Genome-wide co-expression analysis in multiple tissues

Expression quantitative trait loci (eQTLs) represent genetic control points of gene expression, and can be categorized as cis- and trans-acting, reflecting local and distant regulation of gene expression respectively. Although there is evidence of co-regulation within clusters of trans-eQTLs, the extent of co-expression patterns and their relationship with the genotypes at eQTLs are not fully understood. We have mapped thousands of cis- and trans-eQTLs in four tissues (fat, kidney, adrenal and left ventricle) in a large panel of rat recombinant inbred (RI) strains. Here we investigate the genome-wide correlation structure in expression levels of eQTL transcripts and underlying genotypes to elucidate the nature of co-regulation within cis- and trans-eQTL datasets. Across the four tissues, we consistently found statistically significant correlations of cis-regulated gene expression to be rare (<0.9% of all pairs tested). Most (>80%) of the observed significant correlations of cis-regulated gene expression are explained by correlation of the underlying genotypes. In comparison, co-expression of trans-regulated gene expression is more common, with significant correlation ranging from 2.9%-14.9% of all pairs of trans-eQTL transcripts. We observed a total of 81 trans-eQTL clusters (hot-spots), defined as consisting of > or =10 eQTLs linked to a common region, with very high levels of correlation between trans-regulated transcripts (77.2-90.2%). Moreover, functional analysis of large trans-eQTL clusters (> or =30 eQTLs) revealed significant functional enrichment among genes comprising 80% of the large clusters. The results of this genome-wide co-expression study show the effects of the eQTL genotypes on the observed patterns of correlation, and suggest that functional relatedness between genes underlying trans-eQTLs is reflected in the degree of co-expression observed in trans-eQTL clusters. Our results demonstrate the power of an integrative, systematic approach to the analysis of a large gene expression dataset to uncover underlying structure, and inform future eQTL studies

Fatigue analysis-based numerical design of stamping tools made of cast iron

This work concerns stress and fatigue analysis of stamping tools made of cast iron with an essentially pearlitic matrix and containing foundry defects. Our approach consists at first, in coupling the stamping numerical processing simulations and structure analysis in order to improve the tool stiffness geometry for minimizing the stress state and optimizing their fatigue lifetime. The method consists in simulating the stamping process by considering the tool as a perfect rigid body. The estimated contact pressure is then used as boundary condition for FEM structure loading analysis of the tool. The result of this analysis is compared with the critical stress limit depending on the automotive model. The acceptance of this test allows calculating the fatigue lifetime of the critical zone by using the S–N curve of corresponding load ratio. If the prescribed tool life requirements are not satisfied, then the critical region of the tool is redesigned and the whole simulation procedures are reactivated. This method is applied for a cast iron EN-GJS-600-3. The stress-failure (S–N) curves for this material is determined at room temperature under push pull loading with different load ratios R0σmin/σmax0−2, R0−1 and R00.1. The effects of the foundry defects are determined by SEM observations of crack initiation sites. Their presence in tested specimens is associated with a reduction of fatigue lifetime by a factor of 2. However, the effect of the load ratio is more important

Geometric observation for the Bures fidelity between two states of a qubit

In this Brief Report, we present a geometric observation for the Bures fidelity between two states of a qubit.Comment: 4 pages, 1 figure, RevTex, Accepted by Phys. Rev.

Direct Josephson coupling between superconducting flux qubits

We have demonstrated strong antiferromagnetic coupling between two three-junction flux qubits based on a shared Josephson junction, and therefore not limited by the small inductances of the qubit loops. The coupling sign and magnitude were measured by coupling the system to a high-quality superconducting tank circuit. Design modifications allowing to continuously tune the coupling strength and/or make the coupling ferromagnetic are discussed.Comment: REVTeX 4, 4 pages, 5 figures; v2: completely rewritten, added finite-temperature results and proposals for ferromagnetic galvanic couplin

Simulation, Experiment, and Evolution: Understanding Nucleation in Protein S6 Folding

In this study, we explore nucleation and the transition state ensemble of the ribosomal protein S6 using a Monte Carlo Go model in conjunction with restraints from experiment. The results are analyzed in the context of extensive experimental and evolutionary data. The roles of individual residues in the folding nucleus are identified and the order of events in the S6 folding mechanism is explored in detail. Interpretation of our results agrees with, and extends the utility of, experiments that shift f-values by modulating denaturant concentration and presents strong evidence for the realism of the mechanistic details in our Monte Carlo Go model and the structural interpretation of experimental f-values. We also observe plasticity in the contacts of the hydrophobic core that support the specific nucleus. For S6, which binds to RNA and protein after folding, this plasticity may result from the conformational flexibility required to achieve biological function. These results present a theoretical and conceptual picture that is relevant in understanding the mechanism of nucleation in protein folding.Comment: PNAS in pres

Kneadings, Symbolic Dynamics and Painting Lorenz Chaos. A Tutorial

A new computational technique based on the symbolic description utilizing kneading invariants is proposed and verified for explorations of dynamical and parametric chaos in a few exemplary systems with the Lorenz attractor. The technique allows for uncovering the stunning complexity and universality of bi-parametric structures and detect their organizing centers - codimension-two T-points and separating saddles in the kneading-based scans of the iconic Lorenz equation from hydrodynamics, a normal model from mathematics, and a laser model from nonlinear optics.Comment: Journal of Bifurcations and Chaos, 201