Isolation and Characterization of a ssDNA Aptamer against Major Soluble Antigen of Renibacterium salmoninarum

Bacterial kidney disease (BKD) is a major health problem of salmonids, affecting both wild and cultured salmon. The disease is caused by Renibacterium salmoninarum (Rs), a fastidious, slow-growing and strongly Gram-positive diplobacillus that produces chronic, systemic infection characterized by granulomatous lesions in the kidney and other organs, often resulting in death. Fast detection of the pathogen is important to limit the spread of the disease, particularly in hatcheries or aquaculture facilities. Aptamers are increasingly replacing conventional antibodies as platforms for the development of rapid diagnostic tools. In this work, we describe the first instance of isolating and characterizing a ssDNA aptamer that binds with high affinity to p57 or major soluble antigen (MSA), the principal antigen found on the cell wall surface of Rs. Specifically, in this study a construct of the full-length protein containing a DNA binding domain (MSA-R2c) was utilized as target. Aptamers were isolated from a pool of random sequences using GO-SELEX (graphene oxide-systematic evolution of ligands by exponential enrichment) protocol. The selection generated multiple aptamers with conserved motifs in the random region. One aptamer with high frequency of occurrence in different clones was characterized and found to display a strong binding affinity to MSA-R2c with a K_d of 3.0 ± 0.6 nM. The aptamer could be potentially utilized for the future development of a sensor for rapid and onsite detection of Rs in water or in infected salmonids, replacing time-consuming and costly lab analyses.     

Influence of alkyl chain length on the structure of dialkyldithiophosphinic Acid self-assembled monolayers on gold

We report the formation and characterization of self-assembled monolayers (SAMs) based on dialkyldithiophosphinic acid adsorbates {[CH(3)(CH(2))(n)](2)P(S)SH (n = 5, 9, 11, 13, 15)} on gold substrates. SAMs were characterized using X-ray photoelectron spectroscopy, reflection-absorption infrared spectroscopy, contact angle measurements, and electrochemical impedance spectroscopy. Data show that there is a roughly 60:40 mixture of bidentate and monodentate adsorbates in each of these SAMs. The presence of monodentate adsorbates is due to the numerous and deep grain boundaries of the underlying gold substrate, which disrupt chelation. Comparing the characterization data of dialkyldithiophosphinic acid SAMs with those of analogous n-alkanethiolate SAMs shows that both SAMs follow a similar trend: The alkyl chains become increasingly organized and crystalline with increasing alkyl chain length. The alkyl groups of dialkyldithiophosphinic acid SAMs, however, are generally less densely packed than those of n-alkanethiolate SAMs. For short alkyl chains (hexyl, decyl, and dodecyl), the significantly lower packing densities cause the alkyl chains to be liquid-like and disorganized. Long-chain dialkyldithiophosphinic acid SAMs are only slightly less crystalline than analogous n-alkanethiolate SAMs.     

Bottom-up view of water network-mediated CO2 reduction using cryogenic cluster ion spectroscopy and direct dynamics simulations

The transition states of a chemical reaction in solution are generally accessed through exchange of thermal energy between the solvent and the reactants. As such, an ensemble of reacting systems approaches the transition state configuration of reactant and surrounding solvent in an incoherent manner that does not lend itself to direct experimental observation. Here we describe how gas-phase cluster chemistry can provide a detailed picture of the microscopic mechanics at play when a network of six water molecules mediates the trapping of a highly reactive "hydrated electron" onto a neutral CO(2) molecule to form a radical anion. The exothermic reaction is triggered from a metastable intermediate by selective excitation of either the reactant CO(2) or the water network, which is evidenced by the evaporative decomposition of the product cluster. Ab initio molecular dynamics simulations of energized CO(2)·(H(2)O)(6)(-) clusters are used to elucidate the nature of the network deformations that mediate intracluster electron capture, thus revealing the detailed solvent fluctuations implicit in the Marcus theory for electron-transfer kinetics in solution.     

Variable time lag and backward ejection in full-dimensional analysis of strong-field double ionization

Ensembles of 400,000 two-electron trajectories in three space dimensions are used with Newtonian equations of motion to track atomic double ionization under very strong laser fields. We report a variable time lag between e-e collision and double ionization, and find that the time lag plays a key role in the emergence directions of the electrons. These are precursors to production of electron momentum distributions showing substantial new agreement with experimental data.     

A decomposition theorem for χ1-convex sets

A set S in $\text{R}$ is said to be χ-convex if and only if S does not contain a visually independent subset having cardinality χ. It is natural to ask when an χ-convex set may be expressed as a countable union of convex sets. Here it is proved that if S is a closed χ-convex set in the plane and $\text{R}$ has at most finitely many bounded components, then S is a countable union of convex sets. A parallel result holds in $\text{R}$ when S is a closed χ-convex set which contains all triangular regions whose relative boundaries are in S. However, the result fails for arbitrary χ-convex sets, even in the plane.     

