Mutations in modified virus Ankara protein 183 render it a non-functional counterpart of B14, an inhibitor of nuclear factor κB activation

Vaccinia virus (VACV) encodes multiple proteins to evade host innate immunity, including B14, a virulence factor that binds to the inhibitor of κB kinase β (IKKβ) and blocks nuclear factor κB (NF-κB) activation. B14 shares 95 % amino acid identity with the 183 protein encoded by modified virus Ankara (MVA), an attenuated VACV strain being developed as a vaccine vector. To evaluate whether the immunogenicity of MVA might be increased by manipulation of MVA immunomodulatory proteins, the MVA counterpart of B14, protein 183, was characterized. Unlike B14, protein 183 was unstable in eukaryotic cells unless proteasome-mediated protein degradation was inhibited. Furthermore, 183 did not inhibit NF-κB activation in response to cytokine stimulation, and did not restore the virulence of VACV strain Western Reserve lacking gene B14R. The instability and non-functionality of 183 are probably explained by a deletion of 6 aa within α-helix 6 of the B14 crystal structure

Absolute quantitative real-time polymerase chain reaction for the measurement of human papillomavirus E7 mRNA in cervical cytobrush specimens

BACKGROUND: Few reports of the utilization of an accurate, cost-effective means for measuring HPV oncogene transcripts have been published. Several papers have reported the use of relative quantitation or more expensive Taqman methods. Here, we report a method of absolute quantitative real-time PCR utilizing SYBR-green fluorescence for the measurement of HPV E7 expression in cervical cytobrush specimens. RESULTS: The construction of a standard curve based on the serial dilution of an E7-containing plasmid was the key for being able to accurately compare measurements between cervical samples. The assay was highly reproducible with an overall coefficient of variation of 10.4%. CONCLUSION: The use of highly reproducible and accurate SYBR-based real-time polymerase chain reaction (PCR) assays instead of performing Taqman-type assays allows low-cost, high-throughput analysis of viral mRNA expression. The development of such assays will help in refining the current screening programs for HPV-related carcinomas

Standardized two-step testing of antibody activity in COVID-19 convalescent plasma

The COVID-19 pandemic revealed an urgent need for rapid profiling of neutralizing antibody responses and development of antibody therapeutics. The current Food and Drug Administration-approved serological tests do not measure antibody-mediated viral neutralization, and there is a need for standardized quantitative neutralization assays. We report a high-throughput two-step profiling approach for identifying neutralizing convalescent plasma. Screening and downselection for serum antibody binding to the receptor-binding domain are followed by quantitative neutralization testing using a chimeric vesicular stomatitis virus expressing spike protein of SARS-CoV-2 in a real-time cell analysis assay. This approach enables a predictive screening process for identifying plasma units that neutralize SARS-CoV-2. To calibrate antibody neutralizing activity in serum from convalescent plasma donors, we introduce a neutralizing antibody standard reagent composed of two human antibodies that neutralize SARS-CoV strains, including SARS-CoV-2 variants of concern. Our results provide a framework for establishing a standardized assessment of antibody-based interventions against COVID-19

Uranium isotope fractionation during coprecipitation with aragonite and calcite

© 2016 Elsevier Ltd. Natural variations in 238U/235U of marine calcium carbonates might provide a useful way of constraining redox conditions of ancient environments. In order to evaluate the reliability of this proxy, we conducted aragonite and calcite coprecipitation experiments at pH ~7.5 and ~8.5 to study possible U isotope fractionation during incorporation into these minerals.Small but significant U isotope fractionation was observed in aragonite experiments at pH ~8.5, with heavier U isotopes preferentially enriched in the solid phase. 238U/235U of dissolved U in these experiments can be fit by Rayleigh fractionation curves with fractionation factors of 1.00007 + 0.00002/-0.00003, 1.00005 ± 0.00001, and 1.00003 ± 0.00001. In contrast, no resolvable U isotope fractionation was observed in an aragonite experiment at pH ~7.5 or in calcite experiments at either pH. Equilibrium isotope fractionation among different aqueous U species is the most likely explanation for these findings. Certain charged U species are preferentially incorporated into calcium carbonate relative to the uncharged U species Ca2UO2(CO3)3(aq), which we hypothesize has a lighter equilibrium U isotope composition than most of the charged species. According to this hypothesis, the magnitude of U isotope fractionation should scale with the fraction of dissolved U that is present as Ca2UO2(CO3)3(aq). This expectation is confirmed by equilibrium speciation modeling of our experiments. Theoretical calculation of the U isotope fractionation factors between different U species could further test this hypothesis and our proposed fractionation mechanism.These findings suggest that U isotope variations in ancient carbonates could be controlled by changes in the aqueous speciation of seawater U, particularly changes in seawater pH, PCO2, Ca2+, or Mg2+ concentrations. In general, these effects are likely to be small (\u3c0.13‰), but are nevertheless potentially significant because of the small natural range of variation of 238U/235U

