Ultra-stable super-resolution fluorescence cryo-microscopy for correlative light and electron cryo-microscopy

Remarkable progress in correlative light and electron cryo-microscopy(cryo-CLEM) has been made in the past decade. A crucial component for cryo-CLEM is a dedicated cryo-fluorescence microscope(cryo-FM). Here, we describe an ultra-stable superresolution cryo-FM that exhibits excellent thermal and mechanical stability. The temperature fluctuations in 10 h are less than0.06 K, and the mechanical drift over 5 h is less than 200 nm in three dimensions. We have demonstrated the super-resolution imaging capability of this system(average single molecule localization accuracy of ～13.0 nm). The results suggest that our system is particularly suitable for long-term observations, such as single molecule localization microscopy(SMLM) and cryogenic super-resolution correlative light and electron microscopy(csCLEM).     

Fine structure of influenza A virus observed by electron cryo-microscopy.

A rapidly frozen vitrified aqueous suspension of influenza A virus was observed by high resolution electron cryomicroscopy. The influenza particles were grouped into small (diameter < 150 nm) spherical particles with well organized interiors, large spherical ones with less internal organization, and filamentous ones. Envelopes of most of the large virus particles were phospholipid bilayers, and the chromatography fraction containing these large particles was largely devoid of viral activity. The envelopes of most of the filamentous and small spherical virus particles, on the other hand, gave a strange contrast which could be ascribed to a combination of a thin outer lipid monolayer and a 7.2 nm thick protein-containing inner layer. These latter particles represented most of the viral activity in the preparation. Densitometric traces of the near in-focus images confirmed these structural differences. Some viral envelope structures apparently intermediate between these two distinct types of membrane were also detected. A structural model of intact biologically active influenza virus particles was formulated from these results, together with computer simulations.     

Marker-free method for accurate alignment between correlated light,cryo-light,and electron cryo-microscopy data using sample support features

Combining fluorescence microscopy with electron cryo-tomography allows, in principle, spatial localization of tagged macromolecular assemblies and structural features within the cellular environment. To allow precise localization and scale integration between the two disparate imaging modalities, accurate alignment procedures are needed. Here, we describe a marker-free method for aligning images from light or cryo-light fluorescence microscopy and from electron cryo-microscopy that takes advantage of sample support features, namely the holes in the carbon film. We find that the accuracy of this method, as judged by prediction errors of the hole center coordinates, is better than 100?nm.     

Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy

The light-driven proton pump bacteriorhodopsin occurs naturally as two-dimensional crystals. A three-dimensional density map of the structure, at near-atomic resolution, has been obtained by studying the crystals using electron cryo-microscopy to obtain electron diffraction patterns and high-resolution micrographs. New methods were developed for analysing micrographs from tilted specimens, incorporating methods previously developed for untilted specimens that enable large areas to be analysed and corrected for distortions. Data from 72 images, from both tilted and untilted specimens, were analysed to produce the phases of 2700 independent Fourier components of the structure. The amplitudes of these components were accurately measured from 150 diffraction patterns. Together, these data represent about half of the full three-dimensional transform to 3.5 A. The map of the structure has a resolution of 3.5 A in a direction parallel to the membrane plane but lower than this in the perpendicular direction. It shows many features in the density that are resolved from the main density of the seven alpha-helices. We interpret these features as the bulky aromatic side-chains of phenylalanine, tyrosine and tryptophan residues. There is also a very dense feature, which is the beta-ionone ring of the retinal chromophore. Using these bulky side-chains as guide points and taking account of bulges in the helices that indicate smaller side-chains such as leucine, a complete atomic model for bacteriorhodopsin between amino acid residues 8 and 225 has been built. There are 21 amino acid residues, contributed by all seven helices, surrounding the retinal and 26 residues, contributed by five helices, forming the proton pathway or channel. Ten of the amino acid residues in the middle of the proton channel are also part of the retinal binding site. The model also provides a useful basis for consideration of the mechanism of proton pumping and allows a consistent interpretation of a great deal of other experimental data. In particular, the structure suggests that pK changes in the Schiff base must act as the means by which light energy is converted into proton pumping pressure in the channel. Asp96 is on the pathway from the cytoplasm to the Schiff base and Asp85 is on the pathway from the Schiff base to the extracellular surface.     

