Rapid tilt-series acquisition for electron cryotomography

Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ～4?nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.     

TomoAlign: A novel approach to correcting sample motion and 3D CTF in CryoET

TomoAlign is a software package that integrates tools to mitigate two important resolution limiting factors in cryoET, namely the beam-induced sample motion and the contrast transfer function (CTF) of the microscope. The package is especially focused on cryoET of thick specimens where fiducial markers are required for accurate tilt-series alignment and sample motion estimation. TomoAlign models the beam-induced sample motion undergone during the tilt-series acquisition. The motion models are used to produce motion-corrected subtilt-series centered on the particles of interest. In addition, the defocus of each particle at each tilt image is determined and can be corrected, resulting in motion-corrected and CTF-corrected subtilt-series from which the subtomograms can be computed. Alternatively, the CTF information can be passed on so that CTF correction can be carried out entirely within external packages like Relion. TomoAlign serves as a versatile tool that can streamline the cryoET workflow from initial alignment of tilt-series to final subtomogram averaging during in situ structure determination.     

Consideration of sample motion in cryo-tomography based on alignment residual interpolation

Recently, it has been shown that the resolution in cryo-tomography could be improved by considering the sample motion in tilt-series alignment and reconstruction, where a set of quadratic polynomials were used to model this motion. One requirement of this polynomial method is the optimization of a large number of parameters, which may limit its practical applicability. In this work, we propose an alternative method for modeling the sample motion. Starting from the standard fiducial-based tilt-series alignment, the method uses the alignment residual as local estimates of the sample motion at the 3D fiducial positions. Then, a scattered data interpolation technique characterized by its smoothness and a closed-form solution is applied to model the sample motion. The motion model is then integrated in the tomographic reconstruction. The new method improves the tomogram quality similar to the polynomial one, with the important advantage that the determination of the motion model is greatly simplified, thereby overcoming one of the major limitations of the polynomial model. Therefore, the new method is expected to make the beam-induced motion correction methodology more accessible to the cryoET community.     

37 Production, survival and morphology of kelp (protista) "sporophytes" arising from selfings, apogamy and hybridizations

The production and survival of sporophyte morphologies that arose from selfings, parthenogenesis, male apogamy and reciprocal hybridizations of Costaria costata (C.A. Agardh) Saunders, Laminaria saccharina (L) Lamouroux, Alaria marginata Postels and Ruprecht, Eisenia arborea Areschoug, Lessoniopsis littoralis (Tilden) Reinke, Macrocystis integrifolia Bory, and Nereocystis leutkeana (Mertens) Postels and Ruprecht was tracked for 215 hybridization trials for 30 weeks. Each trial consisted of selfings for each species, solo cultures of males and females for each species and reciprocal crossings. At the end of 30 weeks, "sporophyte" survival in the 215 cases was 13% for selfings, 10% for parthenogenesis, 6% for apogamy, and 16% for the reciprocal hybridizations. The morphologies of sporophytes resulting from selfings were typical of the selfed species. Parthenosporophytes and reciprocal hybrids usually had the distinctive morphology of the female parent. Male, apogamously derived "sporophytes" often had reduced morphological features. For example, A. marginata male apogamous sporophytes often lacked a midrib. The sporophyte morphologies that arose in the reciprocal crossings are considered to be putative hybrids. Molecular evidence is required to establish their genetic origins.     

XRayView: a teaching aid for X-ray crystallography.

A software package, XRayView, has been developed that uses interactive computer graphics to introduce basic concepts of x-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography. Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space. XRayView is designed with "user-friendliness" in mind, using pull-down menus to control the program. Many of the experiences of using real x-ray diffraction equipment to examine crystalline diffraction can be simulated. Exercises are available on-line to guide the users through many typical x-ray diffraction experiments.     

Multiple-axis tomography: applications to basal bodies from Paramecium tetraurelia

BACKGROUND INFORMATION: Transmission electron tomography is becoming a powerful tool for studying subcellular components of cells. Classical approaches for electron tomography consist of recording images along a single-tilt axis. This approach is being improved by dual-axis reconstructions and/or high-tilt devices (tilt angle>+/-60 degrees) on microscopes to compensate part of the information loss due to the 'missing wedge' phenomena. RESULTS: In the present work we have evaluated the extension of the dual-axis technique to a multiple-axis approach, and we demonstrate a freely available plug-in for the Java-based freeware image-analysis software ImageJ. Our results from phantom and experimental data sets from Paramecium tetraurelia epon-embedded sections have shown that multiple-axis tomography achieves results equivalent to those obtained by dual-axis approach without the requirement for high-tilt devices. CONCLUSIONS: This new approach allows performance of high-resolution tomography, avoiding the need for high-tilt devices, and therefore will increase the access of electron tomography to a larger community.     

