Energetic changes caused by antigenic module insertion in a virus-like particle revealed by experiment and molecular dynamics simulations

The success of recombinant virus-like particles (VLPs) for human papillomavirus and hepatitis B demonstrates the potential of VLPs as safe and efficacious vaccines. With new modular designs emerging, the effects of antigen module insertion on the self-assembly and structural integrity of VLPs should be clarified so as to better enabling improved design. Previous work has revealed insights into the molecular energetics of a VLP subunit, capsomere, comparing energetics within various solution conditions known to drive or inhibit self-assembly. In the present study, molecular dynamics (MD) simulations coupled with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) method were performed to examine the molecular interactions and energetics in a modular capsomere of a murine polyomavirus (MPV) VLP designed to protect against influenza. Insertion of an influenza antigenic module is found to lower the binding energy within the capsomere, and a more active state is observed in Assembly Buffer as compared with that in Stabilization Buffer, which has been experimentally validated through measurements using differential scanning calorimetry. Further in-depth analysis based on free-energy decomposition indicates that destabilized binding can be attributed to electrostatic interaction induced by the chosen antigen module. These results provide molecular insights into the conformational stability of capsomeres and their abilities to be exploited for antigen presentation, and are expected to be beneficial for the biomolecular engineering of VLP vaccines.Lin Zhang, Ronghong Tang, Shu Bai, Natalie K. Connors, Linda H.L. Lua, Yap P. Chuan, Anton P.J. Middelberg, Yan Su

Longitudinal changes in prospective memory and their clinical correlates at 1-year follow-up in first-episode schizophrenia

This study aimed to investigate prospective memory (PM) and the association with clinical factors at 1-year follow-up in first-episode schizophrenia (FES). Thirty-two FES patients recruited from a university-affiliated psychiatric hospital in Beijing and 17 healthy community controls (HCs) were included. Time- and event-based PM (TBPM and EBPM) performances were measured with the Chinese version of the Cambridge Prospective Memory Test (CCAMPROMPT) at baseline and at one-year follow-up. A number of other neurocognitive tests were also administered. Remission was determined at the endpoint according to the PANSS score _ 3 for selected items. Repeated measures analysis of variance revealed a significant interaction between time (baseline vs. endpoint) and group (FES vs. HCs) for EBPM (F(1, 44) = 8.8, p = 0.005) and for all neurocognitive components. Paired samples ttests showed significant improvement in EBPM in FES (13.1±3.7 vs. 10.3±4.8; t = 3.065, p = 0.004), compared to HCs (15.7±3.6 vs. 16.5±2.3; t = -1.248, p = 0.230). A remission rate of 59.4% was found in the FES group. Analysis of covariance revealed that remitters performed significantly better on EBPM (14.9±2.6 vs. 10.4±3.6; F(1, 25) = 12.2, p = 0.002) than non-remitters at study endpoint. The association between EBPM and 12-month clinical improvement in FES suggests that EBPM may be a potential neurocognitive marker for the effectiveness of standard pharmacotherapy. Furthermore, the findings also imply that PM may not be strictly a trait-related endophenotype as indicated in previous studies

Measuring non-Markovianity of processes with controllable system-environment interaction

Non-Markovian processes have recently become a central topic in the study of open quantum systems. We realize experimentally non-Markovian decoherence processes of single photons by combining time delay and evolution in a polarization-maintaining optical fiber. The experiment allows the identification of the process with strongest memory effects as well as the determination of a recently proposed measure for the degree of quantum non-Markovianity based on the exchange of information between the open system and its environment. Our results show that an experimental quantification of memory in quantum processes is indeed feasible which could be useful in the development of quantum memory and communication devices.Comment: 5 pages, 4 figures. V2: Minor modifications, title change

Measurement Induced Quantum Coherence Recovery

We show that measurement can recover the quantum coherence of a qubit in a non-Markovian environment. The experimental demonstration in an optical system is provided by comparing the visibilities (and fidelities) of the final states with and without measurement. This method can be extended to other two-level quantum systems and entangled states in a non-Markovian evolution environment. It may also be used to implement other quantum information processing.Comment: 9 pages, 5 figure

The controlled teleportation of an arbitrary two-atom entangled state in driven cavity QED

In this paper, we propose a scheme for the controlled teleportation of an arbitrary two-atom entangled state $|\phi>_{12}=a|gg>_{12}+b|ge>_{12}+c|eg>_{12}+d|ee>_{12}$ in driven cavity QED. An arbitrary two-atom entangled state can be teleported perfectly with the help of the cooperation of the third side by constructing a three-atom GHZ entangled state as the controlled channel. This scheme does not involve apparent (or direct) Bell-state measurement and is insensitive to the cavity decay and the thermal field. The probability of the success in our scheme is 1.0.Comment: 10 page

The entanglement in one-dimensional random XY spin chain with Dzyaloshinskii-Moriya interaction

The impurities of exchange couplings, external magnetic fields and Dzyaloshinskii--Moriya (DM) interaction considered as Gaussian distribution, the entanglement in one-dimensional random $XY$ spin systems is investigated by the method of solving the different spin-spin correlation functions and the average magnetization per spin. The entanglement dynamics at central locations of ferromagnetic and antiferromagnetic chains have been studied by varying the three impurities and the strength of DM interaction. (i) For ferromagnetic spin chain, the weak DM interaction can improve the amount of entanglement to a large value, and the impurities have the opposite effect on the entanglement below and above critical DM interaction. (ii) For antiferromagnetic spin chain, DM interaction can enhance the entanglement to a steady value. Our results imply that DM interaction strength, the impurity and exchange couplings (or magnetic field) play competing roles in enhancing quantum entanglement.Comment: 12 pages, 3 figure

