Reconstructions of two packaging vertex deficient particles at 22 and 18 Å resolutions without icosahedral symmetry imposition.

<p>(A) A typical micrograph of Sus526 mutant particles (P6<i>⁻</i>, P9<i>⁻</i>, P20<i>⁻</i> (P22<i>⁻</i>), DNA-P8<i>⁻</i>). (B) The top view and (C) the central slice view of the Sus526 reconstruction. (D) A typical micrographs of Sus42 mutant particles (P6<i>⁻</i>, P9<i>⁻</i>, (P20<i>⁻</i>), P22<i>⁻</i>, DNA-P8<i>⁻</i>). (E) The top view and (F) the central slice view of the Sus42 reconstruction.</p

Reconstruction of PRD1 virion at 12 Å resolution without icosahedral symmetry imposition.

<p>(A) A typical micrograph of the PRD1 virions. (B) The top view and (C) the central slice view of the reconstruction. (D) The unique vertex occupies one of the 12 pentonal positions and interacts with the capsid proteins at its outer edge. (E) The other 11 vertices have a regular 5-fold structure. (F) The crystal structure of the MCP P3 of PRD1 (PDB code 1W8X, chain B) fitted in the corresponding segmented density in the cryo-EM map, allowing the boundary delineation of the unique vertex complex and the MCPs surrounding it.</p

Properties of reconstructions of virion, procapsid, and mutant particles of PRD1.

a<p>Determined at full width half the maximum of the peak.</p>b<p>Based on radially averaging the central section of each reconstruction and comparing the averaged intensity of the membrane layer to the capsid layer.</p><p>Properties of reconstructions of virion, procapsid, and mutant particles of PRD1.</p

PLEMT: A Novel Pseudolikelihood-Based EM Test for Homogeneity in Generalized Exponential Tilt Mixture Models

<p>Motivated by analyses of DNA methylation data, we propose a semiparametric mixture model, namely, the generalized exponential tilt mixture model, to account for heterogeneity between differentially methylated and nondifferentially methylated subjects in the cancer group, and capture the differences in higher order moments (e.g., mean and variance) between subjects in cancer and normal groups. A pairwise pseudolikelihood is constructed to eliminate the unknown nuisance function. To circumvent boundary and nonidentifiability problems as in parametric mixture models, we modify the pseudolikelihood by adding a penalty function. In addition, the test with simple asymptotic distribution has computational advantages compared with permutation-based test for high-dimensional genetic or epigenetic data. We propose a pseudolikelihood-based expectation–maximization test, and show the proposed test follows a simple chi-squared limiting distribution. Simulation studies show that the proposed test controls Type I errors well and has better power compared to several current tests. In particular, the proposed test outperforms the commonly used tests under all simulation settings considered, especially when there are variance differences between two groups. The proposed test is applied to a real dataset to identify differentially methylated sites between ovarian cancer subjects and normal subjects. Supplementary materials for this article are available online.</p

The unique vertex organization.

<p>(A) The side view, (B) the central slice view, and (C) the top slice view of the segmented unique vertex in the mature virion. The cut-through view (C) (location labeled as the orange dashed line in (A) and (B)) shows the 12 arms (numbered 1 to 12) of the central part of the unique vertex and the extra surrounding densities. (D) The side view, (E) the side slice view, and (F) the top slice view of the segmented transmembrane density in the procapsid. The top slice view (F) (location labeled as the orange dashed line in (D)) shows the 12 arms of the structure organized as hexameric dimers (numbered 1 to 6 in circles). The density of the unique vertex in the procapsid (grey) is shown on that of the mature virion (cyan) as a side slice view (G) and top slice view (H).</p

Simulated relative efficiency (RE) for combined (CE) and positive part shrinkage (PP) estimators relative to unrestricted estimator (UE) for different values of <i>ϵ</i>.

<p>Simulated relative efficiency (RE) for combined (CE) and positive part shrinkage (PP) estimators relative to unrestricted estimator (UE) for different values of <i>ϵ</i>.</p

The survival curves of the four Kaplan-Meier (KM) estimates for time to receiving the first unit of RBC from site 1 (n1 = 303, solid line), site 2 (n2 = 137, dashed), site 3 (n3 = 133, dotted), and site 4 (n4 = 125, dot-dashed), respectively.

<p>The survival curves of the four Kaplan-Meier (KM) estimates for time to receiving the first unit of RBC from site 1 (n1 = 303, solid line), site 2 (n2 = 137, dashed), site 3 (n3 = 133, dotted), and site 4 (n4 = 125, dot-dashed), respectively.</p

Delineating the boundary between the unique vertex and the surrounding major capsid proteins.

<p>(A) The ribbon representation of the regular 5-fold vertex structure (PDB code 1W8X). The penton P31 is shown in dark blue and the surrounding peripentonal P3 trimers are shown in five colors, each of which belongs to one asymmetric unit. (B) The top view and (C) the side slice view of the segmented unique vertex density (grey) surrounded by ten P3 trimers. The unique vertex replaces the penton and five peripentonal P3 trimers (shown as transparent gray density in (A)). (D) The electrostatic potential surface of the surrounding peripentonal MCP P3s was calculated with APBS and colored in Chimera ranging from red (negative) to blue (positive) with central slice view.</p

Wt and mutant PRD1 viruses and their properties.

a<p><i>S. enterica</i> serovar Typhimurium LT2 suppressor strain harboring plasmid pLM2 <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002024#pbio.1002024-Mindich3" target="_blank">[74]</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002024#pbio.1002024-Winston1" target="_blank">[75]</a>.</p>b<p><i>S. enterica</i> serovar Typhimurium LT2 DS88 <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002024#pbio.1002024-Bamford7" target="_blank">[73]</a>.</p>c<p>Presence of the protein in the particle is rather uncertain based on biochemical analysis.</p><p>Wt and mutant PRD1 viruses and their properties.</p

Mean of 1000 estimated medians and REs for 0%, 30% and 50% censoring rates for uniform, log-normal and exponential distributions when sample size is 100.

<p>Mean of 1000 estimated medians and REs for 0%, 30% and 50% censoring rates for uniform, log-normal and exponential distributions when sample size is 100.</p