Structural Basis of Vesicle Formation at the Inner Nuclear Membrane.

Vesicular nucleo-cytoplasmic transport is becoming recognized as a general cellular mechanism for translocation of large cargoes across the nuclear envelope. Cargo is recruited, enveloped at the inner nuclear membrane (INM), and delivered by membrane fusion at the outer nuclear membrane. To understand the structural underpinning for this trafficking, we investigated nuclear egress of progeny herpesvirus capsids where capsid envelopment is mediated by two viral proteins, forming the nuclear egress complex (NEC). Using a multi-modal imaging approach, we visualized the NEC in situ forming coated vesicles of defined size. Cellular electron cryo-tomography revealed a protein layer showing two distinct hexagonal lattices at its membrane-proximal and membrane-distant faces, respectively. NEC coat architecture was determined by combining this information with integrative modeling using small-angle X-ray scattering data. The molecular arrangement of the NEC establishes the basic mechanism for budding and scission of tailored vesicles at the INM.

Quantitative Element-Sensitive Analysis of Individual Nanoobjects.

A reliable and quantitative material analysis is crucial for assessing new technological processes, especially to facilitate a quantitative understanding of advanced material properties at the nanoscale. To this end, X-ray fluorescence microscopy techniques can offer an element-sensitive and non-destructive tool for the investigation of a wide range of nanotechnological materials. Since X-ray radiation provides information depths of up to the microscale, even stratified or buried arrangements are easily accessible without invasive sample preparation. However, in terms of the quantification capabilities, these approaches are usually restricted to a qualitative or semi-quantitative analysis at the nanoscale. Relying on comparable reference nanomaterials is often not straightforward or impossible because the development of innovative nanomaterials has proven to be more fast-paced than any development process for appropriate reference materials. The present work corroborates that a traceable quantification of individual nanoobjects can be realized by means of an X-ray fluorescence microscope when utilizing rather conventional but well-calibrated instrumentation instead of reference materials. As a proof of concept, the total number of atoms forming a germanium nanoobject is quantified using soft X-ray radiation. Furthermore, complementary dimensional parameters of such objects are reconstructed.

Laboratory Soft X-Ray Microscopy with an Integrated Visible-Light Microscope-Correlative Workflow for Faster 3D Cell Imaging.

Laboratory transmission soft X-ray microscopy (L-TXM) has emerged as a complementary tool to synchrotron-based TXM and high-resolution biomedical 3D imaging in general in recent years. However, two major operational challenges in L-TXM still need to be addressed: a small field of view and a potentially misaligned rotation stage. As it is not possible to alter the magnification during operation, the field of view in L-TXM is usually limited to a few tens of micrometers. This complicates locating areas and objects of interest in the sample. Additionally, if the rotation axis of the sample stage cannot be adjusted prior to the experiments, an efficient workflow for tomographic imaging cannot be established, as refocusing and sample repositioning will become necessary after each recorded projection. Both these limitations have been overcome with the integration of a visible-light microscope (VLM) into the L-TXM system. Here, we describe the calibration procedure of the goniometer sample stage and the integrated VLM and present the resulting 3D imaging of a test sample. In addition, utilizing this newly integrated VLM, the extracellular matrix of cryofixed THP-1 cells (human acute monocytic leukemia cells) was visualized by L-TXM for the first time in the context of an ongoing biomedical research project.

Near field stacking of zone plates for reduction of their effective zone period.

Here we analyze the potential of a new fabrication method for high resolution zone plates with high aspect ratios based on near field stacking of frequency doubled atomic layer deposited (ALD) zone plates. The proposed method enables reduction of the effective zone period by a factor of four with two zone plate layers compared to the initial e-beam lithography exposed outermost zone period. It also overcomes the problem that very small zone widths with high aspect ratios have to be fabricated for high-resolution hard X-ray microscopy. Using rigorous coupled wave theory, we have analyzed the diffraction behavior of these near field stacked zone plates and investigated strategies to optimize fabrication parameters to compensate for separation of stacked zone plates. The calculations performed for 8 keV photon energy and effective outermost zone widths of 28 nm and 15 nm predict diffraction efficiencies ≥ 20% suggesting that such optics could find widespread practical applications.

