A library of infectious hepatitis C viruses with engineered mutations in the E2 gene reveals growth-adaptive mutations that modulate interactions with scavenger receptor class B type I

While natural hepatitis C virus (HCV) infection results in highly diverse quasispecies of related viruses over time, mutations accumulate more slowly in tissue culture, in part because of the inefficiency of replication in cells. To create a highly diverse population of HCV particles in cell culture and identify novel growth-enhancing mutations, we engineered a library of infectious HCV with all codons represented at most positions in the ectodomain of the E2 gene. We identified many putative growth-adaptive mutations and selected nine highly represented E2 mutants for further study: Q412R, T416R, S449P, T563V, A579R, L619T, V626S, K632T, and L644I. We evaluated these mutants for changes in particle-to-infectious-unit ratio, sensitivity to neutralizing antibody or CD81 large extracellular loop (CD81-LEL) inhibition, entry factor usage, and buoyant density profiles. Q412R, T416R, S449P, T563V, and L619T were neutralized more efficiently by anti-E2 antibodies and T416R, T563V, and L619T by CD81-LEL. Remarkably, all nine variants showed reduced dependence on scavenger receptor class B type I (SR-BI) for infection. This shift from SR-BI usage did not correlate with a change in the buoyant density profiles of the variants, suggesting an altered E2-SR-BI interaction rather than changes in the virus-associated lipoprotein-E2 interaction. Our results demonstrate that residues influencing SR-BI usage are distributed across E2 and support the development of large-scale mutagenesis studies to identify viral variants with unique functional properties. IMPORTANCE Characterizing variant viruses can reveal new information about the life cycle of HCV and the roles played by different viral genes. However, it is difficult to recapitulate high levels of diversity in the laboratory because of limitations in the HCV culture system. To overcome this limitation, we engineered a library of mutations into the E2 gene in the context of an infectious clone of the virus. We used this library of viruses to identify nine mutations that enhance the growth rate of HCV. These growth-enhancing mutations reduced the dependence on a key entry receptor, SR-BI. By generating a highly diverse library of infectious HCV, we mapped regions of the E2 protein that influence a key virus-host interaction and provide proof of principle for the generation of large-scale mutant libraries for the study of pathogens with great sequence variability

Clustering in mixing flows

We calculate the Lyapunov exponents for particles suspended in a random three-dimensional flow, concentrating on the limit where the viscous damping rate is small compared to the inverse correlation time. In this limit Lyapunov exponents are obtained as a power series in epsilon, a dimensionless measure of the particle inertia. Although the perturbation generates an asymptotic series, we obtain accurate results from a Pade-Borel summation. Our results prove that particles suspended in an incompressible random mixing flow can show pronounced clustering when the Stokes number is large and we characterise two distinct clustering effects which occur in that limit.Comment: 5 pages, 1 figur

Higher-order topological pumping

The discovery of the quantization of particle transport in adiabatic pumping cycles of periodic structures by Thouless [Thouless D. J., Phys. Rev. B 27, 6083 (1983)] linked the Chern number, a topological invariant characterizing the quantum Hall effect in two-dimensional electron gases, with the topology of dynamical periodic systems in one dimension. Here, we demonstrate its counterpart for higher-order topology. Specifically, we show that adiabatic cycles in two-dimensional crystals with vanishing dipole moments (and therefore zero `particle transport') can nevertheless be topologically nontrivial. These cycles are associated with higher-order topology and can be diagnosed by their ability to produce corner-to-corner transport in certain metamaterial platforms. We experimentally verify this transport by using an array of photonic waveguides modulated in their separations and refractive indices. By mapping the dynamical phenomenon demonstrated here from two spatial and one temporal to three spatial dimensions, this transport is equivalent to the observation of the chiral nature of the gapless hinge states in a three-dimensional second-order topological insulator.Comment: Main text: 5 pages, 3 figures. Supp. Info: 8 pages, 5 figure

Emission Reduction Performance of Modified Hot Mix Asphalt Mixtures

Three novel asphalt modifiers with pollutant emission reduction effects and new emissions measurement equipment compatible with several preexisting asphalt production systems are developed in this paper. The effects of various modifier, asphalt binder type, and gradation of hot mix asphalt (HMA) on pollutant emissions are evaluated in the lab through a comprehensive experimental design. Furthermore, road performances are monitored to evaluate the emissions reduction of modified HMA mixture for production. With increasing modifier content, the emissions reduction performance is improved markedly, with maximum reduction of 70.5%. However, the impact of modifier content on pollutant emissions reduction tends to be insignificant for dosages greater than 20% of the initial asphalt weight. Changes in asphalt type and asphalt mix gradation are found to moderately impact the emissions reduction effect. Finally, the mechanisms of emissions reduction are investigated, primarily attribute to their physical and chemical adsorption and pollutant reductive degradation characteristics