Genetic analysis assessed by microsatellites for a diallel mating design of two geographical stocks of the blood clam <Emphasis Type="Italic">Tegillarca granosa</Emphasis>

To determine the potential for productive efficiency and genetic improvement in the blood clam Tegillarca granosa, four offspring populations (ZZ, ZK, KZ and KK) were produced from a diallel mating of two different geographical stocks (Z and K). The levels of genetic diversity and population structures of four populations were analyzed using 14 polymorphic microsatellites. The results showed that the mean observed heterozygosities (Ho) of reciprocal cross populations (ZK and KZ) was higher than those of pure populations(ZZ and KK). The largest values of genetic differentiation coefficient (F_st?=?0.067) and Nei’s unbiased genetic distance (Dc?=?0.263) were between ZK and KZ, and the smallest (F_st?=?0.020, Dc?=?0.116) were between ZZ and KK, which revealed that the largest genetic divergence was between the two reciprocal cross populations and the smallest was between two pure populations. This study demonstrated that the reciprocal cross populations of T. granosa had an extensive genetic difference and improvement, which may be advantageous for future breeding studies.     

Reciprocal control of pyruvate dehydrogenase kinase and phosphatase by inositol phosphoglycans. Dynamic state set by "push-pull" system

Reversible phosphorylation of proteins regulates numerous aspects of cell function, and abnormal phosphorylation is causal in many diseases. Pyruvate dehydrogenase complex (PDC) is central to the regulation of glucose homeostasis. PDC exists in a dynamic equilibrium between de-phospho-(active) and phosphorylated (inactive) forms controlled by pyruvate dehydrogenase phosphatases (PDP1,2) and pyruvate dehydrogenase kinases (PDK1-4). In contrast to the reciprocal regulation of the phospho-/de-phospho cycle of PDC and at the level of expression of the isoforms of PDK and PDP regulated by hormones and diet, there is scant evidence for regulatory factors acting in vivo as reciprocal "on-off" switches. Here we show that the putative insulin mediator inositol phosphoglycan P-type (IPG-P) has a sigmoidal inhibitory action on PDK in addition to its known linear stimulation of PDP. Thus, at critical levels of IPG-P, this sigmoidal/linear model markedly enhances the switchover from the inactive to the active form of PDC, a "push-pull" system that, combined with the developmental and hormonal control of IPG-P, indicates their powerful regulatory function. The release of IPGs from cell membranes by insulin is significant in relation to diabetes. The chelation of IPGs with Mn2+ and Zn2+ suggests a role as "catalytic chelators" coordinating the traffic of metal ions in cells. Synthetic inositol hexosamine analogues are shown here to have a similar linear/sigmoidal reciprocal action on PDC exerting push-pull effects, suggesting their potential for treatment of metabolic disorders, including diabetes.     

High-resolution cryo-electron microscopy on macromolecular complexes and cell organelles

Cryo-electron microscopy techniques and computational 3-D reconstruction of macromolecular assemblies are tightly linked tools in modern structural biology. This symbiosis has produced vast amounts of detailed information on the structure and function of biological macromolecules. Typically, one of two fundamentally different strategies is used depending on the specimens and their environment. A: 3-D reconstruction based on repetitive and structurally identical unit cells that allow for averaging, and B: tomographic 3-D reconstructions where tilt-series between approximately ±60 and ±70° at small angular increments are collected from highly complex and flexible structures that are beyond averaging procedures, at least during the first round of 3-D reconstruction. Strategies of group A are averaging-based procedures and collect large number of 2-D projections at different angles that are computationally aligned, averaged together, and back-projected in 3-D space to reach a most complete 3-D dataset with high resolution, today often down to atomic detail. Evidently, success relies on structurally repetitive particles and an aligning procedure that unambiguously determines the angular relationship of all 2-D projections with respect to each other. The alignment procedure of small particles may rely on their packing into a regular array such as a 2-D crystal, an icosahedral (viral) particle, or a helical assembly. Critically important for cryo-methods, each particle will only be exposed once to the electron beam, making these procedures optimal for highest-resolution studies where beam-induced damage is a significant concern. In contrast, tomographic 3-D reconstruction procedures (group B) do not rely on averaging, but collect an entire dataset from the very same structure of interest. Data acquisition requires collecting a large series of tilted projections at angular increments of 1–2° or less and a tilt range of ±60° or more. Accordingly, tomographic data collection exposes its specimens to a large electron dose, which is particularly problematic for frozen-hydrated samples. Currently, cryo-electron tomography is a rapidly emerging technology, on one end driven by the newest developments of hardware such as super-stabile microscopy stages as well as the latest generation of direct electron detectors and cameras. On the other end, success also strongly depends on new software developments on all kinds of fronts such as tilt-series alignment and back-projection procedures that are all adapted to the very low-dose and therefore very noisy primary data. Here, we will review the status quo of cryo-electron microscopy and discuss the future of cellular cryo-electron tomography from data collection to data analysis, CTF-correction of tilt-series, post-tomographic sub-volume averaging, and 3-D particle classification. We will also discuss the pros and cons of plunge freezing of cellular specimens to vitrified sectioning procedures and their suitability for post-tomographic volume averaging despite multiple artifacts that may distort specimens to some degree.     