Analysis of macromolecular structure and dynamics by electron cryo-microscopy.

Electron cryo-microscopy has yielded a wealth of detailed new information on structures of biological macromolecules ranging from alphabeta-tubulin at 3.7 A resolution to hepatitis B virus at 7.4 A resolution, as well as a number of membrane proteins at 6-8 A resolution. Much of this progress was made possible by recent advances in instrumentation and image processing techniques.     

Visualization of the domain structure of an L-type Ca2+ channel using electron cryo-microscopy

The three-dimensional structure of the skeletal muscle voltage-gated L-type calcium channel (Ca(v)1.1; dihydropyridine receptor, DHPR) was determined using electron cryo-microscopy and single-particle averaging. The structure shows a single channel complex with an approximate total molecular mass of 550 kDa, corresponding to the five known subunits of the DHPR, and bound detergent and lipid. Features visible in our structure together with antibody labeling of the beta and alpha(2) subunits allowed us to assign locations for four of the five subunits within the structure. The most striking feature of the structure is the extra-cellular alpha(2) subunit that protrudes from the membrane domain in close proximity to the alpha(1) subunit. The cytosolic beta subunit is located close to the membrane and adjacent to subunits alpha(1), gamma and delta. Our structure correlates well with the functional and biochemical data available for this channel and suggests a three-dimensional model for the excitation-contraction coupling complex consisting of DHPR tetrads and the calcium release channel.     

Structure of native and expanded sobemoviruses by electron cryo-microscopy and image reconstruction

Rice yellow mottle virus (RYMV) and southern bean mosaic virus, cowpea strain (SCPMV) are members of the Sobemovirus genus of RNA-containing viruses. We used electron cryo-microscopy (cryo-EM) and icosahedral image analysis to examine the native structures of these two viruses at 25 A resolution. Both viruses have a single tightly packed capsid layer with 180 subunits assembled on a T=3 icosahedral lattice. Distinctive crown-like pentamers emanate from the 12 5-fold axes of symmetry. The exterior face of SCPMV displays deep valleys along the 2-fold axes and protrusions at the quasi-3-fold axes. While having a similar topography, the surface of RYMV is comparatively smooth. Two concentric shells of density reside beneath the capsid layer of RYMV and SCPMV, which we interpret as ordered regions of genomic RNA. In the presence of divalent cations, SCPMV particles swell and fracture, whereas the expanded form of RYMV is stable. We previously proposed that the cell-to-cell movement of RYMV in xylem involves chelation of Ca(2+) from pit membranes of infected cells, thereby stabilizing the capsid shells and allowing a pathway for spread of RYMV through destabilized membranes. In the context of this model, we propose that the expanded form of RYMV is an intermediate in the in vivo assembly of virions.     

A machine learning approach for the identification of protein secondary structure elements from electron cryo-microscopy density maps

The accuracy of the secondary structure element (SSE) identification from volumetric protein density maps is critical for de-novo backbone structure derivation in electron cryo-microscopy (cryoEM). It is still challenging to detect the SSE automatically and accurately from the density maps at medium resolutions (～5-10 ?). We present a machine learning approach, SSELearner, to automatically identify helices and β-sheets by using the knowledge from existing volumetric maps in the Electron Microscopy Data Bank. We tested our approach using 10 simulated density maps. The averaged specificity and sensitivity for the helix detection are 94.9% and 95.8%, respectively, and those for the β-sheet detection are 86.7% and 96.4%, respectively. We have developed a secondary structure annotator, SSID, to predict the helices and β-strands from the backbone Cα trace. With the help of SSID, we tested our SSELearner using 13 experimentally derived cryo-EM density maps. The machine learning approach shows the specificity and sensitivity of 91.8% and 74.5%, respectively, for the helix detection and 85.2% and 86.5% respectively for the β-sheet detection in cryoEM maps of Electron Microscopy Data Bank. The reduced detection accuracy reveals the challenges in SSE detection when the cryoEM maps are used instead of the simulated maps. Our results suggest that it is effective to use one cryoEM map for learning to detect the SSE in another cryoEM map of similar quality.     

Structure of influenza haemagglutinin at neutral and at fusogenic pH by electron cryo-microscopy

The three-dimensional structures of the complete haemagglutinin (HA) of influenza virus A/Japan/305/57 (H2N2) in its native (neutral pH) and membrane fusion-competent (low pH) form by electron cryo-microscopy at a resolution of 10 A and 14 A, respectively, have been determined. In the fusion-competent form the subunits remain closely associated preserving typical overall features of the trimeric ectodomain at neutral pH. Rearrangements of the tertiary structure in the distal and the stem parts are associated with the formation of a central cavity through the entire ectodomain. We suggest that the cavity is essential for relocation of the so-called fusion sequence of HA towards the target membrane.     

3-dimensional imaging of collagen using second harmonic generation

Collagen is the most important structural protein of the animal body. Its unique triple-helix structure and extremely high level of crystallinity make it exceptionally efficient in generating the second harmonic of incident light, and we show here how this leads to a novel mode of microscopy of immediate practical significance in medicine and biology. In particular, it provides sensitive and high-resolution information on collagen distribution, discriminates between type I and type III collagen, and allows both a greater understanding of and a sensitive test for cirrhosis of the liver. Future research applications could include wound healing and hereditary collagen diseases such as osteogenesis imperfecta.     

A second generation universal microarray for subtyping influenza a virus

The microchip for influenza A subtyping working on the ??one spot-one subtype?? principle was developed. Each spot contains a set of oligonucleotide probes specific for particular subtypes of hemagglutinin, neuraminidase and matrix protein (influenza A marker). Reliability of the proposed chip is the same as for the full-size microchip for separate hemagglutinin and neuraminidase typing which was created in our group earlier. The image was visualized by labeling the analyzed nucleic acid by either fluorescent dye or biotin with the following fixation in streptavidin-gold nanoparticles and development by silver precipitation. In the second case, the image was analyzed using an ordinary scanner that essentially simplifies influenza A subtyping.     

Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy

We explore structural characterization of protein assemblies by a combination of electron cryo-microscopy (cryoEM) and comparative protein structure modeling. Specifically, our method finds an optimal atomic model of a given assembly subunit and its position within an assembly by fitting alternative comparative models into a cryoEM map. The alternative models are calculated by MODELLER [J. Mol. Biol. 234 (1993) 313] from different sequence alignments between the modeled protein and its template structures. The fitting of these models into a cryoEM density map is performed either by FOLDHUNTER [J. Mol. Biol. 308 (2001) 1033] or by a new density fitting module of MODELLER (Mod-EM). Identification of the most accurate model is based on the correlation between the model accuracy and the quality of fit into the cryoEM density map. To quantify this correlation, we created a benchmark consisting of eight proteins of different structural folds with corresponding density maps simulated at five resolutions from 5 to 15 angstroms, with three noise levels each. Each of the proteins in the set was modeled based on 300 different alignments to their remotely related templates (12-32% sequence identity), spanning the range from entirely inaccurate to essentially accurate alignments. The benchmark revealed that one of the most accurate models can usually be identified by the quality of its fit into the cryoEM density map, even for noisy maps at 15 angstroms resolution. Therefore, a cryoEM density map can be helpful in improving the accuracy of a comparative model. Moreover, a pseudo-atomic model of a component in an assembly may be built better with comparative models of the native subunit sequences than with experimentally determined structures of their homologs.     

