Transport of Molecular Motor Dimers in Burnt-Bridge Models

Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic continuous-time burnt-bridge models. In these models the motion of molecular motors is viewed as a random walk along the lattices with periodically distributed weak links (bridges). When the particle crosses the weak link it can be destroyed with a probability $p$, driving the molecular motor motion in one direction. Dynamic properties and effective generated forces of dimer molecular motors are calculated exactly as a function of a concentration of bridges $c$ and burning probability $p$ and compared with properties of the monomer motors. It is found that the ratio of the velocities of the dimer and the monomer can never exceed 2, while the dispersions of the dimer and the monomer are not very different. The relative effective generated force of the dimer (as compared to the monomer) also cannot be larger than 2 for most sets of parameters. However, a very large force can be produced by the dimer in the special case of $c=1/2$ for non-zero shift between the lattices. Our calculations do not show the significant increase in the force generated by collagenase motor proteins in real biological systems as predicted by previous computational studies. The observed behavior of dimer molecular motors is discussed by considering in detail the particle dynamics near burnt bridges.Comment: 21 pages and 11 figure

dimer paramagnetic centers in lead germanate crystals doped with iron and halogen (Cl-, Br-, F-) ions

The dimer complexes Fe3+-Cl-, Fe3+-Br-, and Fe3+-O2- in ferroelectric lead germanate crystals doped with iron and annealed in chlorine-, bromine-, and fluorine-containing atmospheres have been studied using the electron paramagnetic resonance method. These complexes are formed by Fe3+ ions in the trigonal position of lead and their associated anions located in the interstitial channel of the structure. The positions of the charge-compensating anions in the channel have been discussed based on the analysis of the parameters of the spin Hamiltonian and their temperature dependence. © 2013 Pleiades Publishing, Ltd

Interferon lambda protects the female reproductive tract against Zika virus infection

Zika virus infections can cause devastating congenital birth defects but the underlying interactions with the host immune system are not well understood. Here, the authors examine the immune basis of vaginal protection and susceptibility to Zika viral infection, and identify a hormonal dependent role for interferon-lambda-mediated protection against disease

Electron paramagnetic resonance of Gd3+ ions in Ca1-x-yYxGdyF2+x+y crystals

Electron paramagnetic resonance of Ca1-x-yYxGdyF2+x+y single crystals has revealed spectra that are not typical of gadolinium-doped CaF2 crystals. These spectra have a nearly tetragonal symmetry and are most probably caused by Gd3+ ions localized in yttrium clusters. Weak spectra of tetragonal Gd3+ centers, whose parameters are close to those of a cubic gadolinium center caused by an isolated Gd3+ ion, have been also detected. These centers are attributed to isolated Gd3+ ions localized near octahedral rare-earth clusters or their associations. © 2013 Pleiades Publishing, Ltd

Current reversal and exclusion processes with history-dependent random walks

A class of exclusion processes in which particles perform history-dependent random walks is introduced, stimulated by dynamic phenomena in some biological and artificial systems. The particles locally interact with the underlying substrate by breaking and reforming lattice bonds. We determine the steady-state current on a ring, and find current-reversal as a function of particle density. This phenomenon is attributed to the non-local interaction between the walkers through their trails, which originates from strong correlations between the dynamics of the particles and the lattice. We rationalize our findings within an effective description in terms of quasi-particles which we call front barriers. Our analytical results are complemented by stochastic simulations.Comment: 5 pages, 6 figure

Specific features of the electron paramagnetic resonance spectrum in the vicinity of the convergence of the transitions of gadolinium centers in Pb5(Ge1 - xSix)3O11

An anomalous electron paramagnetic resonance spectrum of the transitions -1/2 ↔ +1/2 of four Gd3+-Si dimer clusters in the Pb5(Ge1 - xSix)3O11 crystals doped with gadolinium has been found in the vicinity of the orientation of the magnetic field along the optic axis of the crystal. It has been assumed that this spectrum is caused by rapid transitions between the spin packets of the initial resonances due to the crossrelaxation. A computer simulation of the spectrum has been carried out. The results obtained adequately describe the experiment. © 2013 Pleiades Publishing, Ltd

GAM: a web-service for integrated transcriptional and metabolic network analysis

Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands of metabolites. Such metabolomic profiles, when analyzed together with transcriptional profiles, can reveal novel insights about underlying biological processes. While a number of conceptual approaches have been developed for data integration, easily accessible tools for integrated analysis of mammalian steady-state metabolomic and transcriptional data are lacking. Here we present GAM (‘genes and metabolites’): a web-service for integrated network analysis of transcriptional and steady-state metabolomic data focused on identification of the most changing metabolic subnetworks between two conditions of interest. In the web-service, we have pre-assembled metabolic networks for humans, mice, Arabidopsis and yeast and adapted exact solvers for an optimal subgraph search to work in the context of these metabolic networks. The output is the most regulated metabolic subnetwork of size controlled by false discovery rate parameters. The subnetworks are then visualized online and also can be downloaded in Cytoscape format for subsequent processing. The web-service is available at: https://artyomovlab.wustl.edu/shiny/gam

Leveraging existing data sets to generate new insights into Alzheimer’s disease biology in specific patient subsets

To generate new insights into the biology of Alzheimer’s Disease (AD), we developed methods to combine and reuse a wide variety of existing data sets in new ways. We first identified genes consistently associated with AD in each of four separate expression studies, and confirmed this result using a fifth study. We next developed algorithms to search hundreds of thousands of Gene Expression Omnibus (GEO) data sets, identifying a link between an AD-associated gene (NEUROD6) and gender. We therefore stratified patients by gender along with APOE4 status, and analyzed multiple SNP data sets to identify variants associated with AD. SNPs in either the region of NEUROD6 or SNAP25 were significantly associated with AD, in APOE4+ females and APOE4+ males, respectively. We developed algorithms to search Connectivity Map (CMAP) data for medicines that modulate AD-associated genes, identifying hypotheses that warrant further investigation for treating specific AD patient subsets. In contrast to other methods, this approach focused on integrating multiple gene expression datasets across platforms in order to achieve a robust intersection of disease-affected genes, and then leveraging these results in combination with genetic studies in order to prioritize potential genes for targeted therapy