a single diffraction pattern from a large macromolecule, a virus or a cell before the sample explodes and turns into plasma(1). The continuous diffraction pattern of non-crystalline objects permits oversampling and direct phase retrieval(2). Here we show that high-quality diffraction data can be obtained with a single X-ray pulse from a noncrystalline biological sample, a single mimivirus particle, which was injected into the pulsed beam of a hard-X-ray free-electron laser, the Linac Coherent Light Source(5). Calculations indicate that the energy deposited into the virus by the pulse heated the particle to over 100,000 K after the pulse had left the sample. The reconstructed exit wavefront (image) yielded 32-nm full-period resolution in a single exposure and showed no measurable damage. The reconstruction indicates inhomogeneous arrangement of dense material inside the virion. We expect that significantly higher resolutions will be achieved in such experiments with shorter and brighter photon pulses focused to a smaller area. The resolution in such experiments can be further extended for samples available in multiple identical copies.
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10.
  • van der Schot, Gijs, et al. (author)
  • Imaging single cells in a beam of live cyanobacteria with an X-ray laser
  • 2015
  • In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 6
  • Journal article (peer-reviewed)abstract
    • 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.
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11.
  • van der Schot, Gijs, et al. (author)
  • Open data set of live cyanobacterial cells imaged using an X-ray laser
  • 2016
  • In: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 3
  • Journal article (peer-reviewed)abstract
    • 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.
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12.
  • Yoon, Chun Hong, et al. (author)
  • Unsupervised classification of single-particle X-ray diffraction snapshots by spectral clustering
  • 2011
  • In: Optics Express. - 1094-4087. ; 19:17, s. 16542-16549
  • Journal article (peer-reviewed)abstract
    • Single-particle experiments using X-ray Free Electron Lasers produce more than 10(5) snapshots per hour, consisting of an admixture of blank shots (no particle intercepted), and exposures of one or more particles. Experimental data sets also often contain unintentional contamination with different species. We present an unsupervised method able to sort experimental snapshots without recourse to templates, specific noise models, or user-directed learning. The results show 90% agreement with manual classification.
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13.
  • Bielecki, Johan, 1982, et al. (author)
  • Electrospray sample injection for single-particle imaging with x-ray lasers
  • 2019
  • In: Science advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 5:5
  • Journal article (peer-reviewed)abstract
    • The possibility of imaging single proteins constitutes an exciting challenge for x-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available x-ray lasers and, as we demonstrate here, contamination of the aerosolized molecules by nonvolatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet size during aerosolization. Here, we show that, with our electrospray injector, we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next-generation x-ray lasers, constitute an important stepping stone toward the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.
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14.
  • Bogan, Michael J, et al. (author)
  • Single particle X-ray diffractive imaging
  • 2008
  • In: Nano letters (Print). - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 8:1, s. 310-6
  • Journal article (peer-reviewed)abstract
    • In nanotechnology, strategies for the creation and manipulation of nanoparticles in the gas phase are critically important for surface modification and substrate-free characterization. Recent coherent diffractive imaging with intense femtosecond X-ray pulses has verified the capability of single-shot imaging of nanoscale objects at suboptical resolutions beyond the radiation-induced damage threshold. By intercepting electrospray-generated particles with a single 15 femtosecond soft-X-ray pulse, we demonstrate diffractive imaging of a nanoscale specimen in free flight for the first time, an important step toward imaging uncrystallized biomolecules.
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15.
  • Daurer, Benedikt J., et al. (author)
  • Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses
  • 2017
  • In: IUCrJ. - : INT UNION CRYSTALLOGRAPHY. - 2052-2525. ; 4, s. 251-262
  • Journal article (peer-reviewed)abstract
    • 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.
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16.