Influence of random zone positioning errors on the resolving power of Fresnel zone plates.

Fresnel zone plates produced by electron beam lithography and planar etching techniques provide a resolving power of about 10 nm. An alternative zone plate fabrication approach is based on alternately coating a micro-wire with two different materials. With this process, very thin zone layers with very high aspect ratios can be deposited. However, depending on the fabrication method, random zone positioning errors may introduce strong aberrations. We simulate the effect of positioning errors using different random fluctuations and study their influence on zone plate resolution. We find that random errors significantly decrease the contrast transfer of X-ray microscopes. Additionally, we derive an upper bound for the mean acceptable variance of the deposition rate.

Three-dimensional cellular ultrastructure resolved by X-ray microscopy.

We developed an X-ray microscope using partially coherent object illumination instead of previously used quasi-incoherent illumination. The design permitted the incorporation of a cryogenic tilt stage, enabling tomography of frozen-hydrated, intact adherent cells. We obtained three-dimensional reconstructions of mouse adenocarcinoma cells at ∼36-nm (Rayleigh) and ∼70-nm (Fourier ring correlation) resolution, which allowed us to visualize the double nuclear membrane, nuclear pores, nuclear membrane channels, mitochondrial cristae and lysosomal inclusions.

Ion beam lithography for Fresnel zone plates in X-ray microscopy.

Fresnel Zone Plates (FZP) are to date very successful focusing optics for X-rays. Established methods of fabrication are rather complex and based on electron beam lithography (EBL). Here, we show that ion beam lithography (IBL) may advantageously simplify their preparation. A FZP operable from the extreme UV to the limit of the hard X-ray was prepared and tested from 450 eV to 1500 eV. The trapezoidal profile of the FZP favorably activates its 2nd order focus. The FZP with an outermost zone width of 100 nm allows the visualization of features down to 61, 31 and 21 nm in the 1st, 2nd and 3rd order focus respectively. Measured efficiencies in the 1st and 2nd order of diffraction reach the theoretical predictions.

Cryo X-ray microscope with flat sample geometry for correlative fluorescence and nanoscale tomographic imaging.

X-ray imaging offers a new 3-D view into cells. With its ability to penetrate whole hydrated cells it is ideally suited for pairing fluorescence light microscopy and nanoscale X-ray tomography. In this paper, we describe the X-ray optical set-up and the design of the cryo full-field transmission X-ray microscope (TXM) at the electron storage ring BESSY II. Compared to previous TXM set-ups with zone plate condenser monochromator, the new X-ray optical layout employs an undulator source, a spherical grating monochromator and an elliptically shaped glass capillary mirror as condenser. This set-up improves the spectral resolution by an order of magnitude. Furthermore, the partially coherent object illumination improves the contrast transfer of the microscope compared to incoherent conditions. With the new TXM, cells grown on flat support grids can be tilted perpendicular to the optical axis without any geometrical restrictions by the previously required pinhole for the zone plate monochromator close to the sample plane. We also developed an incorporated fluorescence light microscope which permits to record fluorescence, bright field and DIC images of cryogenic cells inside the TXM. For TXM tomography, imaging with multi-keV X-rays is a straightforward approach to increase the depth of focus. Under these conditions phase contrast imaging is necessary. For soft X-rays with shrinking depth of focus towards 10nm spatial resolution, thin optical sections through a thick specimen might be obtained by deconvolution X-ray microscopy. As alternative 3-D X-ray imaging techniques, the confocal cryo-STXM and the dual beam cryo-FIB/STXM with photoelectron detection are proposed.

Correlative VIS-fluorescence and soft X-ray cryo-microscopy/tomography of adherent cells.

Soft X-ray cryo-microscopy/tomography of vitreous samples is becoming a valuable tool in structural cell biology. Within the 'water-window' wavelength region (2.34-4.37nm), it provides absorption contrast images with high signal to noise ratio and resolution of a few tens of nanometer. Soft X-rays with wavelengths close to the K-absorption edge of oxygen penetrate biological samples with thicknesses in the micrometer range. Here, we report on the application of a recently established extension of the transmission soft X-ray cryo-microscope (HZB TXM) at the beamline U41-XM of the BESSY II electron storage ring by an in-column epi-fluorescence and reflected light cryo-microscope. We demonstrate the new capability for correlative fluorescence and soft X-ray cryo-microscopy/tomography of this instrument along a typical life science experimental approach - the correlation of a fluorophore-tagged protein (pUL34-GFP of pseudorabies virus, PrV, the nuclear membrane-anchored component of the nuclear egress complex of the Herpesviridae which interacts with viral pUL31) in PrV pUL34-GFP/pUL31 coexpressing mammalian cells, with virus-induced vesicular structures in the nucleus, expanding the nucleoplasmic reticulum. Taken together, our results demonstrate new possibilities to study the role of specific proteins in substructures of adherent cells, especially of the nucleus in toto, accessible to electron microscopy in thinned samples only.

Towards an atlas of mammalian cell ultrastructure by cryo soft X-ray tomography.

We provide a catalog of 3D cryo soft X-ray tomography (cryo-SXT) images obtained from ∼6 to 12µm thick mouse adenocarcinoma cells. Included are multiple representative images of nuclei, nucleoli, nuclear membrane, nuclear membrane channels, mitochondria, lysosomes, endoplasmic reticulum, filaments and plasma membrane, plus three structures not previously described by cryo-SXT, namely Golgi, microvilli and nuclear-membrane blebs. Sections from the 3D cryo-SXT tomograms for all the preceding structures closely resemble those seen by thin-section transmission electron microscopy (TEM). Some structures such as nuclear-membrane channels and nuclear-membrane blebs are more easily detected by cryo-SXT than TEM most likely due to their better contrast and cellular preservation in cryo-SXT combined with the ability to rapidly locate these structures within a full 3D image. We identify and discuss two current limitations in cryo-SXT: variability in image quality and difficulties in detecting weaker contrast structures such as chromatin and various nuclear bodies. Progress on these points is likely to come from the solution of several technical problems in image acquisition, plus the implementation of advanced cryo soft X-ray microscopy approaches such as phase contrast or optical sectioning.

Cryo X-ray nano-tomography of vaccinia virus infected cells.

We have performed full-field cryo X-ray microscopy in the water window photon energy range on vaccinia virus (VACV) infected cells to produce tomographic reconstructions. PtK2 cells were infected with a GFP-expressing VACV strain and frozen by plunge fast freezing. The infected cells were selected by light fluorescence microscopy of the GFP marker and subsequently imaged in the X-ray microscope under cryogenic conditions. Tomographic tilt series of X-ray images were used to yield three-dimensional reconstructions showing different cell organelles (nuclei, mitochondria, filaments), together with other structures derived from the virus infection. Among them, it was possible to detect viral factories and two types of viral particles related to different maturation steps of VACV (immature and mature particles), which were compared to images obtained by standard electron microscopy of the same type of cells. In addition, the effect of radiation damage during X-ray tomographic acquisition was analyzed. Thin sections studied by electron microscopy revealed that the morphological features of the cells do not present noticeable changes after irradiation. Our findings show that cryo X-ray nano-tomography is a powerful tool for collecting three-dimensional structural information from frozen, unfixed, unstained whole cells with sufficient resolution to detect different virus particles exhibiting distinct maturation levels.

Characterization of the resolving power and contrast transfer function of a transmission X-ray microscope with partially coherent illumination.

The achievable spatial resolution and the contrast transfer function (CTF) are key parameters characterizing an X-ray microscope. We measured the spatial resolution and the contrast transfer function of the transmission X-ray microscope (TXM) at the electron storage ring BESSY II. The TXM uses the radiation of an undulator source and operates under partially coherent illumination conditions. For spatial resolutions down to 25 nm, our measurements of the CTF's are in good agreement with theoretical CTF data for partial coherence. With higher resolution zone plate objectives, we measured a spatial resolution (half-pitch) of 11 nm in 1st and 3rd order of diffraction. However, with these objectives the stray light level increases significantly.

Soft X-ray nanoscale imaging using a sub-pixel resolution charge coupled device (CCD) camera.