Electron tomographic analysis of frozen-hydrated tissue sections

Electron tomography of frozen-hydrated tissue sections enables analysis of the 3-D structure of cell organelles in situ and in a near-native state. In this study, 160-200-nm-thick sections were cut from high-pressure frozen rat liver, and improved methods were used for handling and mounting the sections. Automated data collection facilitated tilt-series recording at low electron dose (approximately 4000 e(-)/nm(2) at 400 keV). Higher doses (up to 10,000 e(-)/nm(2)) were found to increase contrast and smooth out surface defects, but caused section distortion and movement, with likely loss of high-resolution information. Tomographic reconstruction showed that knife marks were 10-40 nm deep and located on the "knife face" of the section, while crevices were 20-50 nm deep and found on the "block face." The interior of the section was normally free of defects, except for compression, and contained useful structural information. For example, the topology of mitochondrial membranes in tissue was found to be very similar to that in frozen-hydrated whole mounts of isolated mitochondria. In rare cases, a 15-nm banding pattern perpendicular to the cutting direction was observed in the interior of the section, most evident in the uniformly dense, protein-rich material of the mitochondrial matrix.     

Radiation dose reduction and image enhancement in biological imaging through equally-sloped tomography

Electron tomography is currently the highest resolution imaging modality available to study the 3D structures of pleomorphic macromolecular assemblies, viruses, organelles and cells. Unfortunately, the resolution is currently limited to 3-5nm by several factors including the dose tolerance of biological specimens and the inaccessibility of certain tilt angles. Here we report the first experimental demonstration of equally-sloped tomography (EST) to alleviate these problems. As a proof of principle, we applied EST to reconstructing frozen-hydrated keyhole limpet hemocyanin molecules from a tilt-series taken with constant slope increments. In comparison with weighted back-projection (WBP), the algebraic reconstruction technique (ART) and the simultaneous algebraic reconstruction technique (SART), EST reconstructions exhibited higher contrast, less peripheral noise, more easily detectable molecular boundaries and reduced missing wedge effects. More importantly, EST reconstructions including only two-thirds the original images appeared to have the same resolution as full WBP reconstructions, suggesting that EST can either reduce the dose required to reach a given resolution or allow higher resolutions to be achieved with a given dose. EST was also applied to reconstructing a frozen-hydrated bacterial cell from a tilt-series taken with constant angular increments. The results confirmed similar benefits when standard tilts are utilized.     

The Structural Dilemma of Bulk Polyethylene: An Intermediary Structure

Background

The Fourier space (reciprocal space) image of bulk polyethylene consists of lines superimposed on the coherent diffuse background. The mixed character of the image indicates the complex nature of these compounds. The inability in detecting full images of reciprocal space of polymeric substances without Compton radiation and the other undesirable diffuse scatterings has misled the structural analysis (structural characterisation) of these materials.