  • Daurer, Benedikt J., et al. (author)
  • Ptychographic wavefront characterization for single-particle imaging at x-ray lasers
  • 2021
  • In: Optica. - : Optical Society of America. - 2334-2536. ; 8:4, s. 551-562
  • Journal article (peer-reviewed)abstract
    • A well-characterized wavefront is important for many x-ray free-electron laser (XFEL) experiments, especially for single-particle imaging (SPI), where individual biomolecules randomly sample a nanometer region of highly focused femtosecond pulses. We demonstrate high-resolution multiple-plane wavefront imaging of an ensemble of XFEL pulses, focused by Kirkpatrick–Baez mirrors, based on mixed-state ptychography, an approach letting us infer and reduce experimental sources of instability. From the recovered wavefront profiles, we show that while local photon fluence correction is crucial and possible for SPI, a small diversity of phase tilts likely has no impact. Our detailed characterization will aid interpretation of data from past and future SPI experiments and provides a basis for further improvements to experimental design and reconstruction algorithms.
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17.
  • Daurer, Benedikt J, et al. (author)
  • Wavefront sensing of individual XFEL pulses using ptychography
  • Other publication (other academic/artistic)abstract
    • The characterization of the wavefront dynamics is important for many X-ray free-electron laser (XFEL) experiments, in particular for coherent diffractive imaging (CDI), as the reconstructed image is always the product of the incoming wavefront with the object. An accurate understanding of the wavefront is also important for any experiment wishing to achieve peak power densities, making use of the tightest possible focal spots. With the use of ptychography we demonstrate high-resolution imaging of the Linac Coherent Light Source (LCLS) beam focused at the endstation for Atomic, Molecular and Optical (AMO) experiments, including its phase and intensity at every plane along its propagation axis, for each individual pulse. Using a mixed-state approach, we have reconstructed the most dominant beam components that constitute an ensemble of pulses, and from the reconstructed components determined their respective contribution in each of the individual pulses. This enabled us to obtain complete wavefront information about each individual pulse. We hope that our findings aid interpretation of data from past and future LCLS experiments and we propose this method to be used routinely for XFEL beam diagnostics. 
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18.
  • Gorkhover, Tais, et al. (author)
  • Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles
  • 2018
  • In: Nature Photonics. - : Springer Science and Business Media LLC. - 1749-4885 .- 1749-4893. ; 12:3, s. 150-153
  • Journal article (peer-reviewed)abstract
    • Ultrafast X-ray imaging on individual fragile specimens such as aerosols 1 , metastable particles 2 , superfluid quantum systems 3 and live biospecimens 4 provides high-resolution information that is inaccessible with conventional imaging techniques. Coherent X-ray diffractive imaging, however, suffers from intrinsic loss of phase, and therefore structure recovery is often complicated and not always uniquely defined 4,5 . Here, we introduce the method of in-flight holography, where we use nanoclusters as reference X-ray scatterers to encode relative phase information into diffraction patterns of a virus. The resulting hologram contains an unambiguous three-dimensional map of a virus and two nanoclusters with the highest lateral resolution so far achieved via single shot X-ray holography. Our approach unlocks the benefits of holography for ultrafast X-ray imaging of nanoscale, non-periodic systems and paves the way to direct observation of complex electron dynamics down to the attosecond timescale.
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19.
  • Hantke, Max Felix, 1984- (author)
  • Coherent Diffractive Imaging with X-ray Lasers
  • 2016
  • Doctoral thesis (other academic/artistic)abstract
    • The newly emerging technology of X-ray free-electron lasers (XFELs) has the potential to revolutionise molecular imaging. XFELs generate very intense X-ray pulses and predictions suggest that they may be used for structure determination to atomic resolution even for single molecules. XFELs produce femtosecond pulses that outrun processes of radiation damage and permit the study of structures at room temperature and of structural dynamics.While the first demonstrations of flash X-ray diffractive imaging (FXI) on biological particles were encouraging, they also revealed technical challenges. In this work we demonstrated how some of these challenges can be overcome. We exemplified, with heterogeneous cell organelles, how tens of thousands of FXI diffraction patterns can be collected, sorted, and analysed in an automatic data processing pipeline. We improved  image resolution and reduced problems with missing data. We validated, described, and deposited the experimental data in the Coherent X-ray Imaging Data Bank.We demonstrated that aerosol injection can be used to collect FXI data at high hit ratios and with low background. We reduced problems with non-volatile sample contaminants by decreasing aerosol droplet sizes from ~1000 nm to ~150 nm. We achieved this by adapting an electrospray aerosoliser to the Uppsala sample injector. Mie scattering imaging was used as a diagnostic tool to measure positions, sizes, and velocities of individual injected particles.XFEL experiments generate large amounts of data at high rates. Preparation, execution, and data analysis of these experiments benefits from specialised software. In this work we present new open-source software tools that facilitates prediction, online-monitoring, display, and pre-processing of XFEL diffraction data.We hope that this work is a valuable contribution in the quest of transitioning FXI from its first experimental demonstration into a technique that fulfills its potentials.
