A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations

<p>Abstract</p> <p>Background</p> <p>Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, <it>Arabidopsis thaliana</it>, provides means to explore their genomic complexity.</p> <p>Results</p> <p>A genome-wide physical map of a rapid-cycling strain of <it>B. oleracea </it>was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of <it>B. oleracea </it>and <it>Arabidopsis thaliana</it>, a relatively high level of genomic change since their divergence. Comparison of the <it>B. oleracea </it>physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity.</p> <p>Conclusions</p> <p>A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes.</p> <p>All the physical mapping data is freely shared at a WebFPC site (<url>http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/</url>; Temporarily password-protected: account: pgml; password: 123qwe123.</p

Eliminating the undercut phenomenon in interference lithography for the fabrication of nano-imprint lithography stamp

We show an easy method to eliminate the undercut profile of photoresist by fabricating periodic nano-patterns on a substrate using interference lithography. An undercut phenomenon occurs frequently on the sidewall of photoresist patterns because of the 3-dimensional intensity distribution generated when two beams are merged to make an interferogram. This is mainly caused by the vertical interference between the incident beam and the one reflected from the surface of a substrate, and bottom-anti-reflection-coating (BARC) material is usually used to prevent beams from being reflected onto the substrate. We propose a simple post-process which helps researchers fabricate well-defined patterns without using BARC material. We developed this process to fabricate stamps for nano-imprint lithography at low cost, and show the results of our nano-imprint process which transfers patterns on a stamp directly through thermal resist. © 2010 Elsevier B.V. All rights reserved.

Enhanced optical properties of nanopillar light-emitting diodes by coupling localized surface plasmon of Ag/SiO2 nanoparticles

We fabricated nanopillar light-emitting diodes (LEDs) embedded with Ag/SiO&lt;inf&gt;2&lt;/inf&gt; nanoparticles, and investigated the energy coupling processes between the localized surface plasmons of nanoparticles and the active quantum well regions of nanopillar LEDs. These nanoparticle-embedded nanopillar LEDs showed considerable increases in photoluminescence and electroluminescence intensities, compared with reference nanopillar LEDs. The observed optical enhancement was explained by the increased spontaneous emission rate caused by energy coupling from excitons in the InGaN/GaN quantum well active region of the LEDs to the localized surface plasmon modes of the Ag/SiO&lt;inf&gt;2&lt;/inf&gt; nanoparticles. A strongly enhanced characteristic photoluminescence decay also confirmed such an explanation. © 2015 The Japan Society of Applied Physics.

A role for Toll-like receptor 4 in the host response to the lung infection of Yersinia pseudotuberculosis in mice

Although a Yersinia pseudotuberculosis (Yptb) lung infection model has been developed to study Y. pestis pathogenesis, it is still necessary to establish a new animal model to mimic the pathophysiological features induced by Y. pestis infection. Here, we provide a new lung infection model using the Yptb strain, IP2777, which displayed rapid spread of bacteria to the liver, spleen, and blood. In addition, we examined whether TLR4 is involved in Yptb-induced pathogenesis in the lung infection model of mice we generated. Following lung infection of WT and TLR4-deficient mice with the Yptb strain IP2777, the survival rate, bacterial colonization, histopathology, and level of cytokines and chemokines in the lung, spleen, liver, and blood were analyzed. TLR4-deficient mice had a lower survival rate than WT mice in response to Yptb lung infection. Although the bacterial colonization and pathology of the lung were comparable between WT and TLR4-deficient mice, those of the spleen and liver were more severe in TLR4-deficient mice. In addition, the levels of TNF-α and CXCL2 in the liver and IL-and CXCL2 in the blood were higher in TLR4-deficient mice than in WT mice. Our results demonstrate that TLR4 is necessary for optimal host protection against Yptb lung infection and TLR4-deficient mice may serve as a better genetic model of Yptb infection for mimicking Y. pestis infection. © 2016 Elsevier Ltd.