Principal Findings

We propose the use of anomalous diffractometry where, it is possible to obtain a real image of reciprocal space without Compton radiation and other undesirable scatterings. By using classical diffractometry techniques this procedure is not possible. This methodology permitted us to obtain the “Direct Delta function”, in the case of polycrystalline substances that was not previously detected. A new procedure was proposed to interpret the image of reciprocal space of bulk polyethylene. The results show the predominance of the geometry of local order determination compared to the crystal unit cell. The analysis of x-ray diffraction images illustrates that the elementary structural unit is a tetrahedron. This structural unit illustrates the atoms in the network scatter in a coherent diffuse manner. Moreover, the interference function derived from the coherent diffuse scattering dampens out quickly and the degree of randomness is superior to a liquid state. The radial distribution function derived from this interference function shows bond shortening in the tetrahedron configuration. It is this particular effect, which stabilises polyethylene.

Conclusion

Here we show by anomalous diffractometry that the traditional concept of the two-phase or the crystal-defect model is an oversimplification of the complex reality. The exploitation of anomalous diffractometry has illustrated that polyethylene has an intermediate ordered structure.     

The "practical mathematics" of recording three-dimensional eye position using scleral coils.

The "gold standard" for recording the three-dimensional rotation of the eye involves placing two coils of wire, embedded in a soft plastic ring, on the sclera of the eye, then placing the subject inside a set of orthogonal oscillating magnetic fields, and using the currents induced in the eye coils to deduce the position of the coil, and hence of the eye, in space. Eye movements are actually eye rotations, which can be described mathematically by a special class of matrices, rotation matrices, or, alternatively, by a rotation vector related to the axis of the rotation. This article deals with the mathematical tools needed to implement the signal processing from such a multifield, dual-coil system and compute the precise rotational movement of the eye. One reason for making such careful measurements is to study an interesting constraint on eye movements, called Listing's law, which expresses ocular torsion, or rotation of the eye about its line of sight, in terms of the direction of gaze. Techniques for experimentally quantitating these constraints are also presented. Following a treatment of the "ideal" case, with coils and eye in perfect alignment, the additional techniques for dealing with various departures from ideality that are almost always encountered experimentally are examined. A final section deals with developing a validation protocol for eye movement analysis techniques using mechanical and computer simulations of eye movements.     

Quasi-independence,homology and the unity of type: a topological theory of characters

In this paper Lewontin's notion of "quasi-independence" of characters is formalized as the assumption that a region of the phenotype space can be represented by a product space of orthogonal factors. In this picture each character corresponds to a factor of a region of the phenotype space. We consider any region of the phenotype space that has a given factorization as a "type", i.e. as a set of phenotypes that share the same set of phenotypic characters. Using the notion of local factorizations we develop a theory of character identity based on the continuation of common factors among different regions of the phenotype space. We also consider the topological constraints on evolutionary transitions among regions with different regional factorizations, i.e. for the evolution of new types or body plans. It is shown that direct transition between different "types" is only possible if the transitional forms have all the characters that the ancestral and the derived types have and are thus compatible with the factorization of both types. Transitional forms thus have to go over a "complexity hump" where they have more quasi-independent characters than either the ancestral as well as the derived type. The only logical, but biologically unlikely, alternative is a "hopeful monster" that transforms in a single step from the ancestral type to the derived type. Topological considerations also suggest a new factor that may contribute to the evolutionary stability of "types". It is shown that if the type is decomposable into factors which are vertex irregular (i.e. have states that are more or less preferred in a random walk), the region of phenotypes representing the type contains islands of strongly preferred states. In other words types have a statistical tendency of retaining evolutionary trajectories within their interior and thus add to the evolutionary persistence of types.     

Dual-Axis Tomography: An Approach with Alignment Methods That Preserve Resolution

Tomographic reconstructions of biological specimens are now routinely being generated in our high voltage electron microscope by tilting the specimen around two orthogonal axes. Separate tomograms are computed from each tilt series. The two tomograms are aligned to each other with general 3-D linear transformations that can correct for distortions between the two tomograms, thus preserving the inherent resolution of the reconstruction throughout its volume. The 3-D Fourier transforms of the two tomograms are then selectively combined to achieve a single tomogram. Unlike a single-axis tomogram, a dual-axis tomogram shows good resolution for extended features at any orientation in the plane of the specimen; it also has improved resolution in the depth of the specimen. Calculations indicate that the improvements available from double tilting and from tilting to higher angles are largely additive. Actual and model data were used to assess whether varying the increment between tilted views in proportion to the cosine of the tilt angle would allow a reduction in the number of pictures required to achieve a given resolution of reconstruction. Analysis by Fourier sector correlation indicated that the variable tilt increment improved the reconstruction in some respects but degraded it in others. A varying tilt increment thus does not give an unqualified improvement, at least when using back-projection algorithms for the reconstruction.     