Evolution of the Reverse Shock Emission from SNR 1987A

We present new (2004 July) G750L and G140L Space Telescope Imaging Spectrograph (STIS) data of the H-alpha and Ly-alpha emission from supernova remnant (SNR) 1987A. With the aid of earlier data, from Oct 1997 to Oct 2002, we track the local evolution of Ly-alpha emission and both the local and global evolution of H-alpha emission. In addition to emission which we can clearly attribute to the surface of the reverse shock, we also measure comparable emission, in both H-alpha and Ly-alpha, which appears to emerge from supernova debris interior to the surface. New observations taken through slits positioned slightly eastward and westward of a central slit show a departure from cylindrical symmetry in the H-alpha surface emission. Using a combination of old and new observations, we construct a light curve of the total H-alpha flux, F, from the reverse shock, which has increased by a factor ~ 4 over about 8 years. However, due to large systematic uncertainties, we are unable to discern between the two limiting behaviours of the flux - F ~ t (self-similar expansion) and F ~ t^5 (halting of the reverse shock). Such a determination is relevant to the question of whether the reverse shock emission will vanish in less than about 7 years (Smith et al. 2005). Future deep, low- or moderate-resolution spectra are essential for accomplishing this task.Comment: 28 pages, 12 figures. Accepted by Ap

Patterns of Lumbar Disc Degeneration: Magnetic Resonance Imaging Analysis in Symptomatic Subjects

Study Design: Cross-sectional study. Purpose: To evaluate lumbar disc degeneration (LDD) on magnetic resonance imaging (MRI) in symptomatic subjects to accumulate baseline data on the pattern of degeneration. Overview of Literature: LDD plays an important role in the diagnosis and treatment of low-back pain in patients. Few studies have focused on the pattern of LDD to understand how the lumbar spine ages. Methods: This study included 1,095 patients (mean age, 44.29 years; range, 16–85 years) who underwent upright lumbar MRI. LDD was graded into five categories (I–V). Positive LDD was defined as grade III or greater. The prevalence and pattern of LDD were ana-lyzed, and the correlations between age and total grade of LDD were evaluated. Results: The average number of LDD levels and the total grade of LDD increased with age. LDD moved cephalad with age. The rate of LDD increased rapidly during the decade before the prevalence of LDD and became \u3e 50%. In the single-level LDD group, the levels L5–S1 were the most common levels (60.3%). In the two-level group, L4–L5 and L5–S1 were the most common levels (53.5%). In the three-level group, L3–L4, L4–L5, and L5–S1 were the most common levels (55.7%). In the multilevel LDD group, contiguous multilevel disc degeneration (CMDD) was more common than the skipped level disc degeneration (SLDD). The levels L4–L5 were the most com-mon levels in the CMDD group, and L5–S1 were the most common levels among SLDD. Conclusions: LDD was found to correlate with age, and the specific patterns and rates of LDD depended on lumbar disc level and age. These LDD pattern data can be used before spinal procedures to predict the probability of natural LDD progression with age

Photon Management in Two-Dimensional Disordered Media

Elaborating reliable and versatile strategies for efficient light coupling between free space and thin films is of crucial importance for new technologies in energy efficiency. Nanostructured materials have opened unprecedented opportunities for light management, notably in thin-film solar cells. Efficient coherent light trapping has been accomplished through the careful design of plasmonic nanoparticles and gratings, resonant dielectric particles and photonic crystals. Alternative approaches have used randomly-textured surfaces as strong light diffusers to benefit from their broadband and wide-angle properties. Here, we propose a new strategy for photon management in thin films that combines both advantages of an efficient trapping due to coherent optical effects and broadband/wide-angle properties due to disorder. Our approach consists in the excitation of electromagnetic modes formed by multiple light scattering and wave interference in two-dimensional random media. We show, by numerical calculations, that the spectral and angular responses of thin films containing disordered photonic patterns are intimately related to the in-plane light transport process and can be tuned through structural correlations. Our findings, which are applicable to all waves, are particularly suited for improving the absorption efficiency of thin-film solar cells and can provide a novel approach for high-extraction efficiency light-emitting diodes

Antibody Engineering Using Phage Display with a Coiled-Coil Heterodimeric Fv Antibody Fragment

A Fab-like antibody binding unit, ccFv, in which a pair of heterodimeric coiled-coil domains was fused to VH and VL for Fv stabilization, was constructed for an anti-VEGF antibody. The anti-VEGF ccFv showed the same binding affinity as scFv but significantly improved stability and phage display level. Furthermore, phage display libraries in the ccFv format were constructed for humanization and affinity maturation of the anti-VEGF antibody. A panel of VH frameworks and VH-CDR3 variants, with a significant improvement in affinity and expressibility in both E. coli and yeast systems, was isolated from the ccFv phage libraries. These results demonstrate the potential application of the ccFv antibody format in antibody engineering

Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set

Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals. Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^>0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and International HapMap projects. The improved accuracy with the use of the new dataset could increase the power for GWAS by as much as 8% relative to genotyping all variants. This reference dataset is available to the scientific community through the NCBI dbGaP portal. Future versions will include additional genotype data as well as non-European populations