Pseudomonas aeruginosa Enhances Production of a Non-Alginate Exopolysaccharide during Long-Term Colonization of the Cystic Fibrosis Lung

The gram-negative opportunistic pathogen Pseudomonas aeruginosa is the primary cause of chronic respiratory infections in individuals with the heritable disease cystic fibrosis (CF). These infections can last for decades, during which time P. aeruginosa has been proposed to acquire beneficial traits via adaptive evolution. Because CF lacks an animal model that can acquire chronic P. aeruginosa infections, identifying genes important for long-term in vivo fitness remains difficult. However, since clonal, chronological samples can be obtained from chronically infected individuals, traits undergoing adaptive evolution can be identified. Recently we identified 24 P. aeruginosa gene expression traits undergoing parallel evolution in vivo in multiple individuals, suggesting they are beneficial to the bacterium. The goal of this study was to determine if these genes impact P. aeruginosa phenotypes important for survival in the CF lung. By using a gain-of-function genetic screen, we found that 4 genes and 2 operons undergoing parallel evolution in vivo promote P. aeruginosa biofilm formation. These genes/operons promote biofilm formation by increasing levels of the non-alginate exopolysaccharide Psl. One of these genes, phaF, enhances Psl production via a post-transcriptional mechanism, while the other 5 genes/operons do not act on either psl transcription or translation. Together, these data demonstrate that P. aeruginosa has evolved at least two pathways to over-produce a non-alginate exopolysaccharide during long-term colonization of the CF lung. More broadly, this approach allowed us to attribute a biological significance to genes with unknown function, demonstrating the power of using evolution as a guide for targeted genetic studies.open6

Deviations from mean-field behavior in disordered nanoscale superconductor-normal-metal-superconductor arrays

We have fabricated quasi-two-dimensional arrays of nano-scale Pb grains coupled by an overlayer of Ag grains. Their temperature dependent resistive transitions follow predictions for an array of mesoscopic superconductor-normal-superconductor junctions. The decrease of their transition temperatures with Ag overlayer thickness systematically deviates from the Cooper limit theory of the proximity effect as the Pb grain size decreases. The deviations occur when the estimated number of Cooper pairs per grain is less than or equal to 1 and suggest the approach to a superconductor to metal transition.Comment: 11 pages, Pdf only, Revisions include text and figure

KDM1A microenvironment, its oncogenic potential, and therapeutic significance

The lysine-specific histone demethylase 1A (KDM1A) was the first demethylase to challenge the concept of the irreversible nature of methylation marks. KDM1A, containing a flavin adenine dinucleotide (FAD)-dependent amine oxidase domain, demethylates histone 3 lysine 4 and histone 3 lysine 9 (H3K4me1/2 and H3K9me1/2). It has emerged as an epigenetic developmental regulator and was shown to be involved in carcinogenesis. The functional diversity of KDM1A originates from its complex structure and interactions with transcription factors, promoters, enhancers, oncoproteins, and tumor-associated genes (tumor suppressors and activators). In this review, we discuss the microenvironment of KDM1A in cancer progression that enables this protein to activate or repress target gene expression, thus making it an important epigenetic modifier that regulates the growth and differentiation potential of cells. A detailed analysis of the mechanisms underlying the interactions between KDM1A and the associated complexes will help to improve our understanding of epigenetic regulation, which may enable the discovery of more effective anticancer drugs

Identification of new regulators of embryonic patterning and morphogenesis in Xenopus gastrulae by RNA sequencing

During early vertebrate embryogenesis, cell fate specification is often coupled with cell acquisition of specific adhesive, polar and/or motile behaviors. In Xenopus gastrulae, tissues fated to form different axial structures display distinct motility. The cells in the early organizer move collectively and directionally toward the animal pole and contribute to anterior mesendoderm, whereas the dorsal and the ventral-posterior trunk tissues surrounding the blastopore of mid-gastrula embryos undergo convergent extension and convergent thickening movements, respectively. While factors regulating cell lineage specification have been described in some detail, the molecular machinery that controls cell motility is not understood in depth. To gain insight into the gene battery that regulates both cell fates and motility in particular embryonic tissues, we performed RNA sequencing (RNA-seq) to investigate differentially expressed genes in the early organizer, the dorsal and the ventral marginal zone of Xenopus gastrulae. We uncovered many known signaling and transcription factors that have been reported to play roles in embryonic patterning during gastrulation. We also identified many uncharacterized genes as well as genes that encoded extracellular matrix (ECM) proteins or potential regulators of actin cytoskeleton. Co-expression of a selected subset of the differentially expressed genes with activin in animal caps revealed that they had distinct ability to block activin-induced animal cap elongation. Most of these factors did not interfere with mesodermal induction by activin, but an ECM protein, EFEMP2, inhibited activin signaling and acted downstream of the activated type I receptor. By focusing on a secreted protein kinase PKDCC1, we showed with overexpression and knockdown experiments that PKDCC1 regulated gastrulation movements as well as anterior neural patterning during early Xenopus development. Overall, our studies identify many differentially expressed signaling and cytoskeleton regulators in different embryonic regions of Xenopus gastrulae and imply their functions in regulating cell fates and/or behaviors during gastrulation.clos