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20.
  • Hantke, Max Felix, et al. (author)
  • Rayleigh-scattering microscopy for tracking and sizing nanoparticles in focused aerosol beams
  • 2018
  • In: IUCrJ. - 2052-2525. ; 5, s. 673-680
  • Journal article (peer-reviewed)abstract
    • Ultra-bright femtosecond X-ray pulses generated by X-ray free-electron lasers (XFELs) can be used to image high-resolution structures without the need for crystallization. For this approach, aerosol injection has been a successful method to deliver 70-2000 nm particles into the XFEL beam efficiently and at low noise. Improving the technique of aerosol sample delivery and extending it to single proteins necessitates quantitative aerosol diagnostics. Here a lab-based technique is introduced for Rayleigh-scattering microscopy allowing us to track and size aerosolized particles down to 40 nm in diameter as they exit the injector. This technique was used to characterize the 'Uppsala injector', which is a pioneering and frequently used aerosol sample injector for XFEL single-particle imaging. The particle-beam focus, particle velocities, particle density and injection yield were measured at different operating conditions. It is also shown how high particle densities and good injection yields can be reached for large particles (100-500 nm). It is found that with decreasing particle size, particle densities and injection yields deteriorate, indicating the need for different injection strategies to extend XFEL imaging to smaller targets, such as single proteins. This work demonstrates the power of Rayleigh-scattering microscopy for studying focused aerosol beams quantitatively. It lays the foundation for lab-based injector development and online injection diagnostics for XFEL research. In the future, the technique may also find application in other fields that employ focused aerosol beams, such as mass spectrometry, particle deposition, fuel injection and three-dimensional printing techniques.
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21.
  • Ho, Phay J., et al. (author)
  • The role of transient resonances for ultra-fast imaging of single sucrose nanoclusters
  • 2020
  • In: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 11
  • Journal article (peer-reviewed)abstract
    • Intense x-ray free-electron laser (XFEL) pulses hold great promise for imaging function in nanoscale and biological systems with atomic resolution. So far, however, the spatial resolution obtained from single shot experiments lags averaging static experiments. Here we report on a combined computational and experimental study about ultrafast diffractive imaging of sucrose clusters which are benchmark organic samples. Our theoretical model matches the experimental data from the water window to the keV x-ray regime. The large-scale dynamic scattering calculations reveal that transient phenomena driven by non-linear x-ray interaction are decisive for ultrafast imaging applications. Our study illuminates the complex interplay of the imaging process with the rapidly changing transient electronic structures in XFEL experiments and shows how computational models allow optimization of the parameters for ultrafast imaging experiments. X-ray free electron lasers provide high photon flux to explore single particle diffraction imaging of biological samples. Here the authors present dynamic electronic structure calculations and benchmark them to single-particle XFEL diffraction data of sucrose clusters to predict optimal single-shot imaging conditions.
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22.
  • Kurta, Ruslan P., et al. (author)
  • Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses
  • 2017
  • In: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 119:15
  • Journal article (peer-reviewed)abstract
    • We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.
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23.
