CD4+CD25+Foxp3+ Regulatory T Cells Depletion May Attenuate the Development of Silica-Induced Lung Fibrosis in Mice

BACKGROUND: Silicosis is an occupational lung disease caused by inhalation of silica dust characterized by lung inflammation and fibrosis. Previous study showed that Th1 and Th2 cytokines are involved in silicosis, but Th1/Th2 polarization during the development of silicosis is still a matter of debate. Regulatory T cells (Treg cells) represent a crucial role in modulation of immune homeostasis by regulating Th1/Th2 polarization, but their possible implication in silicosis remains to be explored. METHODOLOGY/PRINCIPAL FINDINGS: To evaluate the implication of Treg cells in the development of silicosis, we generated the Treg-depleted mice model by administration of anti-CD25 mAbs and mice were exposed to silica by intratracheal instillation to establish experimental model of silica-induced lung fibrosis. The pathologic examinations show that the Treg-depleted mice are susceptive to severer inflammation in the early stage, with enhanced infiltration of inflammatory cells. Also, depletion of Treg cells causes a delay of the progress of silica-induced lung fibrosis in mice model. Further study of mRNA expression of cytokines reveals that depletion of Tregs leads to the increased production of Th1-cytokines and decreased production of Th2-cytokine. The Flow Cytometry and realtime PCR study show that Treg cells exert the modulation function both directly by expressing CTLA-4 at the inflammatory stage, and indirectly by secreting increasing amount of IL-10 and TGF-β during the fibrotic stage in silica-induced lung fibrosis. CONCLUSION/SIGNIFICANCE: Our study suggests that depletion of Tregs may attenuate the progress of silica-induced lung fibrosis and enhance Th1 response and decelerate Th1/Th2 balance toward a Th2 phenotype in silica-induced lung fibrosis. The regulatory function of Treg cells may depend on direct mechanism and indirect mechanism during the inflammatory stage of silicosis

TEMP: a computational method for analyzing transposable element polymorphism in populations

Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate the frequencies of transposition events in the population and pinpoint junctions of high frequency transposition events at nucleotide resolution. Simulation data indicate that TEMP outperforms other algorithms such as PoPoolationTE, RetroSeq, VariationHunter and GASVPro. TEMP also performs well on whole-genome human data derived from the 1000 Genomes Project. We applied TEMP to characterize the TE frequencies in a wild Drosophila melanogaster population and study the inheritance patterns of TEs during hybrid dysgenesis. We also identified sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production. TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git. Acids Research

Extreme case of Faraday effect: magnetic splitting of ultrashort laser pulses in plasmas

The Faraday effect, caused by a magnetic-field-induced change in the optical properties, takes place in a vast variety of systems from a single atomic layer of graphenes to huge galaxies. Currently, it plays a pivot role in many applications such as the manipulation of light and the probing of magnetic fields and material's properties. Basically, this effect causes a polarization rotation of light during its propagation along the magnetic field in a medium. Here, we report an extreme case of the Faraday effect where a linearly polarized ultrashort laser pulse splits in time into two circularly polarized pulses of opposite handedness during its propagation in a highly magnetized plasma. This offers a new degree of freedom for manipulating ultrashort and ultrahigh power laser pulses. Together with technologies of ultra-strong magnetic fields, it may pave the way for novel optical devices, such as magnetized plasma polarizers. In addition, it may offer a powerful means to measure strong magnetic fields in laser-produced plasmas.Comment: 18 pages, 5 figure

Quantum Information Propagation Preserving Computational Electromagnetics

We propose a new methodology, called numerical canonical quantization, to solve quantum Maxwell's equations useful for mathematical modeling of quantum optics physics, and numerical experiments on arbitrary passive and lossless quantum-optical systems. It is based on: (1) the macroscopic (phenomenological) electromagnetic theory on quantum electrodynamics (QED), and (2) concepts borrowed from computational electromagnetics. It was shown that canonical quantization in inhomogeneous dielectric media required definite and proper normal modes. Here, instead of ad-hoc analytic normal modes, we numerically construct complete and time-reversible normal modes in the form of traveling waves to diagonalize the Hamiltonian. Specifically, we directly solve the Helmholtz wave equations for a general linear, reciprocal, isotropic, non-dispersive, and inhomogeneous dielectric media by using either finite-element or finite-difference methods. To convert a scattering problem with infinite number of modes into one with a finite number of modes, we impose Bloch-periodic boundary conditions. This will sparsely sample the normal modes with numerical Bloch-Floquet-like normal modes. Subsequent procedure of numerical canonical quantization is straightforward using linear algebra. We provide relevant numerical recipes in detail and show an important numerical example of indistinguishable two-photon interference in quantum beam splitters, exhibiting Hong-Ou-Mandel effect, which is purely a quantum effect. Also, the present methodology provides a way of numerically investigating existing or new macroscopic QED theories. It will eventually allow quantum-optical numerical experiments of high fidelity to replace many real experiments as in classical electromagnetics.Comment: 17 pages, 11 figures, journal article submitted to Physical review A (under review