APOBEC3G-UBA2 fusion as a potential strategy for stable expression of APOBEC3G and inhibition of HIV-1 replication

<p>Abstract</p> <p>Background</p> <p>Although APOBEC3G protein is a potent and innate anti-HIV-1 cellular factor, HIV-1 Vif counteracts the effect of APOBEC3G by promoting its degradation through proteasome-mediated proteolysis. Thus, any means that could prevent APOBEC3G degradation could potentially enhance its anti-viral effect. The UBA2 domain has been identified as an intrinsic stabilization signal that protects protein from proteasomal degradation. In this pilot study, we tested whether APOBEC3G, when it is fused with UBA2, can resist Vif-mediated proteasomal degradation and further inhibit HIV-1 infection.</p> <p>Results</p> <p>APOBEC3G-UBA2 fusion protein is indeed more resistant to Vif-mediated degradation than APOBEC3G. The ability of UBA2 domain to stabilize APOBEC3G was diminished when polyubiquitin was over-expressed and the APOBEC3G-UBA2 fusion protein was found to bind less polyubiquitin than APOBEC3G, suggesting that UBA2 stabilizes APOBEC3G by preventing ubiquitin chain elongation and proteasome-mediated proteolysis. Consistently, treatment of cells with a proteasome inhibitor MG132 alleviated protein degradation of APOBEC3G and APOBEC3G-UBA2 fusion proteins. Analysis of the effect of APOBEC3G-UBA2 fusion protein on viral infectivity indicated that infection of virus packaged from HEK293 cells expressing APOBEC3G-UBA2 fusion protein is significantly lower than those packaged from HEK293 cells over-producing APOBEC3G or APOBEC3G-UBA2 mutant fusion proteins.</p> <p>Conclusion</p> <p>Fusion of UBA2 to APOBEC3G can make it more difficult to be degraded by proteasome. Thus, UBA2 could potentially be used to antagonize Vif-mediated APOBEC3G degradation by preventing polyubiquitination. The stabilized APOBEC3G-UBA2 fusion protein gives stronger inhibitory effect on viral infectivity than APOBEC3G without UBA2.</p

Unconventional machine learning of genome-wide human cancer data

Recent advances in high-throughput genomic technologies coupled with exponential increases in computer processing and memory have allowed us to interrogate the complex aberrant molecular underpinnings of human disease from a genome-wide perspective. While the deluge of genomic information is expected to increase, a bottleneck in conventional high-performance computing is rapidly approaching. Inspired in part by recent advances in physical quantum processors, we evaluated several unconventional machine learning (ML) strategies on actual human tumor data. Here we show for the first time the efficacy of multiple annealing-based ML algorithms for classification of high-dimensional, multi-omics human cancer data from the Cancer Genome Atlas. To assess algorithm performance, we compared these classifiers to a variety of standard ML methods. Our results indicate the feasibility of using annealing-based ML to provide competitive classification of human cancer types and associated molecular subtypes and superior performance with smaller training datasets, thus providing compelling empirical evidence for the potential future application of unconventional computing architectures in the biomedical sciences

Cell cycle G2/M arrest through an S phase-dependent mechanism by HIV-1 viral protein R

<p>Abstract</p> <p>Background</p> <p>Cell cycle G2 arrest induced by HIV-1 Vpr is thought to benefit viral proliferation by providing an optimized cellular environment for viral replication and by skipping host immune responses. Even though Vpr-induced G2 arrest has been studied extensively, how Vpr triggers G2 arrest remains elusive.</p> <p>Results</p> <p>To examine this initiation event, we measured the Vpr effect over a single cell cycle. We found that even though Vpr stops the cell cycle at the G2/M phase, but the initiation event actually occurs in the S phase of the cell cycle. Specifically, Vpr triggers activation of Chk1 through Ser³⁴⁵phosphorylation in an S phase-dependent manner. The S phase-dependent requirement of Chk1-Ser³⁴⁵phosphorylation by Vpr was confirmed by siRNA gene silencing and site-directed mutagenesis. Moreover, downregulation of DNA replication licensing factors Cdt1 by siRNA significantly reduced Vpr-induced Chk1-Ser³⁴⁵phosphorylation and G2 arrest. Even though hydroxyurea (HU) and ultraviolet light (UV) also induce Chk1-Ser³⁴⁵phosphorylation in S phase under the same conditions, neither HU nor UV-treated cells were able to pass through S phase, whereas <it>vpr</it>-expressing cells completed S phase and stopped at the G2/M boundary. Furthermore, unlike HU/UV, Vpr promotes Chk1- and proteasome-mediated protein degradations of Cdc25B/C for G2 induction; in contrast, Vpr had little or no effect on Cdc25A protein degradation normally mediated by HU/UV.</p> <p>Conclusions</p> <p>These data suggest that Vpr induces cell cycle G2 arrest through a unique molecular mechanism that regulates host cell cycle regulation in an S-phase dependent fashion.</p

Commensurate lattice distortion in the layered titanium oxypnictides Na2_{2}Ti2Pn2_{2}Pn_{2}O (Pn=Pn = As, Sb) determined by X-ray diffraction

We report single crystal X-ray diffraction measurements on Na$_2$Ti$_{2}Pn_{2}$O ($Pn$ = As, Sb) which reveal a charge superstructure that appears below the density wave transitions previously observed in bulk data. From symmetry-constrained structure refinements we establish that the associated distortion mode can be described by two propagation vectors, ${\bf q}_{1} = (1/2, 0, l)$ and ${\bf q}_{2} = (0, 1/2, l)$, with $l=0$ (Sb) or $l = 1/2$ (As), and primarily involves in-plane displacements of the Ti atoms perpendicular to the Ti--O bonds. The results provide direct evidence for phonon-assisted charge density wave order in Na$_2$Ti$_{2}Pn_{2}$O and identify a proximate ordered phase that could compete with superconductivity in doped BaTi$_{2}$Sb$_{2}$O

The Kinetic Sunyaev-Zel'dovich Effect from Radiative Transfer Simulations of Patchy Reionization

We present the first calculation of the kinetic Sunyaev-Zel'dovich (kSZ) effect due to the inhomogeneous reionization of the universe based on detailed large-scale radiative transfer simulations of reionization. The resulting sky power spectra peak at l=2000-8000 with maximum values of l^2C_l~1\times10^{-12}. The peak scale is determined by the typical size of the ionized regions and roughly corresponds to the ionized bubble sizes observed in our simulations, ~5-20 Mpc. The kSZ anisotropy signal from reionization dominates the primary CMB signal above l=3000. This predicted kSZ signal at arcminute scales is sufficiently strong to be detectable by upcoming experiments, like the Atacama Cosmology Telescope and South Pole Telescope which are expected to have ~1' resolution and ~muK sensitivity. The extended and patchy nature of the reionization process results in a boost of the peak signal in power by approximately one order of magnitude compared to a uniform reionization scenario, while roughly tripling the signal compared with that based upon the assumption of gradual but spatially uniform reionization. At large scales the patchy kSZ signal depends largely on the ionizing source efficiencies and the large-scale velocity fields: sources which produce photons more efficiently yield correspondingly higher signals. The introduction of sub-grid gas clumping in the radiative transfer simulations produces significantly more power at small scales, and more non-Gaussian features, but has little effect at large scales. The patchy nature of the reionization process roughly doubles the total observed kSZ signal for l~3000-10^4 compared to non-patchy scenarios with the same total electron-scattering optical depth.Comment: 14 pages, 13 figures (some in color), submitted to Ap