Precise and unbiased estimation of astigmatism and defocus in transmission electron microscopy

Nano-Structured Materials under Irradiation: Oxide Dispersion-Strengthened Steels

Oxide dispersion-strengthened materials are reinforced by a (Y, Ti, O) nano-oxide dispersion and thus can be considered as nanostructured materials. In this alloy, most of the nanoprecipitates are (Y, Ti, O) nano-oxides exhibiting a Y₂Ti₂O₇ pyrochlore-like structure. However, the lattice structure of the smallest oxides is difficult to determine, but it is likely to be close to the atomic structure of the host matrix. Designed to serve in extreme environments—i.e., a nuclear power plant—the challenge for ODS steels is to preserve the nano-oxide dispersion under irradiation in order to maintain the excellent creep properties of the alloy in the reactor. Under irradiation, the nano-oxides exhibit different behaviour as a function of the temperature. At low temperature, the nano-oxides tend to dissolve owing to the frequent ballistic ejection of the solute atoms. At medium temperature, the thermal diffusion balances the ballistic dissolution, and the nano-oxides display an apparent stability. At high temperature, the nano-oxides start to coarsen, resulting in an increase in their size and a decrease in their number density. If the small nano-oxides coarsen through a radiation-enhanced Ostwald ripening mechanism, some large oxides disappear to the benefit of the small ones through a radiation-induced inverse Ostwald ripening. In conclusion, it is suggested that, under irradiation, the nano-oxide dispersion prevails over dislocations, grain boundaries and free surfaces to remove the point defects created by irradiation.

Dynamics of the charging-induced imaging instability in transmission electron microscopy

Revolutionary microscopy technologies for aberration correction in spatial and energy aspects have exhibited continuous progress, pushing forward the information limit of materials research down to a scale of sub-angstrom and milli-electron voltage. Nevertheless, imaging quality could still suffer due to sample instability, e.g. the charging effect, which always comes along with electron microscopy characterizations. Herein, using a defocus estimation algorithm and an in situ image feature tracking method, we quantitatively studied the image drifting dynamics induced by the charging on transmission electron microscopy (TEM) carrier grids with tunable electrical conductivity. Experimental evidence clarifies the debate about the charge types, proving that the irradiation of the electron beam induces a positive charge on the grid sample of poor electrical conductivity. Such charge accumulation accounts for subsequent imaging instability, including the increase of defocus and the drift of lateral images. Particularly, the competition between charging and discharging was found to dynamically modulate the propagation of electron beam, resulting in a periodically reciprocating movement on TEM images. These findings enrich understanding on the dynamic principle of charging effects as well as the details of image drifting behaviors. It also suggests specific attention on the importance of conductivity control on a TEM specimen, beyond all the efforts for instrumental improvements.

Structure of the mature Rous sarcoma virus lattice reveals a role for IP6 in the formation of the capsid hexamer

Inositol hexakisphosphate (IP6) is an assembly cofactor for HIV-1. We report here that IP6 is also used for assembly of Rous sarcoma virus (RSV), a retrovirus from a different genus. IP6 is ~100-fold more potent at promoting RSV mature capsid protein (CA) assembly than observed for HIV-1 and removal of IP6 in cells reduces infectivity by 100-fold. Here, visualized by cryo-electron tomography and subtomogram averaging, mature capsid-like particles show an IP6-like density in the CA hexamer, coordinated by rings of six lysines and six arginines. Phosphate and IP6 have opposing effects on CA in vitro assembly, inducing formation of T = 1 icosahedrons and tubes, respectively, implying that phosphate promotes pentamer and IP6 hexamer formation. Subtomogram averaging and classification optimized for analysis of pleomorphic retrovirus particles reveal that the heterogeneity of mature RSV CA polyhedrons results from an unexpected, intrinsic CA hexamer flexibility. In contrast, the CA pentamer forms rigid units organizing the local architecture. These different features of hexamers and pentamers determine the structural mechanism to form CA polyhedrons of variable shape in mature RSV particles.

Reducing bias and variance for CTF estimation in single particle cryo-EM

When using an electron microscope for imaging of particles embedded in vitreous ice, the recorded image, or micrograph, is a significantly degraded version of the tomographic projection of the sample. Apart from noise, the image is affected by the optical configuration of the microscope. This transformation is typically modeled as a convolution with a point spread function. The Fourier transform of this function, known as the contrast transfer function (CTF), is oscillatory, attenuating and amplifying different frequency bands, and sometimes flipping their signs. High-resolution reconstruction requires this CTF to be accounted for, but as its form depends on experimental parameters, it must first be estimated from the micrograph. We present a new method for CTF estimation based on multitaper techniques that reduce bias and variance in the estimate. We also use known properties of the CTF and the background power spectrum to further reduce the variance through background subtraction and steerable basis projection. We show that the resulting power spectrum estimates better capture the zero-crossings of the CTF and yield accurate CTF estimates on several experimental micrographs.

Structures of immature EIAV Gag lattices reveal a conserved role for IP6 in lentivirus assembly

Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.