A laboratory apparatus for the generation and biocide efficacy testing of Legionella biofilms

P.N. GREEN AND R.S. PIRRIE. 1993. The construction and operation of a laboratory biofilm generator designed to grow sessile populations of legionellas for biocide efficacy testing is described. Some examples of static biocide testing on both sessile and planktonic populations of Legionella bozemanii are discussed along with other potential applications of the apparatus.     

The generation of non-linear solute gradients for chromatography by using only simple apparatus.

It is shown that by using only a series of tubes with constant cross-sectional area and a single-channel peristaltic pump, it is possible to produce solute gradients with time profiles that are concave, convex, sigmoid or even with turning points. The general theory for predicting gradients, by using tubes in series that are either open or closed to the atmosphere, is presented, and the equations using three compartments are given. Experiments are described that support the usefulness and accuracy of such a theoretical treatment.     

Development of a second generation linkage map for almond using RAPD and SSR markers.

Fifty-four RAPD (random amplified polymorphic DNA) markers and 6 SSRs (simple sequence repeats) were included in a molecular marker map with 120 RFLPs (restriction fragment length polymorphisms) and 7 isozyme genes previously constructed using the offspring of a cross between the almond (Prunus amygdalus) cultivars 'Ferragnès' and 'Tuono'. Only highly reproducible RAPDs segregating 1:1 were used. To identify these markers, a total of 325 primers were screened, from which 41 produced RAPDs useful for mapping. Polymorphism was detected in six of the eight Prunus SSRs (simple sequence repeats) studied, thus enabling these to be mapped. All markers were placed on the 8 linkage groups previously identified. The number of new markers included in the map of 'Ferragnès' was 33 for a total of 126, and 30 in the map of 'Tuono' for a total of 99. The sizes of the maps of 'Ferragnès' (415 cM) and 'Tuono' (416 cM) were similar, representing a 5% increase over the maps constructed solely with isozymes and RFLPs. The estimated total size of the almond map was of 457 cM. Some markers were placed in zones with low density of markers and others in the extreme of linkage groups. The use of RAPD markers to complete genetic maps constructed with transferable markers is discussed.     

A second generation microcomputer controlled binding system for alpine skiing research

In the study of sports biomechanics, alpine skiing injuries have always demanded significant attention. In order to aid in understanding the loading phenomena associated with alpine skiing, a new research binding system has been designed which enables both the recording of boot loading data and actively controlled release of the skier's boot from the ski. The new research binding system consists of three hardware components, a dynamometer which senses all six load components at the boot/ski interface, an electromechanical device capable of releasing the boot from the ski, and a new general purpose microprocessor-based data acquisition and release control module. Constructed integrally with the dynamometer, the release mechanism is activated by electrical command from the control module. The mechanical and electrical design features of the dynamometer/release mechanism as well as important features of the hardware and software of the data acquisition and control module are briefly discussed. The system has been tested both in the laboratory and on the ski slopes. The emphasis of this paper is on the boot loading data acquired through field testing and observations on the loading environment during common recreational skiing maneuvers. Through analysis of the data, insight into both the style and safety aspects of alpine skiing is gained.     

Subunit disassembly and unfolding kinetics of hemoglobin studied by time-resolved electrospray mass spectrometry

We report the use of electrospray ionization (ESI) mass spectrometry (MS) in conjunction with online rapid mixing to monitor the kinetics of acid-induced ferrihemoglobin denaturation. Under equilibrium conditions, the hemoglobin mass spectrum is dominated by the intact heterotetramer. Dimeric and monomeric species are also observed at lower intensities. In addition, ionic signals corresponding to hexameric (tetramer-dimer) and octameric (tetramer x 2) hemoglobin species are observed. These complexes may represent weak solution-phase assemblies. The acid-induced denaturation process was monitored for reaction time ranging from 9 ms to approximately 3 s. The data obtained were subjected to a global analysis procedure which simultaneously fit all kinetic (ESI-MS intensity vs time) profiles to multiexponential expressions. Results of the global analysis are consistent with the coexistence of two subpopulations of tetrameric hemoglobin which differ in their disassembly rates and ESI charge states. The higher-charge state tetramer ions preferentially dissociate via a rapid pathway (tau(1) = 51 ms), resulting in the transient formation of a heme-saturated dimer, holo-alpha-globin, and a heme-deficient dimer. The latter is shown by MS/MS to be comprised of a heme-bound alpha-subunit complexed with an apo-beta-chain. The slow-decaying tetramer population, apparent at a slightly lower average charge state, breaks down into its monomeric constituents with no observable intermediate species (tau(2) = 390 ms). Surprisingly, unfolded apo-alpha-globin is formed more rapidly than unfolded apo-beta-globin. The appearance of the latter occurs with a relaxation time tau(3) of 1.2 s. It is postulated that accumulation of unfolded apo-beta-globin is delayed by transient population of an undetected unfolding intermediate.     