Cross-National Differences in Victimization : Disentangling the Impact of Composition and Context

Varying rates of criminal victimization across countries are assumed to be the outcome of countrylevel structural constraints that determine the supply ofmotivated o¡enders, as well as the differential composition within countries of suitable targets and capable guardianship. However, previous empirical tests of these ‘compositional’ and ‘contextual’ explanations of cross-national di¡erences have been performed upon macro-level crime data due to the unavailability of comparable individual-level data across countries. This limitation has had two important consequences for cross-national crime research. First, micro-/meso-level mechanisms underlying cross-national differences cannot be truly inferred from macro-level data. Secondly, the e¡ects of contextual measures (e.g. income inequality) on crime are uncontrolled for compositional heterogeneity. In this paper, these limitations are overcome by analysing individual-level victimization data across 18 countries from the International CrimeVictims Survey. Results from multi-level analyses on theft and violent victimization indicate that the national level of income inequality is positively related to risk, independent of compositional (i.e. micro- and meso-level) di¡erences. Furthermore, crossnational variation in victimization rates is not only shaped by di¡erences in national context, but also by varying composition. More speci¢cally, countries had higher crime rates the more they consisted of urban residents and regions with lowaverage social cohesion.

X-ray Crystallographic Structure of an Artificial β-Sheet Dimer

This paper describes the X-ray crystallographic structure of a designed cyclic beta-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics beta-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce beta-sheet structure in a heptapeptide strand that forms the dimerization interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the beta-sheet structure and the two delta-linked ornithine turn units that link the Hao-containing template to the heptapeptide beta-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a beta-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide beta-strand. The delta-linked ornithines adopt a conformation that resembles a hydrogen-bonded beta-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic beta-sheet 1a resemble the dimers of many proteins, such as defensin HNP-3, the lambda-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of 1a self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic beta-sheet peptides that were observed in solution

Prediction of Ubiquitination Sites by Using the Composition of k-Spaced Amino Acid Pairs

As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed to predict ubiquitination sites from protein sequences. With the assistance of Support Vector Machine (SVM), the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input. When trained and tested in the dataset of yeast ubiquitination sites (Radivojac et al, Proteins, 2010, 78: 365–380), a 100-fold cross-validation on a 1∶1 ratio of positive and negative samples revealed that the accuracy and MCC of CKSAAP_UbSite reached 73.40% and 0.4694, respectively. The proposed CKSAAP_UbSite has also been intensively benchmarked to exhibit better performance than some existing predictors, suggesting that it can be served as a useful tool to the community. Currently, CKSAAP_UbSite is freely accessible at http://protein.cau.edu.cn/cksaap_ubsite/. Moreover, we also found that the sequence patterns around ubiquitination sites are not conserved across different species. To ensure a reasonable prediction performance, the application of the current CKSAAP_UbSite should be limited to the proteome of yeast

Residual hepatocellular carcinoma after oxaliplatin treatment has increased metastatic potential in a nude mouse model and is attenuated by Songyou Yin

<p>Abstract</p> <p>Background</p> <p>The opposite effects of chemotherapy, which enhance the malignancy of treated cancers such as hepatocellular carcinoma (HCC), are not well understood. We investigated this phenomenon and corresponding mechanisms to develop a novel approach for improving chemotherapy efficacy in HCC.</p> <p>Methods</p> <p>Human hepatocellular carcinoma cell lines HepG2 (with low metastatic potential) and MHCC97L (with moderate metastatic potential) were used for the in vitro study. An orthotopic nude mouse model of human HCC was developed using MHCC97L cells. We then assessed the metastatic potential of surviving tumor cells after in vitro and in vivo oxaliplatin treatment. The molecular changes in surviving tumor cells were evaluated by western blot, immunofluorescence, and immunohistochemistry. The Chinese herbal extract Songyou Yin (composed of five herbs) was investigated in vivo to explore its effect on the metastatic potential of oxaliplatin-treated cancer cells.</p> <p>Results</p> <p>MHCC97L and HepG2 cells surviving oxaliplatin treatment showed enhanced migration and invasion in vitro. Residual HCC after in vivo oxaliplatin treatment demonstrated significantly increased metastasis to the lung (10/12 vs. 3/12) when re-inoculated into the livers of new recipient nude mice. Molecular changes consistent with epithelial-mesenchymal transition (EMT) were observed in oxaliplatin-treated tumor tissues and verified by in vitro experiments. The Chinese herbal extract Songyou Yin (4.2 and 8.4 g/kg) attenuated EMT and inhibited the enhanced metastatic potential of residual HCC in nude mice (6/15 vs. 13/15 and 3/15 vs. 13/15, respectively).</p> <p>Conclusions</p> <p>The surviving HCC after oxaliplatin treatment underwent EMT and demonstrated increased metastatic potential. Attenuation of EMT by Songyou Yin may improve the efficacy of chemotherapy in HCC.</p