Selection and analytical applications of aptamers binding microbial pathogens

DNA aptamers specifically recognizing microbial cells and viruses have a range of analytical and therapeutic applications. This article describes recent advances in the development of aptamers targeting specific pathogens (e.g., live bacteria, whole viral particles, and virally-infected mammalian cells). Specific aptamers against pathogens have been used as affinity reagents to develop sandwich assays, to label and to image cells, to bind with cells for flow-cytometry analysis, and to act as probes for development of whole-cell biosensors. Future applications of aptamers to pathogens will benefit from recent advances in improved selection and new aptamers containing modified nucleotides, particularly slow off-rate modified aptamers (SOMAmers).     

Spatial resolution optimization of backscattered electron images using Monte Carlo simulation

The relation between probe size and spatial resolution of backscattered electron (BSE) images was studied. In addition, the effect of the accelerating voltage, the current intensity and the sample geometry and composition were analyzed. An image synthesis method was developed to generate the images from backscattered electron coefficients obtained from Monte Carlo simulations. Spatial resolutions of simulated images were determined with the SMART-J method, which is based on the Fourier transform of the image. The resolution can be improved by either increasing the signal or decreasing the noise of the backscattered electron image. The analyses demonstrate that using a probe size smaller than the size of the observed object (sample features) does not improve the spatial resolution. For a probe size larger than the feature size, the spatial resolution is proportional to the probe size.     

Oxygenated Metabolites of n‐3 Polyunsaturated Fatty Acids as Potential Oxidative Stress Biomarkers: Total Synthesis of 8‐F3t‐IsoP, 10‐F4t‐NeuroP and [D4]‐10‐F4t‐NeuroP

A wide variety of metabolic products of polyunsaturated fatty acids is of paramount importance for improving our medical knowledge in the field of oxidized lipids. Two novel metabolites of n‐3 polyunsaturated fatty acids, 8‐F_3t‐IsoP and 10‐F_4t‐NeuroP as well as a deuterated derivative thereof were synthesized based on an acetylenic intermediate. An original approach achieved lateral chain insertion of 8‐F_3t‐IsoP by a ring‐closing alkyne metathesis/semi‐reduction strategy together with a temporary tether.     

(+)-(1S, 3S, 6S, 8S)-und (−)-(1R, 3R, 6R, 8R)-4, 9-Twistadien: Synthese und Bestimmung der absoluten Konfiguration

(+)-(1S, 3S, 6S, 8S)-and (?)-(1R, 3R, 6R, 8R)-4, 9-Twistadiene: Synthesis and Absolute Configuration A synthesis and the determination of the absolute configuration of (+)-(1S, 3S, 6S, 8S)- and (?)-(1R, 3R, 6R, 8R)-4, 9-twistadiene ((+)- and (?)- 4 , respectively) is described. Their chiroptical properties are compared with those of saturated twistane ((+)- and (?)- 5 ) as well as with those of the unsaturated and saturated 2, 7-dioxatwistane analogs (+)- and (?)- 9 , and (+)- and (?)- 10 , respectively, which also are compounds of known absolute configurations.     

Spontaneous Isomerization of Peptide Cation Radicals Following Electron Transfer Dissociation Revealed by UV-Vis Photodissociation Action Spectroscopy

Peptide cation radicals of the z-type were produced by electron transfer dissociation (ETD) of peptide dications and studied by UV-Vis photodissociation (UVPD) action spectroscopy. Cation radicals containing the Asp (D), Asn (N), Glu (E), and Gln (Q) residues were found to spontaneously isomerize by hydrogen atom migrations upon ETD. Canonical N-terminal [z₄ + H]^+● fragment ion-radicals of the R-C^●H-CONH- type, initially formed by N?C_α bond cleavage, were found to be minor components of the stable ion fraction. Vibronically broadened UV-Vis absorption spectra were calculated by time-dependent density functional theory for several [^●DAAR + H]⁺ isomers and used to assign structures to the action spectra. The potential energy surface of [^●DAAR + H]⁺ isomers was mapped by ab initio and density functional theory calculations that revealed multiple isomerization pathways by hydrogen atom migrations. The transition-state energies for the isomerizations were found to be lower than the dissociation thresholds, accounting for the isomerization in non-dissociating ions. The facile isomerization in [^●XAAR + H]⁺ ions (X = D, N, E, and Q) was attributed to low-energy intermediates having the radical defect in the side chain that can promote hydrogen migration along backbone C_α positions. A similar side-chain mediated mechanism is suggested for the facile intermolecular hydrogen migration between the c- and [z + H]^●-ETD fragments containing Asp, Asn, Glu, and Gln residues.

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Dynamics of Ultracold Bosons in Artificial Gauge Fields—Angular Momentum,Fragmentation, and the Variance of Entropy

We consider the dynamics of two-dimensional interacting ultracold bosons triggered by suddenly switching on an artificial gauge field. The system is initialized in the ground state of a harmonic trapping potential. As a function of the strength of the applied artificial gauge field, we analyze the emergent dynamics by monitoring the angular momentum, the fragmentation as well as the entropy and variance of the entropy of absorption or single-shot images. We solve the underlying time-dependent many-boson Schrödinger equation using the multiconfigurational time-dependent Hartree method for indistinguishable particles (MCTDH-X). We find that the artificial gauge field implants angular momentum in the system. Fragmentation—multiple macroscopic eigenvalues of the reduced one-body density matrix—emerges in sync with the dynamics of angular momentum: the bosons in the many-body state develop non-trivial correlations. Fragmentation and angular momentum are experimentally difficult to assess; here, we demonstrate that they can be probed by statistically analyzing the variance of the image entropy of single-shot images that are the standard projective measurement of the state of ultracold atomic systems.