Al Katz

Zika virus-like particle (VLP) based vaccine

The newly emerged mosquito-borne Zika virus poses a major public challenge due to its ability to cause significant birth defects and neurological disorders. The impact of sexual transmission is unclear but raises further concerns about virus dissemination. No specific treatment or vaccine is currently available, thus the development of a safe and effective vaccine is paramount. Here we describe a novel strategy to assemble Zika virus-like particles (VLPs) by co-expressing the structural (CprME) and non-structural (NS2B/NS3) proteins, and demonstrate their effectiveness as vaccines. VLPs are produced in a suspension culture of mammalian cells and self-assembled into particles closely resembling Zika viruses as shown by electron microscopy studies. We tested various VLP vaccines and compared them to analogous compositions of an inactivated Zika virus (In-ZIKV) used as a reference. VLP immunizations elicited high titers of antibodies, as did the In-ZIKV controls. However, in mice the VLP vaccine stimulated significantly higher virus neutralizing antibody titers than comparable formulations of the In-ZIKV vaccine. The serum neutralizing activity elicited by the VLP vaccine was enhanced using a higher VLP dose and with the addition of an adjuvant, reaching neutralizing titers greater than those detected in the serum of a patient who recovered from a Zika infection in Brazil in 2015. Discrepancies in neutralization levels between the VLP vaccine and the In-ZIKV suggest that chemical inactivation has deleterious effects on neutralizing epitopes within the E protein. This along with the inability of a VLP vaccine to cause infection makes it a preferable candidate for vaccine development.

Morphology of Influenza B/Lee/40 Determined by Cryo-Electron Microscopy

Cryo-electron microscopy projection image analysis and tomography is used to describe the overall architecture of influenza B/Lee/40. Algebraic reconstruction techniques with utilization of volume elements (blobs) are employed to reconstruct tomograms of this pleomorphic virus and distinguish viral surface spikes. The purpose of this research is to examine the architecture of influenza type B virions by cryo-electron tomography and projection image analysis. The aims are to explore the degree of ribonucleoprotein disorder in irregular shaped virions; and to quantify the number and distribution of glycoprotein surface spikes (hemagglutinin and neuraminidase) on influenza B. Projection image analysis of virion morphology shows that the majority (∼83%) of virions are spherical with an average diameter of 134±19 nm. The aspherical virions are larger (average diameteru200a=u200a155±47 nm), exhibit disruption of the ribonucleoproteins, and show a partial loss of surface protein spikes. A count of glycoprotein spikes indicates that a typical 130 nm diameter type B virion contains ∼460 surface spikes. Configuration of the ribonucleoproteins and surface glycoprotein spikes are visualized in tomogram reconstructions and EM densities visualize extensions of the spikes into the matrix. The importance of the viral matrix in organization of virus structure through interaction with the ribonucleoproteins and the anchoring of the glycoprotein spikes to the matrix is demonstrated.

Protein P7 of the cystovirus φ6 is located at the three-fold axis of the unexpanded procapsid.

The objective of this study was to determine the location of protein P7, the RNA packaging factor, in the procapsid of the φ6 cystovirus. A comparison of cryo-electron microscopy high-resolution single particle reconstructions of the φ6 complete unexpanded procapsid, the protein P2-minus procapsid (P2 is the RNA directed RNA-polymerase), and the P7-minus procapsid, show that prior to RNA packaging the P7 protein is located near the three-fold axis of symmetry. Difference maps highlight the precise position of P7 and demonstrate that in P7-minus particles the P2 proteins are less localized with reduced densities at the three-fold axes. We propose that P7 performs the mechanical function of stabilizing P2 on the inner protein P1 shell which ensures that entering viral single-stranded RNA is replicated.

Influence of cations on aggregation rates in Mg-montmorillonite

Critical-zone reactions involve inorganic and biogenic colloids in a cation-rich environment. The present research defines the rates and structure of purified Mg-montmorillonite aggregates formed in the presence of monovalent (K+) and divalent (Ca2+, Mg 2+) cations using light-extinction measurements. Time evolution of turbidity was employed to determine early-stage aggregation rates. Turbidity spectra were used to measure the fractal dimension at later stages. The power law dependence of the stability ratios on cation concentration was found to vary with the reciprocal of the valence rather than the predicted reciprocal of valence-squared, indicating that the platelet structure may be a factor influencing aggregation rates. The critical coagulation concentrations (CCC) (3 mM for CaCl2, 4 mM for MgCl2, and 70 mM for KCl) were obtained from the stability ratios. At a later time and above a minimal cation concentration, turbidity reached a quasi-stable state, indicating the formation of large aggregates. Under this condition, an approximate turbidity forward-scattering correction factor was applied and the fractal dimension was determined from the extinction spectra. For the divalent cations, the fractal dimensions were 1.65 ± 0.3 for Ca2+ and 1.75 ± 0.3 for Mg2+ and independent of cation concentrations above the CCC. For the monovalent cation, the fractal dimension increased with K+ concentration from 1.35 to 1.95, indicating a transition to a face-to-face geometry from either an edge-to-edge or edge-to-face orientation.

Disassembly of the cystovirus ϕ6 envelope by montmorillonite clay

Prior studies of clay–virus interactions have focused on the stability and infectivity of nonenveloped viruses, yielding contradictory results. We hypothesize that the surface charge distribution of the clay and virus envelope dictates how the components react and affect aggregation, viral stability, and infectivity. The bacteriophage Cystoviridae species φ6 used in this study is a good model for enveloped pathogens. The interaction between φ6 and montmorillonite (MMT) clay (the primary component of bentonite) is explored by transmission electron microscopy. The analyses show that MMT–φ6 mixtures undergo heteroaggregation, forming structures in which virtually all the virions are either sequestered between MMT platelet layers or attached to platelet edges. The virions swell and undergo disassembly resulting in partial or total envelope loss. Edge‐attached viral envelopes distort to increase contact area with the positively charged platelet edges indicating that the virion surface is negatively charged. The nucleocapsid (NCs) remaining after envelope removal also exhibit distortion, in contrast to detergent‐produced NCs which exhibit no distortion. This visually discernible disassembly is a mechanism for loss of infectivity previously unreported by studies of nonenveloped viruses. The MMT‐mediated sequestration and disassembly result in reduced infectivity, suggesting that clays may reduce infectivity of enveloped pathogenic viruses in soils and sediments.

Computational Methods for Electron Tomography of Influenza Virus

Influenza is a rapidly changing virus that appears seasonally in the human population. Every year a new strain of the influenza virus appears with the potential to cause a serious global pandemic. Knowledge of the structure and density of the surface proteins is of critical importance in a vaccine candidate. Reconstruction techniques from a series of tilted electron-tomographic projection images provide quantification of surface proteins. Two major categories of reconstruction techniques are transform methods such as weighted backprojection (WBP) and series expansion methods such as the algebraic reconstruction techniques (ART) and the simultaneous iterative reconstruction technique (SIRT). Series expansion methods aim at estimating the object to be reconstructed by a linear combination of some fixed basis functions and they typically estimate the coefficients in such an expansion by an iterative algorithm. The choice of the set of basis functions greatly influences the result of a series expansion method. It has been demonstrated repeatedly that using spherically symmetric basis functions (blobs), instead of the more traditional voxels, results in reconstructions of superior quality, provided that the free parameters that occur in the definition of the family of blobs are appropriately tuned. In this chapter, it is demonstrated that, with the recommended data-processing steps performed on the projection images prior to reconstruction, series expansion methods such as ART (with its free parameters appropriately tuned) will provide 3D reconstructions of viruses from tomographic tilt series that allow reliable quantification of the surface proteins and that the same is not achieved using WBP.

Component tree analysis of cystovirus φ6 nucleocapsid Cryo-EM single particle reconstructions

The 3-dimensional structure of the nucleocapsid (NC) of bacteriophage φ6 is described utilizing component tree analysis, a topological and geometric image descriptor. The component trees are derived from density maps of cryo-electron microscopy single particle reconstructions. Analysis determines position and occupancy of structure elements responsible for RNA packaging and transcription. Occupancy of the hexameric nucleotide triphosphorylase (P4) and RNA polymerase (P2) are found to be essentially complete in the NC. The P8 protein lattice likely fixes P4 and P2 in place during maturation. We propose that the viral procapsid (PC) is a dynamic structural intermediate where the P4 and P2 can attach and detach until held in place in mature NCs. During packaging, the PC expands to accommodate the RNA, and P2 translates from its original site near the inner 3-fold axis (20 sites) to the inner 5-fold axis (12 sites) with excess P2 positioned inside the central region of the NC.