  • Kördel, Mikael, et al. (author)
  • Biological Laboratory X-Ray Microscopy
  • 2019
  • In: X-Ray Nanoimaging. - : SPIE - International Society for Optical Engineering. - 9781510629189
  • Conference paper (peer-reviewed)abstract
    • Zone-plate-based soft x-ray microscopes operating in the water window allow high-resolution and high-contrast imaging of intact cells in their near-native state. Laboratory-source-based x-ray microscopes are an important complement to the accelerator-based instruments, providing high accessibility and allowing close integration with other cell-biological techniques. Here we present recent biological applications using the Stockholm laboratory water-window x-ray microscope, which is based on a liquid-nitrogen-jet laser-plasma source. Technical improvements to the microscope in the last few years have resulted in increased x-ray flux at the sample and significantly improved stability and reliability. In addition to this, vibrations in key components have been measured, analyzed and reduced to improve the resolution to 25 nm half-period. The biological applications include monitoring the development of carbon-dense vesicles in starving human embryonic kidney cells (HEK293T), imaging the interaction between natural killer (NK) cells and HEK293T target cells, and most recently studying a newly discovered giant DNA virus and the process of viral replication inside a host amoeba. All biological imaging was done on cryo-frozen hydrated samples in 2D and in some cases 3D.
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24.
  • Kördel, Mikael, et al. (author)
  • Biological Laboratory X-ray Microscopy
  • 2018
  • In: Microscopy and Microanalysis. - 1431-9276 .- 1435-8115. ; 24:S2, s. 346-347
  • Journal article (peer-reviewed)
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25.
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26.
  • Kördel, Mikael, et al. (author)
  • Quantitative conversion of biomass in giant DNA virus infection
  • 2021
  • In: Scientific Reports. - : Springer Nature. - 2045-2322. ; 11:1
  • Journal article (peer-reviewed)abstract
    • Bioconversion of organic materials is the foundation of many applications in chemical engineering, microbiology and biochemistry. Herein, we introduce a new methodology to quantitatively determine conversion of biomass in viral infections while simultaneously imaging morphological changes of the host cell. As proof of concept, the viral replication of an unidentified giant DNA virus and the cellular response of an amoebal host are studied using soft X-ray microscopy, titration dilution measurements and thermal gravimetric analysis. We find that virions produced inside the cell are visible from 18 h post infection and their numbers increase gradually to a burst size of 280-660 virions. Due to the large size of the virion and its strong X-ray absorption contrast, we estimate that the burst size corresponds to a conversion of 6-12% of carbonaceous biomass from amoebal host to virus. The occurrence of virion production correlates with the appearance of a possible viral factory and morphological changes in the phagosomes and contractile vacuole complex of the amoeba, whereas the nucleus and nucleolus appear unaffected throughout most of the replication cycle.
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27.
  • Li, Haoyuan, et al. (author)
  • Diffraction data from aerosolized Coliphage PR772 virus particles imaged with the Linac Coherent Light Source
  • 2020
  • In: Scientific Data. - : NATURE RESEARCH. - 2052-4463. ; 7:1
  • Journal article (peer-reviewed)abstract
    • Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 mu m x 1.7 mu m full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.
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28.
  • Li, Yuyang, et al. (author)
  • Synthesis and Cytotoxicity Studies on Ru and Rh Nanoparticles as Potential X-Ray Fluorescence Computed Tomography (XFCT) Contrast Agents
  • 2020
  • In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 10:2
  • Journal article (peer-reviewed)abstract
    • X-Ray fluorescence computed tomography (XFCT) is an emerging biomedical imaging technique, which demands the development of new contrast agents. Ruthenium (Ru) and rhodium (Rh) have spectrally attractive K ff edge energies, qualifying them as new XFCT bio-imaging probes. Metallic Ru and Rh nanoparticles are synthesized by polyol method, in the presence of a stabilizer. The effect of several reaction parameters, including reaction temperature time, precursor and stabilizer concentration, and stabilizer molecular weight, on the size of particles, were studied. Resultant materials were characterized in detail using XRD, TEM, FT-IR, DLS-zeta potential and TGA techniques. Ru particles in the size range of 1-3 nm, and Rh particles of 6-9 nm were obtained. At physiological pH, both material systems showed agglomeration into larger assemblies ranging from 12-104 nm for Ru and 25-50 nm for Rh. Cytotoxicity of the nanoparticles (NPs) was evaluated on macrophages and ovarian cancer cells, showing minimal toxicity in doses up to 50 mu g/mL. XFCT performance was evaluated on a small-animal-sized phantom model, demonstrating the possibility of quantitative evaluation of the measured dose with an expected linear response. This work provides a detailed route for the synthesis, size control and characterization of two materials systems as viable contrast agents for XFCT bio-imaging.
