Large-scale pyrosequencing of synthetic DNA: a comparison with results from Sanger dideoxy sequencing

Pyrosequencing is a relatively recent method for sequencing short stretches of DNA. Because both Pyrosequencing and Sanger dideoxy sequencing were recently used to characterize and validate DNA molecular barcodes in a large yeast gene-deletion project, a meta-analysis of those data allow an excellent and timely opportunity for evaluating Pyrosequencing against the current gold standard, Sanger dideoxy sequencing. Starting with yeast genomic DNA, parallel PCR amplification methods were used to prepared 4747 short barcode-containing constructs from 6000 Saccharomyces cerevisiae gene-deletion strains. Pyrosequencing was optimized for average read lengths of 25-30 bases, which included in each case a 20-mer barcode sequence. Results were compared with sequence data obtained by the standard Sanger dideoxy chain termination method. In most cases, sequences obtained by Pyrosequencing and Sanger dideoxy sequencing were of comparable accuracy, and the overall rate of failure was similar. The DNA in the barcodes is derived from synthetic oligonucleotide sequences that were inserted into yeast-deletion-strain genomic DNA by homologous recombination and represents the most significant amount of DNA from a synthetic source that has been sequenced to date. Although more automation and quality control measures are needed, Pyrosequencing was shown to be a fast and convenient method for determining short stretches of DNA sequence.     

Lability of nanoparticulate metal complexes in electrochemical speciation analysis

Lability concepts are elaborated for metal complexes with soft (3D) and hard (2D) aqueous nanoparticles. In the presence of a non-equilibrium sensor, e.g. a voltammetric electrode, the notion of lability for nanoparticulate metal complexes, M-NP, reflects the ability of the M-NP to maintain equilibrium with the reduced concentration of the electroactive free M²⁺ in its diffusion layer. Since the metal ion binding sites are confined to the NP body, the conventional reaction layer in the form of a layer adjacent to the electrode surface is immaterial. Instead an intraparticulate reaction zone may develop at the particle/medium interface. Thus the chemodynamic features of M-NP complexes should be fundamentally different from those of molecular systems in which the reaction layer is a property of the homogeneous solution (μ?=?(D _M/k _a ^′)^1/2). For molecular complexes, the characteristic timescale of the electrochemical technique is crucial in the lability towards the electrode surface. In contrast, for nanoparticulate complexes it is the dynamics of the exchange of the electroactive metal ion with the surrounding medium that governs the effective lability towards the electrode surface.     

Rapid micromachining of high aspect ratio holes in fused silica glass by high repetition rate picosecond laser

We present multiple methods of high aspect ratio hole drilling in fused silica glass, taking advantage of high power and high repetition rate picosecond lasers and flexible beam delivery methods to excise deep holes with minimal collateral damage. Combinations of static and synchronous scanning of laser focus were explored over a range of laser repetition rates and burst-train profiles that dramatically vary laser plume interaction dynamics, heat-affected zone, and heat accumulation physics. Chemically assisted etching of picosecond laser modification tracks are also presented as an extension from femtosecond laser writing of volume nanograting to form high aspect ratio (77) channels. Processing windows are identified for the various beam delivery methods that optimize the laser exposure over energy, wavelength, and repetition rate to reduce microcracking and deleterious heating effects. The results show the benefits of femtosecond laser interactions in glass extend into the picosecond domain, where the attributes of higher power further yield wide processing windows and significantly faster fabrication speed. High aspect ratio holes of 400 μm depth were formed over widely varying rates of 333 holes per second for mildly cracked holes in static-focal positioning through to one hole per second for low-damage and taper free holes in synchronous scanning.     

Ring‐Extended Gramicidin S Analogs Containing cis δ‐Sugar Amino Acid Turn Mimetics with Varying Ring Size

This article presents a series of ring‐extended gramicidin S derivatives, 9 – 14 , that have four ornithine residues as polar protonated side chains and one modified turn region containing a mono‐functionalized cis‐δ‐oxetane, δ‐furanoid, or δ‐pyranoid sugar amino acid residue. Of the GS analogs evaluated, we identified compound 7 , which contains the mono‐benzyloxy cis‐δ‐pyranoid sugar amino acid, as having a better biological profile than the clinically applied topical antibiotic gramicidin S.     

Fluorescent-Magnetic Nanostructures Based on Polymer-Quantum Dots Conjugates

Summary: In this study it is presented the synthesis and the characterization of Fluorescent-Magnetic Nanostructures based on polymer-quantum dots conjugates. Polyvinyl alcohol (PVA) was used as the capping-ligand for the preparation of Cd_xMn_1-xS semiconductor nanocrystals via aqueous colloidal chemistry. Different substitution ratios of Cd²⁺ by Mn⁺² ions were investigated aiming at the formation of stable nanoparticles with photo-luminescent and semi-magnetic properties. UV-visible spectroscopy (UV-vis), photoluminescence spectroscopy (PL), Electric Paramagnetic Resonance Spectroscopy (EPR), and transmission electron microscopy (TEM) were used to characterize the formation and the relative stability of Cd_xMn_1-xS nanoparticles. The results have showed the influence of the Mn²⁺partially replacing Cd²⁺ in the optical behavior of the quantum dots (QDs) produced. In addition, the Cd_xMn_1-xS QDs have evidenced luminescent and semi-magnetic properties. Thus, the biocompatible water-soluble polymer was effective as ligand for synthesizing and stabilizing QDs conjugates with properties allowing them to be potentially applied as imaging and labeling probes in the biomedical field.     

Non-reciprocal transmission via phase conjugation in multimode optical fibres

We demonstrate phase conjugate correction of modal distortion of a single mode beam on double-passing a passive highly multimode fibre. Phase conjugation is achieved in a self-pumped photorefractive BaTiO₃ crystal which conjugates only the e-polarised input component. We show that only a small fraction of the multimode fibre output is required to faithfully conjugate the single mode input beam. This technique enables the demonstration of a novel non-reciprocal transmission device, which for example has immediate application in gain-grating holographic resonator designs with multimode fibres as the active gain medium.