Sub-wavelength focusing of high intensities in microfibre tips

Sub-wavelength efficient intensity confinement has been demonstrated in nanostructured optical microfibre tips. Focus Ion Beam (FIB) milling was used to nanostructure gold-coated optical microfibre tips and form apertures at the apex. Simulations were carried out to optimize the device design. Enhanced transmission efficiency (higher than 10-2) was achieved in spot sizes of ~λ/10. Nanostructured microfibre tips have the potential for a number of applications including optical recording, photolithography and scanning near-field optical microscopy (SNOM)

User\u27s Guide to SNAP for ArcGIS : ArcGIS Interface for Scheduling and Network Analysis Program

This document introduces a computer software named SNAP for ArcGIS®, which has been developed to streamline scheduling and transportation planning for timber harvest areas. Using modern optimization techniques, it can be used to spatially schedule timber harvest with consideration of harvesting costs, multiple products, alternative destinations, and transportation systems. SNAP for ArcGIS attempts either to maximize a net present value or minimize discounted costs of harvesting and transportation over the planning horizon while meeting given harvest volume and acreage constraints. SNAP for ArcGIS works in the ArcGIS environment and provides an easy-to-use analytical tool for sophisticated spatial planning of timber harvest

Cells exhibiting strong p16INK4a promoter activation in vivo display features of senescence

The activation of cellular senescence throughout the lifespan promotes tumor suppression, whereas the persistence of senescent cells contributes to aspects of aging. This theory has been limited, however, by an inability to identify and isolate individual senescent cells within an intact organism. Toward that end, we generated a murine reporter strain by “knocking-in” a fluorochrome, tandem-dimer Tomato (tdTom), into exon 1α of the p16 INK4a locus. We used this allele (p16 tdTom ) for the enumeration, isolation, and characterization of individual p16 INK4a -expressing cells (tdTom + ). The half-life of the knocked-in transcript was shorter than that of the endogenous p16 INK4a mRNA, and therefore reporter expression better correlated with p16 INK4a promoter activation than p16 INK4a transcript abundance. The frequency of tdTom + cells increased with serial passage in cultured murine embryo fibroblasts from p16 tdTom/+ mice. In adult mice, tdTom + cells could be readily detected at low frequency in many tissues, and the frequency of these cells increased with aging. Using an in vivo model of peritoneal inflammation, we compared the phenotype of cells with or without activation of p16 INK4a and found that tdTom + macrophages exhibited some features of senescence, including reduced proliferation, senescence-associated β-galactosidase (SA-β-gal) activation, and increased mRNA expression of a subset of transcripts encoding factors involved in SA-secretory phenotype (SASP). These results indicate that cells harboring activation of the p16 INK4a promoter accumulate with aging and inflammation in vivo, and display characteristics of senescence

Novel anti-inflammatory peptides based on chemokine – glycosaminoglycan interactions reduce leukocyte migration and disease severity in a model of rheumatoid arthritis

Inflammation is characterized by the infiltration of leukocytes from the circulation and into the inflamed area. Leukocytes are guided throughout this process by chemokines. These are basic proteins that interact with leukocytes to initiate their activation and extravasation via chemokine receptors. This is enabled through chemokine immobilization by glycosaminoglycans (GAGs) at the luminal endothelial surface of blood vessels. A specific stretch of basic amino acids on the chemokine, often at the C terminus, interacts with the negatively charged GAGs, which is considered an essential interaction for the chemokine function. Short-chain peptides based on this GAG-binding region of the chemokines CCL5, CXCL8, and CXCL12γ were synthesized using standard Fmoc chemistry. These peptides were found to bind to GAGs with high affinity, which translated into a reduction of leukocyte migration across a cultured human endothelial monolayer in response to chemokines. The leukocyte migration was inhibited upon removal of heparan sulfate from the endothelial surface and was found to reduce the ability of the chemokine and peptide to bind to endothelial cells in binding assays and to human rheumatoid arthritis tissue. The data suggest that the peptide competes with the wild-type chemokine for binding to GAGs such as HS and thereby reduces chemokine presentation and subsequent leukocyte migration. Furthermore, the lead peptide based on CXCL8 could reduce the disease severity and serum levels of the proinflammatory cytokine TNF-α in a murine Ag-induced arthritis model. Taken together, evidence is provided for interfering with the chemokine-GAG interaction as a relevant therapeutic approach

Directed -in vitro- evolution of Precambrian and extant Rubiscos

Rubisco is an ancient, catalytically conserved yet slow enzyme, which plays a central role in the biosphere’s carbon cycle. The design of Rubiscos to increase agricultural productivity has hitherto relied on the use of in vivo selection systems, precluding the exploration of biochemical traits that are not wired to cell survival. We present a directed -in vitro- evolution platform that extracts the enzyme from its biological context to provide a new avenue for Rubisco engineering. Precambrian and extant form II Rubiscos were subjected to an ensemble of directed evolution strategies aimed at improving thermostability. The most recent ancestor of proteobacteria -dating back 2.4 billion years- was uniquely tolerant to mutagenic loading. Adaptive evolution, focused evolution and genetic drift revealed a panel of thermostable mutants, some deviating from the characteristic trade-offs in CO2-fixing speed and specificity. Our findings provide a novel approach for identifying Rubisco variants with improved catalytic evolution potential.This work was supported by the REPSOL Research contracts Rubolution (RC020401120018), Rubolution 2.0 (RC 020401140042), the CSIC project PIE-201780E043 and the Australian Research Council grant CE140100015

Nitrogen oxides and PAN in plumes from boreal fires during ARCTAS-B and their impact on ozone: an integrated analysis of aircraft and satellite observations

We determine enhancement ratios for NO<sub>x</sub>, PAN, and other NO<sub>y</sub> species from boreal biomass burning using aircraft data obtained during the ARCTAS-B campaign and examine the impact of these emissions on tropospheric ozone in the Arctic. We find an initial emission factor for NO<sub>x</sub> of 1.06 g NO per kg dry matter (DM) burned, much lower than previous observations of boreal plumes, and also one third the value recommended for extratropical fires. Our analysis provides the first observational confirmation of rapid PAN formation in a boreal smoke plume, with 40% of the initial NO<sub>x</sub> emissions being converted to PAN in the first few hours after emission. We find little clear evidence for ozone formation in the boreal smoke plumes during ARCTAS-B in either aircraft or satellite observations, or in model simulations. Only a third of the smoke plumes observed by the NASA DC8 showed a correlation between ozone and CO, and ozone was depleted in the plumes as often as it was enhanced. Special observations from the Tropospheric Emission Spectrometer (TES) also show little evidence for enhanced ozone in boreal smoke plumes between 15 June and 15 July 2008. Of the 22 plumes observed by TES, only 4 showed ozone increasing within the smoke plumes, and even in those cases it was unclear that the increase was caused by fire emissions. Using the GEOS-Chem atmospheric chemistry model, we show that boreal fires during ARCTAS-B had little impact on the median ozone profile measured over Canada, and had little impact on ozone within the smoke plumes observed by TES

Alterations in the Aedes aegypti Transcriptome during Infection with West Nile, Dengue and Yellow Fever Viruses

West Nile (WNV), dengue (DENV) and yellow fever (YFV) viruses are (re)emerging, mosquito-borne flaviviruses that cause human disease and mortality worldwide. Alterations in mosquito gene expression common and unique to individual flaviviral infections are poorly understood. Here, we present a microarray analysis of the Aedes aegypti transcriptome over time during infection with DENV, WNV or YFV. We identified 203 mosquito genes that were ≥5-fold differentially up-regulated (DUR) and 202 genes that were ≥10-fold differentially down-regulated (DDR) during infection with one of the three flaviviruses. Comparative analysis revealed that the expression profile of 20 DUR genes and 15 DDR genes was quite similar between the three flaviviruses on D1 of infection, indicating a potentially conserved transcriptomic signature of flaviviral infection. Bioinformatics analysis revealed changes in expression of genes from diverse cellular processes, including ion binding, transport, metabolic processes and peptidase activity. We also demonstrate that virally-regulated gene expression is tissue-specific. The overexpression of several virally down-regulated genes decreased WNV infection in mosquito cells and Aedes aegypti mosquitoes. Among these, a pupal cuticle protein was shown to bind WNV envelope protein, leading to inhibition of infection in vitro and the prevention of lethal WNV encephalitis in mice. This work provides an extensive list of targets for controlling flaviviral infection in mosquitoes that may also be used to develop broad preventative and therapeutic measures for multiple flaviviruses

A monodisperse transmembrane α-helical peptide barrel

The fabrication of monodisperse transmembrane barrels formed from short synthetic peptides has not been demonstrated previously. This is in part because of the complexity of the interactions between peptides and lipids within the hydrophobic environment of a membrane. Here we report the formation of a transmembrane pore through the self-assembly of 35 amino acid α-helical peptides. The design of the peptides is based on the C-terminal D4 domain of the Escherichia coli polysaccharide transporter Wza. By using single-channel current recording, we define discrete assembly intermediates and show that the pore is most probably a helix barrel that contains eight D4 peptides arranged in parallel. We also show that the peptide pore is functional and capable of conducting ions and binding blockers. Such α-helix barrels engineered from peptides could find applications in nanopore technologies such as single-molecule sensing and nucleic-acid sequencing