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29.
  • Li, Yuyang, et al. (author)
  • Synthesis, Physicochemical Characterization, and Cytotoxicity Assessment of Rh Nanoparticles with Different Morphologies-as Potential XFCT Nanoprobes
  • 2020
  • In: Nanomaterials. - : MDPI AG. - 2079-4991. ; 10:11, s. 2129-2129
  • Journal article (peer-reviewed)abstract
    • Morphologically controllable synthesis of Rh nanoparticles (NPs) was achieved by the use of additives during polyol synthesis. The effect of salts and surfactant additives including PVP, sodium acetate, sodiumcitrate, CTAB,CTAC,andpotassiumbromideonRhNPsmorphologywasinvestigated. When PVP was used as the only additive, trigonal NPs were obtained. Additives containing Br− ions (CTAB and KBr) resulted in NPs with a cubic morphology, while those with carboxyl groups (sodium citrate and acetate) formed spheroid NPs. The use of Cl− ions (CTAC) resulted in a mixture of polygon morphologies. Cytotoxicity of these NPs was evaluated on macrophages and ovarian cancer cell lines. Membrane integrity and cellular activity are both influenced to a similar extent, for both the cell lines, with respect to the morphology of Rh NPs. The cells exposed to trigonal Rh NPs showed the highest viability, among the NP series. Particles with a mixed polygon morphology had the highest cytotoxic impact, followed by cubic and spherical NPs. The Rh NPs were further demonstrated as contrast agents for X-ray fluorescence computed tomography (XFCT) in a small-animal imaging setting. This work provides a detailed route for the synthesis, morphology control, and characterization of Rh NPs as viable contrast agents for XFCT bio-imaging. 
  •  
30.
  • Lundholm, Ida V., et al. (author)
  • Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging
  • 2018
  • In: IUCrJ. - : International Union of Crystallography. - 2052-2525. ; 5, s. 531-541
  • Journal article (peer-reviewed)abstract
    • Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.
  •  
31.
  • Mikael, Kördel, et al. (author)
  • Giant DNA virus infection reveals high bioconversion from amoeba to virus
  • Other publication (other academic/artistic)abstract
    • 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.
  •  
32.
  • Mühlig, Kerstin, et al. (author)
  • Nanometre-sized droplets from a gas dynamic virtual nozzle
  • 2019
  • In: Journal of Applied Crystallography. - : INT UNION CRYSTALLOGRAPHY. - 1600-5767 .- 0021-8898. ; 52, s. 800-808
  • Journal article (peer-reviewed)abstract
    • This paper reports on improved techniques to create and characterize nanometre-sized droplets from dilute aqueous solutions by using a gas dynamic virtual nozzle (GDVN). It describes a method to measure the size distribution of uncharged droplets, using an environmental scanning electron microscope, and provides theoretical models for the droplet sizes created. The results show that droplet sizes can be tuned by adjusting the gas and liquid flow rates in the GDVN, and at the lowest liquid flow rates, the size of the water droplets peaks at about 120 nm. This droplet size is similar to droplet sizes produced by electrospray ionization but requires neither electrolytes nor charging of the solution. The results presented here identify a new operational regime for GDVNs and show that predictable droplet sizes, comparable to those obtained by electrospray ionization, can be produced by purely mechanical means in GDVNs.
  •  
33.
  • Munke, Anna, et al. (author)
  • Coherent diffraction of single Rice Dwarf Virus particles using soft X-rays at the Linac Coherent Light Source
  • 2018
  • In: Nature Scientific Data.