A second generation climate index for tourism (CIT): specification and verification

Climate is a key resource for many types of tourism and as such can be measured and evaluated. An index approach is required for this task because of the multifaceted nature of weather and the complex ways that weather variables come together to give meaning to climate for tourism. Here we address the deficiencies of past indices by devising a theoretically sound and empirically tested method that integrates the various facets of climate and weather into a single index called the Climate Index for Tourism (CIT). CIT rates the climate resource for activities that are highly climate/weather sensitive, specifically, beach “sun, sea and sand” (3S) holidays. CIT integrates thermal (T), aesthetic (A) and physical (P) facets of weather, which are combined in a weather typology matrix to determine a climate satisfaction rating that ranges from very poor (1 = unacceptable) to very good (7 = optimal). Parameter A refers to sky condition and P to rain or high wind. T is the body-atmosphere energy balance that integrates the environmental and physiological thermal variables, such as solar heat load, heat loss by convection (wind) and by evaporation (sweating), longwave radiation exchange and metabolic heat (activity level). Rather than use T as a net energy (calorific) value, CIT requires that it be expressed as thermal sensation using the standard nine-point ASHRAE scale (“very hot” to “very cold”). In this way, any of the several body-atmosphere energy balance schemes available may be used, maximizing the flexibility of the index. A survey (N = 331) was used to validate the initial CIT. Respondents were asked to rate nine thermal states (T) with different sky conditions (A). They were also asked to assess the impact of high winds or prolonged rain on the perceived quality of the overall weather condition. The data was analysed statistically to complete the weather typology matrix, which covered every possible combination of T, A and P. Conditions considered to be optimal (CIT class 6–7) for 3S tourism were those that were “slightly warm” with clear skies or scattered cloud (≤25% cloud). Acceptable conditions (CIT = 4–5) fell within the thermal range “indifferent” to “hot” even when the sky was overcast. Wind equal to or in excess of 6 m/s (22 km/h) or rain resulted in the CIT rating dropping to 1 or 2 (unacceptable) and was thus an override of pleasant thermal conditions. Further cross-cultural research is underway to examine whether climate preferences vary with different social and cultural tourist segments internationally.     

Assessing the capabilities of a 4kx4k CCD camera for electron cryo-microscopy at 300kV

CCD cameras have numerous advantages over photographic film for detecting electrons; however the point spread function of these cameras has not been sufficient for single particle data collection to subnanometer resolution with 300kV microscopes. We have adopted spectral signal to noise ratio (SNR) as a parameter for assessing detector quality for single particle imaging. The robustness of this parameter is confirmed under a variety of experimental conditions. Using this parameter, we demonstrate that the SNR of images of either amorphous carbon film or ice embedded virus particles collected on a new commercially available 4kx4k CCD camera are slightly better than photographic film at low spatial frequency (<1/5 Nyquist frequency), and as good as photographic film out to half of the Nyquist frequency. In addition it is slightly easier to visualize ice embedded particles on this CCD camera than on photographic film. Based on this analysis it is realistic to collect images containing subnanometer resolution data (6-9A) using this CCD camera at an effective magnification of approximately 112000x on a 300kV electron microscope.