The ϕ6 Cystovirus Protein P7 Becomes Accessible to Antibodies in the Transcribing Nucleocapsid: A Probe for Viral Structural Elements

Protein P7 is a component of the cystovirus viral polymerase complex. In the unpackaged procapsid, the protein is situated in close proximity to the viral directed RNA polymerase, P2. Cryo-electron microscopy difference maps from the species ϕ6 procapsid have demonstrated that P7 and P2 likely interact prior to viral RNA packaging. The location of P7 in the post-packaged nucleocapsid (NC) remains unknown. P7 may translocate closer to the five-fold axis of a filled procapsid but this has not been directly visualized. We propose that monoclonal antibodies (Mabs) can be selected that serve as probe- reagents for viral assembly and structure. A set of Mabs have been isolated that recognize and bind to the ϕ6 P7. The antibody set contains five unique Mabs, four of which recognize a linear epitope and one which recognizes a conformational epitope. The four unique Mabs that recognize a linear epitope display restricted utilization of Vκ and VH genes. The restricted genetic range among 4 of the 5 antibodies implies that the antibody repertoire is limited. The limitation could be the consequence of a paucity of exposed antigenic sites on the ϕ6 P7 surface. It is further demonstrated that within ϕ6 nucleocapsids that are primed for early-phase transcription, P7 is partially accessible to the Mabs, indicating that the nucleocapsid shell (protein P8) has undergone partial disassembly exposing the protein’s antigenic sites.

Heteroaggregation of an enveloped bacteriophage with colloidal sediments and effect on virus viability

n Abstractn n Four sediments in the colloidal size range: goethite, montmorillonite, illite, and kaolinite, were suspended with the bacteriophage φ6, a model enveloped virus, to determine relative rates of heteroaggregation and the effect of aggregation on virus viability. Turbidity was measured on combinations of virus and each sediment type at low concentration to determine aggregation rates. Aggregation of sediment with virus occurred regardless of mineral type, and larger fraction of virus is expected to aggregate with increasing sediment concentration leading to higher deposition rates. The negatively charged sediments, aggregated with φ6 (also negatively charged at neutral pH) at a faster rate than the positively charged sediments, yielding turbidity slopes of 4.94u202f×u202f10−3u202fs−1 and 7.50u202f×u202f10−4u202fs−1 for φ6-montmorillonite and φ6-illite aggregates, respectively, and 2.98u202f×u202f10−5u202fs−1 and 2.84u202f×u202f10−5u202fs−1, for φ6-goethite and φ6-kaolinite, respectively. This indicates that the interaction between sediments and virus is hydrophobic, rather than electrostatic. Large numbers of virions remained viable post-aggregation, despite the fragility of the viral envelope, indicating that small-sized aggregates, which may travel more readily through porous media, may pose an infection risk. The fraction of φ6 that remained viable varied with sediment type, with montmorillonite-φ6 aggregates experiencing the greatest reduction in infectivity at 35%. TEM analyses reveal that in all sediment-φ6 combinations, infectivity loss was likely due to disassembly of the viral envelope as a result of aggregation.n n

Using a Topological Descriptor to Investigate Structures of Virus Particles

An understanding of the three-dimensional structure of a biological macromolecular complex is essential to fully understand its function. A component tree is a topological and geometric image descriptor that captures information regarding the structure of an image based on the connected components determined by different grayness thresholds. We believe interactive visual exploration of component trees of the density maps of macromolecular complexes can yield much information about their structure. To illustrate how component trees can convey important structural information, we consider component trees of four recombinant procapsids of a bacteriophage cystovirus i¾?6, and show how differences between the component trees reflect the fact that each non-wild-type mutant of the procapsid has an incomplete set of constituent proteins.