Скрининг белков-биомаркеров рака легкого с помощью мультиплексной электрохимической сенсорной системы на основе аптамеров

The aim of this work is the development and demonstration of the method of simultaneous detection of several biomarkers of lung cancer in the blood plasma of patients using a multiplex electrochemical testing system based on DNA aptamers. DNA aptamers are a new class of synthetic affinity probes obtained by in vitro or in vivo selection procedure by the systematic evolution of ligands by exponential enrichment (SELEX).Materials and methods. A set of aptamers obtained previously by selection for postoperative lung cancer tissue was used to create a multiplex electrochemical biochip. Identification of aptamer target proteins was performed using a modified affinity enrichment method (AptaBID). Molecular targets for the used set of aptamers to lung cancer were defined as vimentin, defensin, a light chain of myosin, tubulin alpha 1-B, neutrophil elastase and A1 elongation factor 1.Measurements of the presence of these biomarker proteins in blood plasma were carried out using electrochemical detection. The difference between peak heights before and after plasma deposition on the electrodes modified by aptamers was considered as a response of the system to the presence of protein onco-markers in blood plasma. Blood plasma of healthy volunteers was used as control.Results. Research showed that in the blood plasma of all the patients with lung cancer the content of biomarker proteins that bind to aptamers on electrode surfaces was increased. The increased content of these proteins in the blood plasma of patients suggests the presence of invasiveness and metastasis of tumors and their chemo-resistance.Цель. Разработка и демонстрация метода одновременного определения нескольких биомаркеров рака легкого в плазме крови больных с помощью мультиплексной электрохимической сенсорной системы, основанной на ДНК-аптамерах. ДНК-аптамеры представляют собой новый класс синтетических аффинных реагентов, получаемых с помощью процедуры селекции in vitro или in vivo методом систематической эволюции лигандов экспоненциальным обогащением (SELEX).Материалы и методы. Для создания мультиплексного электрохимического биочипа использовалось несколько аптамеров, полученных ранее путем селекции к послеоперационным тканям рака легкого. Идентификацию белков-мишеней аптамеров проводили с помощью модифицированного метода аффинного обогащения (AptaBID). В качестве молекулярных мишеней для использованного набора аптамеров к раку легкого были определены виментин, дефензин, легкая цепь миозина, тубулин альфа 1-B, нейтрофил эластаза и фактор удлинения 1 A1. Определение наличия этих белков-биомаркеров в плазме крови проводили с помощью электрохимической детекции. В качестве отклика системы на присутствие белков-онкомаркеров в плазме крови выступала разница между величинами пиков на квадратно-волновой вольтамперограмме до и после нанесения плазмы на электроды с предварительно иммобилизированными на их поверхности аптамерами. Для контрольного сравнения использовалась плазма крови здоровых добровольцев.Результаты. Показано, что в плазме крови всех исследованных больных раком легкого повышено содержание белков-биомаркеров, связывающихся с аптамерами на поверхностях электродов. Повышенное содержание этих белков в плазме крови больных предполагает их химиорезистентность и высокую степень инвазивности и метастазирования опухолей

The Not-So-Easy Task of Computing Class Subsumptions in OWL RL.

The lightweight ontology language OWL RL is used for reasoning with large amounts of data. To this end, the W3C standard provides a simple system of deduction rules, which operate directly on the RDF syntax of OWL. Several similar systems have been studied. However, these approaches are usually complete for instance retrieval only. This paper asks if and how such methods could also be used for computing entailed subclass relationships. Checking entailment for arbitrary OWL RL class subsumptions is co-NP-hard, but tractable rule-based reasoning is possible when restricting to subsumptions between atomic classes. Surprisingly, however, this cannot be achieved in any RDF-based rule system, i.e., the W3C calculus cannot be extended to compute all atomic class subsumptions. We identify syntactic restrictions to mitigate this problem, and propose a rule system that is sound and complete for many OWL RL ontologies. © 2012 Springer-Verlag Berlin Heidelberg

Screening of lung cancer biomarker-proteins with a multiplex electrochemical sensor system based on aptamers

The aim of this work is the development and demonstration of the method of simultaneous detection of several biomarkers of lung cancer in the blood plasma of patients using a multiplex electrochemical testing system based on DNA aptamers. DNA aptamers are a new class of synthetic affinity probes obtained by in vitro or in vivo selection procedure by the systematic evolution of ligands by exponential enrichment (SELEX).Materials and methods. A set of aptamers obtained previously by selection for postoperative lung cancer tissue was used to create a multiplex electrochemical biochip. Identification of aptamer target proteins was performed using a modified affinity enrichment method (AptaBID). Molecular targets for the used set of aptamers to lung cancer were defined as vimentin, defensin, a light chain of myosin, tubulin alpha 1-B, neutrophil elastase and A1 elongation factor 1.Measurements of the presence of these biomarker proteins in blood plasma were carried out using electrochemical detection. The difference between peak heights before and after plasma deposition on the electrodes modified by aptamers was considered as a response of the system to the presence of protein onco-markers in blood plasma. Blood plasma of healthy volunteers was used as control.Results. Research showed that in the blood plasma of all the patients with lung cancer the content of biomarker proteins that bind to aptamers on electrode surfaces was increased. The increased content of these proteins in the blood plasma of patients suggests the presence of invasiveness and metastasis of tumors and their chemo-resistance