MMP7 Shedding of Syndecan-1 Facilitates Re-Epithelialization by Affecting α2β1 Integrin Activation

Lung injury promotes the expression of matrix metalloproteinase-7 (MMP7, matrilysin), which is required for neutrophil recruitment and re-epithelialization. MMP7 governs the lung inflammatory response through the shedding of syndecan-1. Because inflammation and repair are related events, we evaluated the role of syndecan-1 shedding in lung re-epithelialization.Epithelial injury induced syndecan-1 shedding from wild-type epithelium but not from Mmp7(-/-) mice in vitro and in vivo. Moreover, cell migration and wound closure was enhanced by MMP7 shedding of syndecan-1. Additionally, we found that syndecan-1 augmented cell adhesion to collagen by controlling the affinity state of the alpha(2)beta(1) integrin.MMP7 shedding of syndecan-1 facilitates wound closure by causing the alpha(2)beta(1) integrin to assume a less active conformation thereby removing restrictions to migration. MMP7 acts in the lungs to regulate inflammation and repair, and our data now show that both these functions are controlled through the shedding of syndecan-1

Large-scale synthesis of high moment FeCo nanoparticles using modified polyol synthesis

Binary alloys of Fe and Co have among the highest magnetizations of any transition metal alloy systems, but their affinity to form oxides act to reduce the magnetization of nanoparticles as their size is reduced below ∼30 nm. Here, we demonstrate the synthesis of single phase, size-controlled FeCo nanoparticles having magnetization greater than 200 emu/g via a non-aqueous method in which ethylene glycol served as solvent and reducing agent as well as surfactant. Experiments indicated pure-phase FeCo nanoparticles, having saturationmagnetization up to 221 emu/g for sizes of 20–30 nm, in single batch processes resulting in \u3e 2 g/batch. Post-synthesis oxidation of nanoparticles was investigated until very stable nanoparticles were realized with constant magnetization over time

Light with a self-torque: extreme-ultraviolet beams with time-varying orbital angular momentum

Twisted light fields carrying orbital angular momentum (OAM) provide powerful capabilities for applications in optical communications, microscopy, quantum optics and microparticle rotation. Here we introduce and experimentally validate a new class of light beams, whose unique property is associated with a temporal OAM variation along a pulse: the self-torque of light. Self-torque is a phenomenon that can arise from matter-field interactions in electrodynamics and general relativity, but to date, there has been no optical analog. In particular, the self-torque of light is an inherent property, which is distinguished from the mechanical torque exerted by OAM beams when interacting with physical systems. We demonstrate that self-torqued beams in the extreme-ultraviolet (EUV) naturally arise as a necessary consequence of angular momentum conservation in non-perturbative high-order harmonic generation when driven by time-delayed pulses with different OAM. In addition, the time-dependent OAM naturally induces an azimuthal frequency chirp, which provides a signature for monitoring the self-torque of high-harmonic EUV beams. Such self-torqued EUV beams can serve as unique tools for imaging magnetic and topological excitations, for launching selective excitation of quantum matter, and for manipulating molecules and nanostructures on unprecedented time and length scales.Comment: 24 pages, 4 figure

Investigating Graduate Education and Undergraduate Research Intentions of College Science Students

The current study examined predictors of undergraduate science students’ intentions to attend graduate school and participate in undergraduate research. We used social cognitive career theory to test our hypothesized model using a sample (N ¼ 411) of life science and physical science majors and examined basic interests in these disciplines as mediating variables. Among life science majors, results of structural equation modeling indicated that microbiology interest mediated the relationship between scientific self-efficacy (SSE) and graduate education intentions (GEIs) and the latter variable also mediated the relationship between microbiology interest and undergraduate research intentions (URIs). The model for physical science majors did not provide a good fit to the data, therefore path coefficients associated with this model were not interpreted. Implications for counseling interventions based on patterns of career intention formation in the life and physical sciences are discussed

Discovery and genotyping of structural variation from long-read haploid genome sequence data

In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that &gt;89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF &gt; 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.</jats:p

Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)

.Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted "modified panhandle" structure, the 5' and 3' termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3'- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3' adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5'- and 3'-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties