Complex lithium ion dynamics in simulated LiPO3 glass studied by means of multi-time correlation functions

Molecular dynamics simulations are performed to study the lithium jumps in LiPO3 glass. In particular, we calculate higher-order correlation functions that probe the positions of single lithium ions at several times. Three-time correlation functions show that the non-exponential relaxation of the lithium ions results from both correlated back-and-forth jumps and the existence of dynamical heterogeneities, i.e., the presence of a broad distribution of jump rates. A quantitative analysis yields that the contribution of the dynamical heterogeneities to the non-exponential depopulation of the lithium sites increases upon cooling. Further, correlated back-and-forth jumps between neighboring sites are observed for the fast ions of the distribution, but not for the slow ions and, hence, the back-jump probability depends on the dynamical state. Four-time correlation functions indicate that an exchange between fast and slow ions takes place on the timescale of the jumps themselves, i.e., the dynamical heterogeneities are short-lived. Hence, sites featuring fast and slow lithium dynamics, respectively, are intimately mixed. In addition, a backward correlation beyond the first neighbor shell for highly mobile ions and the presence of long-range dynamical heterogeneities suggest that fast ion migration occurs along preferential pathways in the glassy matrix. In the melt, we find no evidence for correlated back-and-forth motions and dynamical heterogeneities on the length scale of the next-neighbor distance.Comment: 12 pages, 13 figure

Gliotoxin, identified from a screen of fungal metabolites, disrupts 7SK snRNP, releases P-TEFb, and reverses HIV-1 latency

A leading pharmacological strategy toward HIV cure requires "shock" or activation of HIV gene expression in latently infected cells with latency reversal agents (LRAs) followed by their subsequent clearance. In a screen for novel LRAs, we used fungal secondary metabolites as a source of bioactive molecules. Using orthogonal mass spectrometry (MS) coupled to latency reversal bioassays, we identified gliotoxin (GTX) as a novel LRA. GTX significantly induced HIV-1 gene expression in latent ex vivo infected primary cells and in CD4+ T cells from all aviremic HIV-1+ participants. RNA sequencing identified 7SK RNA, the scaffold of the positive transcription elongation factor b (P-TEFb) inhibitory 7SK small nuclear ribonucleoprotein (snRNP) complex, to be significantly reduced upon GTX treatment of CD4+ T cells. GTX directly disrupted 7SK snRNP by targeting La-related protein 7 (LARP7), releasing active P-TEFb, which phosphorylated RNA polymerase II (Pol II) C-terminal domain (CTD), inducing HIV transcription

Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach

The acquisition and analysis of datasets including multi-level omics and physiology from non-model species, sampled from field populations, is a formidable challenge, which so far has prevented the application of systems biology approaches. If successful, these could contribute enormously to improving our understanding of how populations of living organisms adapt to environmental stressors relating to, for example, pollution and climate. Here we describe the first application of a network inference approach integrating transcriptional, metabolic and phenotypic information representative of wild populations of the European flounder fish, sampled at seven estuarine locations in northern Europe with different degrees and profiles of chemical contaminants. We identified network modules, whose activity was predictive of environmental exposure and represented a link between molecular and morphometric indices. These sub-networks represented both known and candidate novel adverse outcome pathways representative of several aspects of human liver pathophysiology such as liver hyperplasia, fibrosis, and hepatocellular carcinoma. At the molecular level these pathways were linked to TNF alpha, TGF beta, PDGF, AGT and VEGF signalling. More generally, this pioneering study has important implications as it can be applied to model molecular mechanisms of compensatory adaptation to a wide range of scenarios in wild populations

Oligomeric ferrocene rings

Cyclic oligomers comprising strongly interacting redox-active monomer units represent an unknown, yet highly desirable class of nanoscale materials. Here we describe the synthesis and properties of the first family of molecules belonging to this compound category—differently sized rings comprising only 1,1′-disubstituted ferrocene units (cyclo[n], n = 5–7, 9). Due to the close proximity and connectivity of centres (covalent Cp–Cp linkages; Cp = cyclopentadienyl) solution voltammograms exhibit well-resolved, separated 1e– waves. Theoretical interrogations into correlations based on ring size and charge state are facilitated using values of the equilibrium potentials of these transitions, as well as their relative spacing. As the interaction free energies between the redox centres scale linearly with overall ring charge and in conjunction with fast intramolecular electron transfer (∼107 s−1), these molecules can be considered as uniformly charged nanorings (diameter ∼1–2 nm)