A sub-pixel 16 bit charge coupled device camera featuring superresolution for the soft X-ray regime is presented. Superresolution images (SRIs) are reconstructed from a set of 4 × 4 individual low-resolution images that are recorded for different sub-pixel shifts of the detector. SRIs have a 1.3 times higher resolution than individual low-resolution images which is close to the maximum achievable enhancement factor of about 1.5 in the X-ray regime under ideal conditions. To characterize this camera and demonstrate its potential, an X-ray microscope setup is used to image different objects at different photon energies.

Multimodal nanoparticles as alignment and correlation markers in fluorescence/soft X-ray cryo-microscopy/tomography of nucleoplasmic reticulum and apoptosis in mammalian cells.

Correlative fluorescence and soft X-ray cryo-microscopy/tomography on flat sample holders is perfectly suited to study the uncompromised physiological status of adherent cells at its best possible preservation by imaging after fast cryo-immobilization. To understand the mechanism by which herpesviruses induce nucleoplasmic reticulum, i.e. invaginations of the nuclear envelope, during their egress from the host cell nucleus, morphologically similar structures found in laminopathies and after chemical induction were investigated as a potentially more easily accessible model system. For example, anti-retroviral protease inhibitors like Saquinavir also induce invaginations of the nuclear membranes. With the help of newly designed multimodal nanoparticles as alignment and correlation markers, and by optimizing fluorescence cryo-microscopy data acquisition, an elaborate three-dimensional network of nucleoplasmic reticulum was demonstrated in nuclei of Saquinavir-treated rabbit kidney cells expressing a fluorescently labeled inner nuclear membrane protein. In part of the protease inhibitor-treated samples, nuclei exhibited dramatic ultrastructural changes indicative of programmed cell death/apoptosis. This unexpected observation highlights another unique feature of soft X-ray microscopy, i.e. high absorption contrast information not relying on labeled cellular components, at a 3D resolution of approximately 40 nm (half-pitch) and through a sample thickness of several micrometers. These properties make it a valuable part of the cell biology imaging toolbox to visualize the cellular ultrastructure in its completeness.

Hard X ray holographic diffraction imaging.

We determine the absolute electron density of a lithographically grown nanostructure with 25 nm resolution by combining hard x-ray Fourier transform holography with iterative phase retrieval methods. While holography immediately reveals an unambiguous image of the object, we deploy in addition iterative phase retrieval algorithms for pushing the resolution close to the diffraction limit. The use of hard (8 keV) x rays eliminates practically all constraints on sample environment and enables a destruction-free investigation of relatively thick or buried samples, making holographic diffraction imaging a very attractive tool for materials science. We note that the technique is ideally suited for subpicosecond imaging that will become possible with the emerging hard x-ray free-electron lasers.

Direct images of the virtual source in a supersonic expansion.

Direct images of the virtual source in a supersonic expansion of helium are presented. The images were obtained using a Fresnel zone plate with free-standing zones, 540 microm in diameter and with an outermost zone width of 50 nm. The general method can be extended to other beams, including seeded beams. Measurements were carried out at absolute source pressures ranging from 11 to 171 bar using a 10 microm nozzle with a source temperature of 320 K. The size of the virtual source was found to be strongly dependent on pressure, changing from a diameter of 67+/-6 microm at an absolute nozzle pressure of 11 bar to 180+/-9 microm at 171 bar. The virtual-source brightness displays a maximum at an absolute nozzle pressure of around 30 bar. This phenomenon occurs because of two competing effects: As the pressure increases, the total flux also increases, but at the same time the virtual source broadens. We modeled the expansion process by calculating the velocity distribution with solutions from the Boltzmann equation to estimate the location of the quitting surface where the frequency of interatomic collisions is assumed negligible. Realistic potentials have been used to calculate the cross section for atomic collisions and, for the velocity distribution perpendicular to the center streamline, a proper scaling with distance derived from the continuum expansion model has been introduced. A good agreement between experiments and model has been found and we discuss its approximation limits. For instance, backscattering effects are not included in the calculations and at present we cannot exclude that they also contribute to a broadening of the virtual-source size for the highest pressure regime. The results presented here are important for improving the understanding of the supersonic expansion process. The experimental method might eventually be used as a new way to test molecular and atomic interaction potentials.