Development of a real-time wave field reconstruction TEM system (I): incorporation of an auto focus tracking system

We have developed a real-time wave field reconstruction transmission electron microscope system that enables auto focus tracking at a video rate. In the developed system, a high-speed image calculation technique using a graphical processing unit was incorporated along with two techniques facilitating high-speed focus control using high-voltage modulation and weighted image integration using exposure time control. By utilizing these techniques, the sample drift induced in the Z-axis direction can be measured and automatically corrected for every 1/30 of a second. The auto focus tracking system can be operated in the sample drift range of ±150 nm with a precision of ~0.4 nm. In addition to amorphous samples, the system can be used to examine thin crystalline samples, which indicates that atomic structure analysis can be performed in real time with high reliability even when heavy drift occurs in the Z-axis direction.

Automatic software correction of residual aberrations in reconstructed HRTEM exit waves of crystalline samples

We develop an automatic and objective method to measure and correct residual aberrations in atomic-resolution HRTEM complex exit waves for crystalline samples aligned along a low-index zone axis. Our method uses the approximate rotational point symmetry of a column of atoms or single atom to iteratively calculate a best-fit numerical phase plate for this symmetry condition, and does not require information about the sample thickness or precise structure. We apply our method to two experimental focal series reconstructions, imaging a β-Si₃N₄ wedge with O and N doping, and a single-layer graphene grain boundary. We use peak and lattice fitting to evaluate the precision of the corrected exit waves. We also apply our method to the exit wave of a Si wedge retrieved by off-axis electron holography. In all cases, the software correction of the residual aberration function improves the accuracy of the measured exit waves.

Real-time detection and single-pass minimization of TEM objective lens astigmatism

Minimization of the astigmatism of the objective lens is a critical daily instrument alignment task essential for high resolution TEM imaging. Fast and sensitive detection of astigmatism is needed to provide real-time feedback and adjust the stigmators to efficiently reduce astigmatism. Currently the method used by many microscopists is to visually examine the roundness of a diffractogram (Thon rings) and iteratively adjust the stigmators to make the Thon rings circular. This subjective method is limited by poor sensitivity and potentially biased by the astigmatism of human eyes. In this study, an s² power spectra based method, s²stigmator, was developed to allow fast and sensitive detection of the astigmatism in TEM live images. The "radar"-style display provides real-time feedback to guide the adjustment of the objective lens stigmators. Such unique capability allowed us to discover the mapping of the two stigmators to the astigmatism amplitude and angle, which led us to develop a single-pass tuning strategy capable of significantly quicker minimization of the objective lens astigmatism.

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation

Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1.

Visualization and quality assessment of the contrast transfer function estimation

The contrast transfer function (CTF) describes an undesirable distortion of image data from a transmission electron microscope. Many users of full-featured processing packages are often new to electron microscopy and are unfamiliar with the CTF concept. Here we present a common graphical output to clearly demonstrate the CTF fit quality independent of estimation software. Separately, many software programs exist to estimate the four CTF parameters, but their results are difficult to compare across multiple runs and it is all but impossible to select the best parameters to use for further processing. A new measurement is presented based on the correlation falloff of the calculated CTF oscillations against the normalized oscillating signal of the data, called the CTF resolution. It was devised to provide a robust numerical quality metric of every CTF estimation for high-throughput screening of micrographs and to select the best parameters for each micrograph. These new CTF visualizations and quantitative measures will help users better assess the quality of their CTF parameters and provide a mechanism to choose the best CTF tool for their data.

Graphene oxide single sheets as substrates for high resolution cryoTEM

CryoTEM is an important tool in the analysis of soft matter, where generally defocus conditions are used to enhance the contrast in the images, but this is at the expense of the maximum resolution that can be obtained. Here, we demonstrate the use of graphene oxide single sheets as support for the formation of 10 nm thin films for high resolution cryoTEM imaging, using DNA as an example. With this procedure, the overlap of objects in the vitrified film is avoided. Moreover, in these thin films less background scattering occurs and as a direct result, an increased contrast can be observed in the images. Hence, imaging closer to focus as compared with conventional cryoTEM procedures is achieved, without losing contrast. In addition, we demonstrate an ~1.8 fold increase in resolution, which is crucial for accurate size analysis of nanostructures.

Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations

Cryo-electron tomography (CET) is the only available technique capable of characterizing the structure of biological macromolecules in conditions close to the native state. With the advent of subtomogram averaging, as a post-processing step to CET, resolutions in the (sub-) nanometer range have become within reach. In addition to advances in instrumentation and experiments, the reconstruction scheme has improved by inclusion of more accurate contrast transfer function (CTF) correction methods, better defocus estimation, and better alignments of the tilt-series and subtomograms. To quantify the importance of each contribution, we have split the full process from data collection to reconstruction into different steps. For the purpose of evaluation we have acquired tilt-series of ribosomes in such a way that we could precisely determine the defocus of each macromolecule. Then, we simulated tilt-series using the InSilicoTEM package and applied tomogram reconstruction and subtomogram averaging. Through large scale simulations under different conditions and parameter settings we find that tilt-series alignment is the resolution limiting factor for our experimental data. Using simulations, we find that when this alignment inaccuracy is alleviated, tilted CTF correction improves the final resolution, or equivalently, the same resolution can be achieved using less particles. Furthermore, we predict from which resolution onwards better CTF correction and defocus estimation methods are required. We obtain a final average using 3198 ribosomes with a resolution of 2.2nm on the experimental data. Our simulations suggest that with the same number of particles a resolution of 1.2nm could be achieved by improving the tilt-series alignment.

Image formation modeling in cryo-electron microscopy

Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.

FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy

In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].