Implementation of High-Throughput Sequencing (HTS) in Aptamer Selection Technology

Aptamers are nucleic acid ligands that bind specifically to a target of interest. Aptamers have gained in popularity due to their high potential for different applications in analysis, diagnostics, and therapeutics. The procedure called systematic evolution of ligands by exponential enrichment (SELEX) is used for aptamer isolation from large nucleic acid combinatorial libraries. The huge number of unique sequences implemented in the in vitro evolution in the SELEX process imposes the necessity of performing extensive sequencing of the selected nucleic acid pools. High-throughput sequencing (HTS) meets this demand of SELEX. Analysis of the data obtained from sequencing of the libraries produced during and after aptamer isolation provides an informative basis for precise aptamer identification and for examining the structure and function of nucleic acid ligands. This review discusses the technical aspects and the potential of the integration of HTS with SELEX

Point Mutations of Nicotinic Receptor α1 Subunit Reveal New Molecular Features of G153S Slow-Channel Myasthenia

Slow-channel congenital myasthenic syndromes (SCCMSs) are rare genetic diseases caused by mutations in muscle nicotinic acetylcholine receptor (nAChR) subunits. Most of the known SCCMS-associated mutations localize at the transmembrane region near the ion pore. Only two SCCMS point mutations are at the extracellular domains near the acetylcholine binding site, α1(G153S) being one of them. In this work, a combination of molecular dynamics, targeted mutagenesis, fluorescent Ca2+ imaging and patch-clamp electrophysiology has been applied to G153S mutant muscle nAChR to investigate the role of hydrogen bonds formed by Ser 153 with C-loop residues near the acetylcholine-binding site. Introduction of L199T mutation to the C-loop in the vicinity of Ser 153 changed hydrogen bonds distribution, decreased acetylcholine potency (EC50 2607 vs. 146 nM) of the double mutant and decay kinetics of acetylcholine-evoked cytoplasmic Ca2+ rise (τ 14.2 ± 0.3 vs. 34.0 ± 0.4 s). These results shed light on molecular mechanisms of nAChR activation-desensitization and on the involvement of such mechanisms in channelopathy genesis

Cognitive Modeling as a Tool Fuel Management at the Station

Let’s consider the solution of fuel management in the warehouse to solve the applied cognitive modeling and cognitive graphics method for displaying the cycle of fuel supplies. In order to effectively manage inventory software-based “canvas”, is constructed a model of fuel consumption at the station, consider the scenario and the evaluation of the results.В данной статье рассматривается решение задачи управления запасами топлива на складе. Для решения применены когнитивное моделирование и метод когнитивной графики для отображения ритмичности поставки топлива. С целью эффективного управления запасами на основе программного обеспечения «Канва» построена модель потребления топлива на станции, рассмотрены сценарии и дана оценка полученным результатам

Cognitive Modeling as a Tool Fuel Management at the Station

Let’s consider the solution of fuel management in the warehouse to solve the applied cognitive modeling and cognitive graphics method for displaying the cycle of fuel supplies. In order to effectively manage inventory software-based “canvas”, is constructed a model of fuel consumption at the station, consider the scenario and the evaluation of the results.В данной статье рассматривается решение задачи управления запасами топлива на складе. Для решения применены когнитивное моделирование и метод когнитивной графики для отображения ритмичности поставки топлива. С целью эффективного управления запасами на основе программного обеспечения «Канва» построена модель потребления топлива на станции, рассмотрены сценарии и дана оценка полученным результатам

Highly selective and sensitive detection of glutamate by an electrochemical aptasensor

An electrochemical aptamer-based sensor was developed for glutamate, the major excitatory neurotransmitter in the central nervous system. Determining glutamic acid release and glutamic acid levels is crucial for studying signal transmission and for diagnosing pathological conditions in the brain. Glutamic acid-selective oligonucleotides were isolated from an ssDNA library using the Capture-SELEX protocol in complex medium. The selection permitted the isolation of an aptamer 1d04 with a dissociation constant of 12 µM. The aptamer sequence was further used in the development of an electrochemical aptamer sensor. For this purpose, a truncated aptamer sequence named glu1 was labelled with a ferrocene redox tag at the 3′-end and immobilized on a gold electrode surface via Au-thiol bonds. Using 6-mercapto-1-hexanol as the backfill, the sensor performance was characterized by alternating current voltammetry. The glu1 aptasensor showed a limit of detection of 0.0013 pM, a wide detection range between 0.01 pM and 1 nM, and good selectivity for glutamate in tenfold diluted human serum. With this enzyme-free aptasensor, the highly selective and sensitive detection of glutamate was demonstrated, which possesses great potential for implementation in microelectrodes and for in vitro as well as in vivo monitoring of neurotransmitter release

Kinetics of the Gas-Phase Reaction of Hydroxyl Radicals with Dimethyl Methylphosphonate (DMMP) over an Extended Temperature Range (273–837 K)

The kinetics of the reaction of hydroxyl radical (OH) with dimethyl methylphosphonate (DMMP, (CH3O)2CH3PO) (reaction 1) OH + DMMP → products (1) was studied at the bath gas (He) pressure of 1 bar over the 295–837 K temperature range. Hydroxyl radicals were produced in the fast reaction of electronically excited oxygen atoms O(1D) with H2O. The time-resolved kinetic profiles of hydroxyl radicals were recorded via UV absorption at around 308 nm using a DC discharge H2O/Ar lamp. The reaction rate constant exhibits a pronounced V-shaped temperature dependence, negative in the low temperature range, 295–530 K (the rate constant decreases with temperature), and positive in the elevated temperature range, 530–837 K (the rate constant increases with temperature), with a turning point at 530 ± 10 K. The rate constant could not be adequately fitted with a standard 3-parameter modified Arrhenius expression. The data were fitted with a 5-parameter expression as: k1 = 2.19 × 10−14(T/298)2.43exp(15.02 kJ mol−1/RT) + 1.71 × 10−10exp(−26.51 kJ mol−1/RT) cm3molecule−1s−1 (295–837 K). In addition, a theoretically predicted pressure dependence for such reactions was experimentally observed for the first time