A novel dual-axis iterative algorithm for electron tomography

A new algorithm for computing electron microscopy tomograms which combines iterative methods with dual-axis geometry is presented. Initial modelling using test data shows several improvements over both the weighted back-projection and simultaneous iterative reconstruction technique methods, with increased stability and tomogram fidelity under high-noise conditions. Preliminary experimental dual-axis reconstructions confirm the viability of the new algorithm.     

Cytogenetic analysis of reciprocal hybrids and their parents between <Emphasis Type="Italic">Larix leptolepis</Emphasis> and <Emphasis Type="Italic">Larix gmelinii</Emphasis>: implications for identifying hybrids

We studied the parental taxa and the interspecific reciprocal hybrids between Larix leptolepis with Larix gmelinii, using classical cytogenetic methods, as well as fluorescence in situ hybridization (FISH) and genomic in situ hybridization. A high frequency (>90%) of complete bivalent formation was observed in reciprocal hybrids. Less than 10% of pollen mother cells exhibited abnormalities. The most frequent abnormalities were bridges. Multivalent chromosome associations were also observed in both reciprocal hybrids, suggesting that some chromosome interchange events did occur, and introgressions from one to the other species were possible. Intergenomic recombination indicates that genes might be readily introgressed into one species from the other in the genus Larix. Interspecific hybridization may be a potential method for genetic improvement in larch. FISH markers documented that the recombinant genomes of reciprocal hybrids were strictly additive and stable, indicating that FISH also might be a useful tool in Larix breeding.     

Rapid deformation of "passive" polymorphonuclear leukocytes: the effects of pentoxifylline

Entry times for spherical (no pseudopods) polymorphonuclear leukocytes (PMNs) into a 4 microns micropipet have been measured as a function of pipet suction pressure (2,500-20,000 dyn/cm2) and concentration of the drug pentoxifylline (PTX, 0.1-10.0 mM). For control cells (0 mM PTX), entry rates (reciprocal entry times) increased almost linearly with increasing suction pressure, indicating a Newtonian-like behavior. With incubation in PTX solutions, entry rate vs. suction pressure became increasingly non-linear, suggesting a shear-thinning effect for the dissipative structure. At a given suction pressure the rate of entry showed a dose-dependent increase with increasing PTX concentration, the effect being most pronounced at high suction pressures (20,000 dyn/cm2). Also, with increasing PTX concentration two other effects were observed: i) there was a decreased incidence of cells that displayed pseudopodia, and ii) there was an increased incidence of cells forming hernias and an increased streaming of cell cytoplasm during aspiration. The first observation points to a down-regulation of the cell's functional ability to "activate" in response to surface/chemical stimuli, and the second indicates that both the cortical and cytoskeletal networks are weakened either by disruption and/or reduction in density of the protein polymers. These observations are in line with other recently published experiments which suggest that the rheological effects of pentoxifylline on PMNs may be associated with the state of actin.     

Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes

Reciprocal crosses between species can yield hybrids with different viabilities. The high frequency of this asymmetric hybrid viability ("Darwin's corollary") places it alongside Haldane's rule and the "large-X effect" as a general feature of postmating reproductive isolation. Recent theory suggests that reciprocal cross asymmetries can arise from stochastic substitutions in uniparentally inherited loci such as mitochondrial genomes, although large systematic differences in mitochondrial substitution rates can also contribute to asymmetries. Although the magnitude of asymmetry will be relatively insensitive to unequal rates of mitochondrial evolution in diverging species, we show here that rate asymmetries can have a large effect on the direction of viability asymmetries. In reciprocal crosses between species, the maternal parent with faster mitochondrial evolution will tend to produce less viable F(1) hybrids owing to an increased probability of mito-nuclear incompatibilities. We test this prediction using data on reciprocal hybrid viability and molecular evolution rates from a clade of freshwater fishes, Centrarchidae. As predicted, species with accelerated mitochondrial evolution tend to be the worse maternal parent for F(1) hybrids, providing the first comparative evidence for a systematic basis to Darwin's corollary. This result is consistent with the hypothesis that mito-nuclear incompatibilities can play an important role in reproductive isolation. Such asymmetrical reproductive isolation may help explain the asymmetrical mitochondrial introgression observed between many hybridizing species. However, as with any comparative study, we cannot rule out the possibility that our results arise from a mutual correlation with a third variable such as body size.