Complete genome sequences of five Ackermannviridae that infect Enterobacteriaceae hosts.

This announcement contains the whole genome sequences of five Ackermannviridae that infect members of the Enterobacteriaceae family of bacteria. Four of the five phages were isolated using Salmonella enterica serovar Typhimurium as a bacterial host: AR2819, Sajous1, SilasIsHot, and FrontPhageNews. ChubbyThor was isolated using Shigella boydii.

Simulation of field-assisted ion exchange in glass regarding the space-charge density and pseudo-mixed-alkali effect: erratum.

This erratum reports corrections for the original publication, Appl. Opt.60, 6632 (2021)APOPAI0003-693510.1364/AO.427171.

Asymmetric optical multimode splitters by field-assisted ion exchange using patterned mask openings.

Asymmetric optical multimode splitters based on optical waveguides were fabricated in glass substrates using a field-assisted ion exchange process. Accompanying simulations, conducted to study the light propagation, revealed the possibility to realize asymmetric splitters based on waveguides with different width. In the exchange process, broad mask openings in the blocking layer are compared to those consisting of closely spaced parallel lines with various widths. The waveguide profiles of the resulting splitters were recorded and the optical losses and splitting ratios were determined for a wavelength of 850 nm. Additionally data transmission tests were conducted and showed the suitability of the splitters for a bandwidth of 28 GBit/s.

Complete Genome Sequences of Six Chi-Like Bacteriophages That Infect Proteus and Klebsiella.

Proteus mirabilis and Klebsiella aerogenes are Gram-negative opportunistic pathogens that are responsible for nosocomial and health care-associated infections, including urinary tract infections. Here, the full genome sequences of six Chi-like Proteus (DanisaurMW, DoubleBarrel, Inception, Jing313, and NotEvenPhaged) or Klebsiella (Phraden) bacteriophages are announced, contributing to the understanding of Chi-like phages.

Simulation of field-assisted ion exchange in glass regarding the space-charge density and pseudo-mixed-alkali effect.

A model is proposed to describe the field-assisted molten salt ion exchange of Na+ with Ag+ in glass. It accounts for the buildup of space-charge zones and for the pseudo-mixed-alkali effect. Simulations in 1D proved to be consistent with experimental results. The 1D model has been expanded to 2D, making it suitable for simulating the fabrication of channel waveguides. Using a first-order approximation, a good agreement between the simulations and the experimental data can be achieved.

Optically transparent and environmentally durable superhydrophobic coating based on functionalized SiO2 nanoparticles.

Optical surfaces such as mirrors and windows that are exposed to outdoor environmental conditions are susceptible to dust buildup and water condensation. The application of transparent superhydrophobic coatings on optical surfaces can improve outdoor performance via a 'self-cleaning' effect similar to the Lotus effect. The contact angle (CA) of water droplets on a typical hydrophobic flat surface varies from 100° to 120°. Adding roughness or microtexture to a hydrophobic surface leads to an enhancement of hydrophobicity and the CA can be increased to a value in the range of 160°-175°. This result is remarkable because such behavior cannot be explained using surface chemistry alone. When surface features are on the order of 100 nm or smaller, they exhibit superhydrophobic behavior and maintain their optical transparency. In this work we discuss our results on transparent superhydrophobic coatings that can be applied across large surface areas. We have used functionalized silica nanoparticles to coat various optical elements and have measured the CA and optical transmission between 190 and 1100 nm on these elements. The functionalized silica nanoparticles were dissolved in a solution of the solvents, while the binder used was a polyurethane clearcoat. This solution was spin-coated onto a variety of test glass substrates, and following a curing period of about 30 min, these coatings exhibited superhydrophobic behavior with a static CA ≥ 160°.

Processing of loose carbon nanotubes into isolated, high density submicron channels.

Loose multi-wall carbon nanotubes (MWNTs) were processed into a bundle of 19,600 individual channels with an individual channel diameter of 0.4 microm using a fiber drawing process. First, a powder of sodium silicate solution containing purified MWNTs was created. A glass capillary tube was filled with the powder and drawn into fibers. The fibers were cut into segments, bundled and redrawn multiple times to create fibers with multiple channels containing MWNTs. This processing approach created thousands of uniformly ordered channels containing dispersed MWNTs in a glass matrix while simultaneously aligning the MWNTs. The bulk resistivity of the MWNT-silicate channel has been improved by 38% after two consecutive draws as a result of the increased MWNT fraction.

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

The Paragon Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2-5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.

Discovering known and unanticipated protein modifications using MS/MS database searching.

We present an MS/MS database search algorithm with the following novel features: (1) a novel protein database structure containing extensive preindexing and (2) zone modification searching, which enables the rapid discovery of protein modifications of known (i.e., user-specified) and unanticipated delta masses. All of these features are implemented in Interrogator, the search engine that runs behind the Pro ID, Pro ICAT, and Pro QUANT software products. Speed benchmarks demonstrate that our modification-tolerant database search algorithm is 100-fold faster than traditional database search algorithms when used for comprehensive searches for a broad variety of modification species. The ability to rapidly search for a large variety of known as well as unanticipated modifications allows a significantly greater percentage of MS/MS scans to be identified. We demonstrate this with an example in which, out of a total of 473 identified MS/MS scans, 315 of these scans correspond to unmodified peptides, while 158 scans correspond to a wide variety of modified peptides. In addition, we provide specific examples where the ability to search for unanticipated modifications allows the scientist to discover: unexpected modifications that have biological significance; amino acid mutations; salt-adducted peptides in a sample that has nominally been desalted; peptides arising from nontryptic cleavage in a sample that has nominally been digested using trypsin; other unintended consequences of sample handling procedures.