  • Journal article (other academic/artistic)abstract
    • Single particle imaging using X-ray Free Electron Lasers has recently made major advancements that have facilitated experiments on smaller samples compared to the earliest reported works on giant viruses and cells. Here, the technique was used to image the 70 nm Rice dwarf virus, for which the generated dataset is described here. The virus particles were aerosolized and injected into the X-ray beam of the Linac Coherent Light Source. A total number of 36534 diffraction patterns were recorded, of which approximately 10 % were classified as ‘single hits’ by the RedFlamingo software. With the anticipation to advance method development, the dataset along with usage instructions are deposited in the Coherent X-ray imaging data bank, free to access and analyze.
  •  
34.
  • Munke, Anna, et al. (author)
  • Data Descriptor : Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source
  • 2016
  • In: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 3
  • Journal article (peer-reviewed)abstract
    • Single particle diffractive imaging data from Rice Dwarf Virus (RDV) were recorded using the Coherent X-ray Imaging (CXI) instrument at the Linac Coherent Light Source (LCLS). RDV was chosen as it is a wellcharacterized model system, useful for proof-of-principle experiments, system optimization and algorithm development. RDV, an icosahedral virus of about 70 nm in diameter, was aerosolized and injected into the approximately 0.1 mu m diameter focused hard X-ray beam at the CXI instrument of LCLS. Diffraction patterns from RDV with signal to 5.9 angstrom ngstrom were recorded. The diffraction data are available through the Coherent X-ray Imaging Data Bank (CXIDB) as a resource for algorithm development, the contents of which are described here.
  •  
35.
  • Narayana Reddy, Hemanth Kumar (author)
  • Structural Studies of Large dsDNA Viruses using Single Particle Methods
  • 2019
  • Doctoral thesis (other academic/artistic)abstract
    • 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.
  •  
36.
  • Okamoto, Kenta, et al. (author)
  • Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly
  • 2018
  • In: Virology. - : Elsevier BV. - 0042-6822 .- 1096-0341. ; 516, s. 239-245
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
37.
  • Okamoto, Kenta, et al. (author)
  • Structural variability and complexity of the giant Pithovirus sibericum particle revealed by high-voltage electron cryo-tomography and energy-filtered electron cryo-microscopy
  • 2017
  • In: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 7
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
38.
  • Okamoto, Kenta, et al. (author)
  • The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes
  • 2016
  • In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 6
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
39.
  • Rath, Asawari D., et al. (author)
  • 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
  • 2014
  • In: Optics Express. - 1094-4087. ; 22:23, s. 28914-28925
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
40.
  • Reddy, Hemanth K. N., et al. (author)
  • Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source
  • 2017
  • In: Scientia Danica. Series H. Humanistica 4. - : Nature Publishing Group. - 1904-5506 .- 2052-4463. ; 4
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
41.
  • Reddy, Hemanth K.N., et al. (author)
  • CryoEM of coliphage PR772 reveals the composition & structure of the elusive vertex complex and the capsid architecture.
  • In: eLIFE. - 2050-084X.
  • Journal article (peer-reviewed)abstract
    • 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.
  •  
42.
  • Reddy, Hemanth K.N., et al. (author)
  • Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture
  • 2019
  • In: eLIFE. - : ELIFE SCIENCES PUBLICATIONS LTD. - 2050-084X. ; 8
  • Journal article (peer-reviewed)abstract
    • 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 angstrom, while the resolution of the protein capsid is 2.3 angstrom. 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.
  •  
43.
  • Saladino, Giovanni Marco, et al. (author)
  • Functional Coatings for X-ray Fluorescent Nanoparticles
  • 2022
  • In: Proceedings of the 6th International Conference on Theoretical and Applied Nanoscience and Nanotechnology, TANN 2022. - : Avestia Publishing.
  • Conference paper (peer-reviewed)abstract
    • In recent years, the design and synthesis of bio-compatible coatings leading to hybrid nanoparticles (NPs) as the contrast agents have gained substantial relevance. Furthermore, the addition of several functionalities for bio-imaging applications represents a key step for non-invasive bio-diagnostics. In this context, we design and utilize hybrid nanostructures for X-ray fluorescence computed tomography (XFCT). The combination of a ceramic or metallic core–based on MoO2, Rh or Ru–with a protective shell allows the generation of bio-compatible nanohybrids for dual mode bio-imaging, where the core NPs constitute the X-ray fluorescence (XRF) contrast agents [1]–[3]. Core NPs are synthesized via polyol, hydrothermal or microwave-assisted hydrothermal methods, yielding uniform shape and high dispersibility in aqueous media. Different approaches have been pursued for the fabrication of a bio-compatible shell coating. A modified sol-gel based silica coating process, doped with a commercial fluorophore (Cy5.5), was developed and shown to be applicable to both ceramic and metallic NPs [4], forming core-shell NPs with both optical and X-ray fluorescence properties. Alternatively, carbon quantum dots (CQDs) were synthesized via citrate pyrolysis using microwave-assisted hydrothermal method, exhibiting uniform size distribution (1.6±0.4 nm) and excitation-independent emission (440 nm). Conjugation of these CQDs, via cross-linking, with Rh NPs led to excitation-independent hybrid NPs, with a red-shifted emission wavelength (520 nm), attributed to the reduction of pyrrolic nitrogen on CQDs [5]. These hybrid NPs exhibit improved in vitro biocompatibility in comparison with bare XRF contrast agents. Furthermore, the optical fluorescence–provided by Cy5.5 or CQDs–allows the localization of the NPs in the intracellular environment while the XRF signal from the core NPs is utilized for XFCT, in small animals, leading to both a microscopic and macroscopic bio-imaging contrast agent.
  •  
44.
  • Saladino, Giovanni, et al. (author)
  • Optical and X-ray Fluorescent Nanoparticles for Dual Mode Bioimaging
  • 2021
  • In: ACS Nano. - : American Chemical Society (ACS). - 1936-0851 .- 1936-086X. ; 15:3, s. 5077-5085
  • Journal article (peer-reviewed)abstract
    • Nanoparticle (NP) based contrast agents detectable via different imaging modalities (multimodal properties) provide a promising strategy for noninvasive diagnostics. Core-shell NPs combining optical and X-ray fluorescence properties as bioimaging contrast agents are presented. NPs developed earlier for X-ray fluorescence computed tomography (XFCT), based on ceramic molybdenum oxide (MoO2) and metallic rhodium (Rh) and ruthenium (Ru), are coated with a silica (SiO2) shell, using ethanolamine as the catalyst. The SiO2 coating method introduced here is demonstrated to be applicable to both metallic and ceramic NPs. Furthermore, a fluorophore (Cy5.5 dye) was conjugated to the SiO2 layer, without altering the morphological and size characteristics of the hybrid NPs, rendering them with optical fluorescence properties. The improved biocompatibility of the SiO2 coated NPs without and with Cy5.5 is demonstrated in vitro by Real-Time Cell Analysis (RTCA) on a macrophage cell line (RAW 264.7). The multimodal characteristics of the core-shell NPs are confirmed with confocal microscopy, allowing the intracellular localization of these NPs in vitro to be tracked and studied. In situ XFCT successfully showed the possibility of in vivo multiplexed bioimaging for multitargeting studies with minimum radiation dose. Combined optical and X-ray fluorescence properties empower these NPs as effective macroscopic and microscopic imaging tools.
  •  
45.
  • Seibert, M. Marvin, et al. (author)
  • Femtosecond diffractive imaging of biological cells
  • 2010
  • In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 43:19, s. 194015-
  • Journal article (peer-reviewed)abstract
    • In a flash diffraction experiment, a short and extremely intense x-ray pulse illuminates the sample to obtain a diffraction pattern before the onset of significant radiation damage. The over-sampled diffraction pattern permits phase retrieval by iterative phasing methods. Flash diffractive imaging was first demonstrated on an inorganic test object (Chapman et al 2006 Nat. Phys. 2 839-43). We report here experiments on biological systems where individual cells were imaged, using single, 10-15 fs soft x-ray pulses at 13.5 nm wavelength from the FLASH free-electron laser in Hamburg. Simulations show that the pulse heated the sample to about 160 000 K but not before an interpretable diffraction pattern could be obtained. The reconstructed projection images return the structures of the intact cells. The simulations suggest that the average displacement of ions and atoms in the hottest surface layers remained below 3 angstrom during the pulse.
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