Superiority of N2O plasma annealing over O2 plasma annealing for amorphous tantalum pentoxide (Ta2O5) films

Japanese Journal of Applied Physics, Part 2: Letters374 BL435-L437JAPL

<i>pslA</i> transcription and translation in over-expression strains.

<p>(A) Fold change in the <i>pslA</i> transcriptional response to gene over-expression. (B) Fold change in the <i>pslA</i> translational response to gene over-expression. β-galactosidase activity was measured at both exponential (black bars) and stationary phase (white bars). Bars represent fold change in <i>pslA</i> transcription or translation compared to the empty vector control strain, PAO1 pJN105 (dashed line). While fold change in <i>pslA</i> transcription or translation is reported for clarity, statistics were performed on normalized luminesence values of empty vector control and over-expression strains assayed on the same day (see Materials and Methods). At least 3 biological replicates were performed in duplicate. Error bars represent standard error of the mean, n=3. *, <i>P</i> value < 0.05 by Student’s <i>t</i> test compared to the empty vector control strain.</p

Protein abundances are more conserved than mRNA abundances across diverse taxa

Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post-transcriptional, translational and protein degradation control clearly influence protein concentration and functionality, it is often thought that protein abundances are primarily determined by the abundances of the corresponding mRNAs. Hence surprisingly, a recent study showed that abundances of orthologous nematode and fly proteins correlate better than their corresponding mRNA abundances. We tested if this phenomenon is general by collecting and testing matching large-scale protein and mRNA expression datasets from seven different species: two bacteria, yeast, nematode, fly, human, and plant. We find that steady-state abundances of proteins show significantly higher correlation across these diverse phylogenetic taxa than the abundances of their corresponding mRNAs (p=0.0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge

Biofilm formation and Psl production in over-expression strains.

<p>(A) Fold change in biofilm formation of wild-type PAO1 over-expression strains. Bars represent the average fold change in biofilm formation compared to the empty vector control strain, PAO1 pJN105 (dashed line). Δ<i>pslA</i> pJN105, a strain that cannot produce Psl, served as a negative control. While fold change in biofilm formation is reported for clarity, statistics were performed on absorbance values for empty vector control and over-expression strains assayed on the same day. At least 3 biological replicates were performed in octuplicate. *, <i>P</i> value < 0.001 by Student’s <i>t</i> test. Error bars represent standard error of the mean, n=3. (B) Fold change in biofilm formation of Δ<i>pslA</i> over-expression strains. Bars represent the average fold change in biofilm formation compared to the empty vector control strain, Δ<i>pslA</i> pJN105 (dashed line). Statistics and error bars are reported as in A. (C) Psl production in PAO1 pJN105 (top) and PAO1 over-expression strains (bottom). The top panels represent Psl production in the wild-type empty vector control strain, PAO1 pJN105, while the bottom panels represent Psl production in the over-expression strains, or as in the last bottom panel, the negative control strain Δ<i>pslA</i> pJN105. At least 3 biological replicates were performed.</p

Protein abundances are more conserved than mRNA abundances across diverse taxa.

Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post-transcriptional, translational and protein degradation control clearly influence protein concentration and functionality, it is often thought that protein abundances are primarily determined by the abundances of the corresponding mRNAs. Hence surprisingly, a recent study showed that abundances of orthologous nematode and fly proteins correlate better than their corresponding mRNA abundances. We tested if this phenomenon is general by collecting and testing matching large-scale protein and mRNA expression data sets from seven different species: two bacteria, yeast, nematode, fly, human, and rice. We find that steady-state abundances of proteins show significantly higher correlation across these diverse phylogenetic taxa than the abundances of their corresponding mRNAs (p=0.0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge