Polarity and proliferation are controlled by distinct signaling pathways downstream of PI3-kinase in breast epithelial tumor cells

Loss of tissue polarity and increased proliferation are the characteristic alterations of the breast tumor phenotype. To investigate these processes, we used a three-dimensional (3D) culture system in which malignant human breast cells can be reverted to a normal phenotype by exposure to inhibitors of phosphatidylinositol 3-kinase (PI3K). Using this assay, we find that Akt and Rac1 act as downstream effectors of PI3K and function as control points of cellular proliferation and tissue polarity, respectively. Our results also demonstrate that the PI3K signaling pathway is an integral component of the overall signaling network induced by growth in 3D, as reversion affected by inhibition of PI3K signaling also down-modulates the endogenous levels of β1 integrin and epidermal growth factor receptor, the upstream modulators of PI3K, and up-regulates PTEN, the antagonist of PI3K. These findings reveal key events of the PI3K pathway that play distinct roles to maintain tissue polarity and that when disrupted are instrumental in the malignant phenotype

Femtosecond photonic viral inactivation probed using solid-state nanopores

We report on detection of virus inactivation using femtosecond laser radiation by measuring the conductance of a solid state nanopore designed for detecting single particles. Conventional methods of assaying for viral inactivation based on plaque forming assays require 24–48 h for bacterial growth. Nanopore conductance measurements provide information on morphological changes at a single virion level.We show that analysis of a time series of nanopore conductance can quantify the detection of inactivation, requiring only a few minutes from collection to analysis. Morphological changes were verified by dynamic light scattering. Statistical analysis maximizing the information entropy provides a measure of the log reduction value. This work provides a rapid method for assaying viral inactivation with femtosecond lasers using solid-state nanopores.First author draf

<em>Aspergillus luchuensis</em>, an industrially important black <em>Aspergillus</em> in East Asia

Aspergilli known as black- and white-koji molds which are used for awamori, shochu, makgeolli and other food and beverage fermentations, are reported in the literature as A. luchuensis, A. awamori, A. kawachii, or A. acidus. In order to elucidate the taxonomic position of these species, available ex-type cultures were compared based on morphology and molecular characters. A. luchuensis, A. kawachii and A. acidus showed the same banding patterns in RAPD, and the three species had the same rDNA-ITS, β-tubulin and calmodulin sequences and these differed from those of the closely related A. niger and A. tubingensis. Morphologically, the three species are not significantly different from each other or from A. niger and A. tubingensis. It is concluded that A. luchuensis, A. kawachii and A. acidus are the same species, and A. luchuensis is selected as the correct name based on priority. Strains of A. awamori which are stored in National Research Institute of Brewing in Japan, represent A. niger (n = 14) and A. luchuensis (n = 6). The neotype of A. awamori (CBS 557.65 = NRRL 4948) does not originate from awamori fermentation and it is shown to be identical with the unknown taxon Aspergillus welwitschiae. Extrolite analysis of strains of A. luchuensis showed that they do not produce mycotoxins and therefore can be considered safe for food and beverage fermentations. A. luchuensis is also frequently isolated from meju and nuruk in Korea and Puerh tea in China and the species is probably common in the fermentation environment of East Asia. A re-description of A. luchuensis is provided because the incomplete data in the original literature. © 2013 Hong et al

Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa

<p>Abstract</p> <p>Background</p> <p>In view of the immense value of <it>Brassica rapa </it>in the fields of agriculture and molecular biology, the multinational <it>Brassica rapa </it>Genome Sequencing Project (BrGSP) was launched in 2003 by five countries. The developing BrGSP has valuable resources for the community, including a reference genetic map and seed BAC sequences. Although the initial <it>B. rapa </it>linkage map served as a reference for the BrGSP, there was ambiguity in reconciling the linkage groups with the ten chromosomes of <it>B. rapa</it>. Consequently, the BrGSP assigned each of the linkage groups to the project members as chromosome substitutes for sequencing.</p> <p>Results</p> <p>We identified simple sequence repeat (SSR) motifs in the <it>B. rapa </it>genome with the sequences of seed BACs used for the BrGSP. By testing 749 amplicons containing SSR motifs, we identified polymorphisms that enabled the anchoring of 188 BACs onto the <it>B. rapa </it>reference linkage map consisting of 719 loci in the 10 linkage groups with an average distance of 1.6 cM between adjacent loci. The anchored BAC sequences enabled the identification of 30 blocks of conserved synteny, totaling 534.9 cM in length, between the genomes of <it>B. rapa </it>and <it>Arabidopsis thaliana</it>. Most of these were consistent with previously reported duplication and rearrangement events that differentiate these genomes. However, we were able to identify the collinear regions for seven additional previously uncharacterized sections of the A genome. Integration of the linkage map with the <it>B. rapa </it>cytogenetic map was accomplished by FISH with probes representing 20 BAC clones, along with probes for rDNA and centromeric repeat sequences. This integration enabled unambiguous alignment and orientation of the maps representing the 10 <it>B. rapa </it>chromosomes.</p> <p>Conclusion</p> <p>We developed a second generation reference linkage map for <it>B. rapa</it>, which was aligned unambiguously to the <it>B. rapa </it>cytogenetic map. Furthermore, using our data, we confirmed and extended the comparative genome analysis between <it>B. rapa </it>and <it>A. thaliana</it>. This work will serve as a basis for integrating the genetic, physical, and chromosome maps of the BrGSP, as well as for studies on polyploidization, speciation, and genome duplication in the genus <it>Brassica</it>.</p

Femtosecond Photonic Viral Inactivation Probed Using Solid-State Nanopores

We report on the detection of inactivation of virus particles using femtosecond laser radiation by measuring the conductance of a solid state nanopore designed for detecting single virus particles. Conventional methods of assaying for viral inactivation based on plaque forming assays require 24-48 hours for bacterial growth. Nanopore conductance measurements provide information on morphological changes at a single virion level. We show that analysis of a time series of nanopore conductance can quantify the detection of inactivation, requiring only a few minutes from collection to analysis. Morphological changes were verified by Dynamic Light Scattering (DLS). Statistical analysis maximizing the information entropy provides a measure of the Log-reduction value. Taken together, our work provides a rapid method for assaying viral inactivation with femtosecond lasers using solid-state nanopores.Comment: 6 Figures with caption