Silver stain removal using H2O2 for enhanced peptide mass mapping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Hydrogen peroxide solutions are reported for the removal of silver stain from proteins isolated in polyacrylamide gels. Removal of silver stain prior to in-gel digestion is shown to enhance sensitivity and sequence coverage of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) peptide mass maps. The rate of silver removal using H2O2 is influenced by H2O2 concentration and increases with increasing pH. The presence of complexation reagents such as ammonia from mass spectrometry compatible ammonium bicarbonate solutions enhances the efficiency and speed of H2O2-mediated silver removal. H2O2-mediated silver removal using the described procedure does not appear to have any detrimental effects on proteins but is observed to produce a slightly elevated level of methionine oxidization over that usually observed in in-gel tryptic digestion.     

The diameter of domination k-critical graphs

A graph is k-domination-critical if γ(G) = k, and for any edge e not in G, γ(G + e) = k ? 1. In this paper we show that the diameter of a domination k-critical graph with k ≧ 2 is at most 2k ? 2. We also show that for every k ≧ 2, there is a k-domination-critical graph having diameter [(3/2)k ? 1]. We also show that the diameter of a 4-domination-critical graph is at most 5.     

Membrane selectivity for an aqueous system by dynamic osmometry

Commercial and fractionated samples of poly(ethylene glycol) and a sample of Dextran were used as standards to show the limitation of a cellulose acetate membrane for osmotic pressure determination of molecular weight in an aqueous system. The leakage of this membrane was much greater in the aqueous system than in organic solvents.     

The edge nucleus of a point-determining graph

In this paper we investigate the edge nucleus E⁰(G) of a point-determining graph G. We observe several relationships between E⁰(G) and the nucleus G⁰ = {v ∈ V(G)∣ G ? v is point determining} and use these relationships to prove several properties of E⁰(G). In particular, we show that there are only a finite number of graphs with a given edge nucleus and we determine those graphs G for which |E⁰(G)| ≤ 2. We also show that an n-clique of a point-determining graph G contains at least n?2 edges of E⁰(G) and if G is totally point determining, then every odd cycle of G meets E⁰(G).     

Predicting particle trajectories on an electrodynamic screen – Theory and experiment

The electrodynamic screen, or EDS, was first introduced to the electrostatics community in the early 1970's. Since that time, it has been studied by several research groups who have investigated its use as a means to remove unwanted particles from insulator surfaces. In the typical EDS, interdigitated electrodes are embedded or deposited on the surface, then energized by three-phase square or sinusoidal voltages of magnitude 500–1200 V at frequencies between 5 and 200 Hz. The resulting electric field entrains previously deposited particles and moves them laterally across the surface. Electrodynamic screens have been proposed for use on solar cells in Mars and Moon space missions, as well as the removal of dust from renewable-energy solar collectors such as photovoltaic panels, solar reflectors, and mirrors. Though often considered merely a nuisance, dust has the potential to partially or totally obscure the solar flux incident on any solar collector.Development of EDS technology has evolved mostly from a “trial and error” approach to choosing such parameters as electrode spacing, depth, and width, as well as voltage magnitude and frequency. Though some theoretical studies may be found in the literature, a more detailed understanding would be valuable in optimizing EDS performance for a particular application and composition of ambient dust, which may vary with geographical location with respect to size, permittivity, and conductivity. A theoretical understanding of how particles are entrained and made to move on an EDS will facilitate proper choice of relevant parameters in future EDS systems. Our work thus attempts to analyze the motion of dust particles subject to all the forces encountered at the surface of an EDS, including the coulomb and dielectrophoretic forces, as well as aerodynamic drag, gravity, and friction. Previous work has shown that particles entrained in the traveling-wave electrostatic field of an EDS exhibit one of two behaviors: ordered, lateral motion; and semi-chaotic motion. These two behaviors have been found both experimentally and in theoretical simulations. This paper attempts to correlate trajectory computations with video observations of these behaviors as recorded in a laboratory setting.     

A conserved asparagine in a ubiquitin-conjugating enzyme positions the substrate for nucleophilic attack

The mechanism used by the ubiquitin-conjugating enzyme, Ubc13, to catalyze ubiquitination is probed with three computational techniques: Born–Oppenheimer molecular dynamics, single point quantum mechanics/molecular mechanics energies, and classical molecular dynamics. These simulations support a long-held hypothesis and show that Ubc13-catalyzed ubiquitination uses a stepwise, nucleophilic attack mechanism. Furthermore, they show that the first step—the formation of a tetrahedral, zwitterionic intermediate—is rate limiting. However, these simulations contradict another popular hypothesis that supposes that the negative charge on the intermediate is stabilized by a highly conserved asparagine (Asn79 in Ubc13). Instead, calculated reaction profiles of the N79A mutant illustrate how charge stabilization actually increases the barrier to product formation. Finally, an alternate role for Asn79 is suggested by simulations of wild-type, N79A, N79D, and H77A Ubc13: it stabilizes the motion of the electrophile prior to the reaction, positioning it for nucleophilic attack. © 2019 Wiley Periodicals, Inc.     

A dynamic study of earthworm feeding ecology -using stable isotopes

Changes in the specific diet of earthworms with time in relation to landuse changes and two different climates were studied by analysing (13)C and (15)N natural abundance in soils and animals. Soil samples from three depths (0-10, 10-20 and 20-30 cm) and earthworms were collected from two sites: Santiago (Northwest Spain) and North Wyke (Southwest England) both consisting of replicated long-term grasslands and recently converted to maize plots. Earthworms were hand-sorted in the field at the peak of the maize growth and after harvesting at both sites. In the Spanish plots, nine and eight earthworm species, all belonging to the three ecological categories (epigeic, anecic and endogeic), were found under maize and permanent pasture, whereas at the English site five and seven different species were, respectively, identified. At both sites (13)C isotopic values of the earthworm tissues reflected changes in diet from C(3) to C(4) with epigeic and epi/anecic worms in the maize plots showing one delta unit difference in relation to the ones found in the grassland plots. Anecic worms seemed to be less responsive to landuse changes. The higher (13)C values of the Spanish soils were also reflected in the earthworm tissues when compared with the English samples. (15)N values showed no clear relationship with the cropping treatments but were clearly related to the ecological grouping, with endogeic worms reaching the highest values whereas for the epigeic and epi/anecic species the lowest values were obtained. This finding was also previously recorded by other authors1 and suggests that, in the future, stable isotope techniques could also be a useful tool in taxonomic studies. Copyright 1999 John Wiley & Sons, Ltd.     

Secondary ion yields produced by keV atomic and polyatomic ion impacts on a self-assembled monolayer surface

A suite of keV polyatomic or 'cluster' projectiles was used to bombard unoxidized and oxidized self-assembled monolayer surfaces. Negative secondary ion yields, collected at the limit of single ion impacts, were measured and compared for both molecular and fragment ions. In contrast to targets that are orders of magnitude thicker than the penetration range of the primary ions, secondary ion yields from polyatomic projectile impacts on self-assembled monolayers show little to no enhancement when compared with monatomic projectiles at the same velocity. This unusual trend is most likely due to the structural arrangement and bonding characteristics of the monolayer molecules with the Au(111). Copyright 1999 John Wiley & Sons, Ltd.