Visible shorelines inR d

Summary LetC be a closed set inR ^d and letj be a fixed integer,j 1. The setS R ^d ~C is said to have aj-partition relative toC if there existj or fewer pointsc ₁,, c _j ofC such that each point ofS sees via the complement ofC at least one pointc _i. For every triple of integersd, p, j withd 0, p d + 1, j 1, there exists a smallest integerf(d, p, j) such that the following is true: IfC is a convexd-polytope inR ^d havingp vertices and ifS R ^d ~C, S has aj-partition relative toC if and only if everyf(d, p, j)-member subset of S has such a partition.ForC a convex polytope inR ² andS R ² ~C, all points ofS see via the complement ofC a common neighborhood in the boundary ofC if and only if every three points ofS see via the complement ofC such a neighborhood.A weak analogue of this result holds for arbitrary compact convex sets inR ^d .     

Semi-empirical molecular orbital calculations on some tautomers of cytosine

The stability of a series of cytosine tautomers has been investigated using both all valence electron and -electron SCF methods. The effect of general and selective scaling of the bond lengths was studied in the CNDO/2 calculations. The enol tautomer of cytosine exceeded the keto form in stability in these calculations. -electron SCF CI calculations were performed on the cytosine tautomers using two different parameterization schemes. The calculated transitions obtained for the enol form showed a close proximity to that of the keto and imino structures. Comparison was made with the experimental electronic spectrum in water and acetonitrile. No clear distiction between the keto and enol forms could be made on the basis of these calculations.

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Zusammenfassung Die StabilitÄt einer Reihe von Cytosin-Tautomeren wurde mit einer Allvalenzelektronen- und mit einer -Elektronen-SCF-Methode untersucht. Die Auswirkung einer allgemeinen als auch selektiven Skalierung der BindungslÄngen wurde bei den CNDO2-Berechnungen untersucht. Das Enoltautomere des Cytosins übertrifft nach diesen Rechnungen die Ketoform an StabilitÄt. Bei den -Elektronen-SCF-CI-Rechnungen wurden zwei Methoden der Parametrisierung angewandt. Die für die Enolform berechneten übergÄnge zeigten eine gro\e Ähnlichkeit zu denjenigen der Keto- und Iminostrukturen. Die berechneten Werte wurden mit dem experimentellen Spektrum von Cytosin in Wasser sowie Acetonitril verglichen. Auf Grund der Berechnungen konnte keine klare Unterscheidung zwischen der Keto- und der Enolform getroffen werden.

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Résumé Etude de la stabilité d'une série de tautomères de la cytosine par les méthodes SCF à électrons de valence et à électrons . L'effet d'ajustement global ou selectif des longueurs de liaison a été étudié dans le cadre CNDO/2. Le tautomère énolique de la cytosine s'avère dans ces calculs plus stable que la forme cétonique. Des calculs d'électrons SCF CI ont été effectués sur les tautomères de la cytosine en utilisant deux schémas différents pour la paramétrisation. Les transitions calculées obtenues pour la forme énolique montrent une grande analogie avec celles des structures cétoniques et iminiques. La comparaison a été faite avec le spectre électronique expérimental dans l'eau et l'acétonitrile. Aucune distinction claire entre les formes cétoniques et énoliques n'a pu Être faite à partir de ces calculs.

     

Automatic poisson peak harvesting for high throughput protein identification

High throughput identification of proteins by peptide mass fingerprinting requires an efficient means of picking peaks from mass spectra. Here, we report the development of a peak harvester to automatically pick monoisotopic peaks from spectra generated on matrix-assisted laser desorption/ionisation time of flight (MALDI-TOF) mass spectrometers. The peak harvester uses advanced mathematical morphology and watershed algorithms to first process spectra to stick representations. Subsequently, Poisson modelling is applied to determine which peak in an isotopically resolved group represents the monoisotopic mass of a peptide. We illustrate the features of the peak harvester with mass spectra of standard peptides, digests of gel-separated bovine serum albumin, and with Escherictia coli proteins prepared by two-dimensional polyacrylamide gel electrophoresis. In all cases, the peak harvester proved effective in its ability to pick similar monoisotopic peaks as an experienced human operator, and also proved effective in the identification of monoisotopic masses in cases where isotopic distributions of peptides were overlapping. The peak harvester can be operated in an interactive mode, or can be completely automated and linked through to peptide mass fingerprinting protein identification tools to achieve high throughput automated protein identification.