Sequence selective capture, release and analysis of DNA using a magnetic microbead-assisted toehold-mediated DNA strand displacement reaction

This paper reports on the modification of magnetic beads with oligonucleotide capture probes with a specially designed pendant toehold (overhang) aimed specifically to capture double-stranded PCR products. After capture, the PCR products were selectively released from the magnetic beads by means of a toehold-mediated strand displacement reaction using short artificial oligonucleotide triggers and analysed using capillary electrophoresis. The approach was successfully shown on two genes widely used in human DNA genotyping, namely human c-fms (macrophage colony-stimulating factor) proto-oncogene for the CSF-1 receptor (CSF1PO) and amelogenin

O sistema de tecnologias profissional-educacionais no sistema de formação de especialistas no perfil social

The paper studies the problem of the use of modern educational technologies for training specialists in the social profile. The quality of university professional training is an integrity of several educational technologies, each of which separately has a fairly independent character, but only together can provide a new quality of breeding professionals in the field of social work. The results of the introduction of modern educational technologies in the teaching and education process of the university social system show: the increase of graduates competing in the labor market, in addition to the development and growth of their social, professional and research competence. Therefore, the quality of university professional training of experts in the social sphere is caused by the synergistic integrity of several educational technologies that together provide a new quality of education in the field of social work.El artículo estudia el problema del uso de tecnologías educativas modernas para los especialistas en capacitación en el perfil social. La calidad de la formación profesional universitaria es una integridad de varias tecnologías educativas, cada una de las cuales por separado tiene un carácter bastante independiente, pero solo juntas pueden proporcionar una nueva calidad de profesionales de la cría en el campo del trabajo social. Los resultados de la introducción de tecnologías educativas modernas en el proceso de enseñanza y educación del sistema social universitario muestran: el aumento de los graduados que compiten en el mercado laboral, ademas del desarrollo y crecimiento de su competencia social, profesional y de investigación. Por lo tanto, la calidad de la formación profesional universitaria de los expertos de la esfera social está causada por la integridad sinérgica de varias tecnologías educativas que juntas proporcionan una nueva calidad de educación en el campo del trabajo social.O artigo estuda o problema do uso de tecnologias educacionais modernas para formação de especialistas no perfil social. A qualidade da formação profissional universitária é uma integridade de várias tecnologias educacionais, cada uma das quais separadamente tem um caráter bastante independente, mas apenas em conjunto pode fornecer uma nova qualidade de profissionais de criação no campo do trabalho social. Os resultados da introdução de modernas tecnologias educacionais no processo de ensino e educação do sistema social universitário mostram: o aumento de graduados competindo no mercado de trabalho, além do desenvolvimento e crescimento de sua competência social, profissional e de pesquisa. Portanto, a qualidade da formação profissional universitária de especialistas na esfera social é causada pela integridade sinérgica de várias tecnologias educacionais que, juntas, proporcionam uma nova qualidade de educação no campo do trabalho social

Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.Dmitriy A. Khodakov, Anastasia S. Khodakova, David M. Huang, Adrian Linacre, Amanda V. Elli

КРУПНОПЛОДНОСТЬ МИНИ-СВИНЕЙ ИЦиГ СО РАН: ПОТЕНЦИАЛ НЕРЕАЛИЗУЕМЫХ ВОЗМОЖНОСТЕЙ

This publication presents the results of the analysis of the dynamics of changes in the largefruited indicators of the breeding group of minipigs of the ICG SB RAS. The analysis showed that the four large-copious indicators are divided into two pairs. The first pair is made up of sample values of the characteristic: average and maximum. These indicators are characterized by stability throughout the studied period. The second pair includes the sample minimum values and standard deviations of the trait. These two indicators are dynamic: the sample minimum values are characterized by a decrease, and the sample standard deviations are characterized by a uniform increase, described by linear regression equations. It is shown that the dynamic characteristics are related to each other. It is determined that in this complex, the leader is the minimum value, and the follower is the standard deviation. This is explained by the fact that an increase in the standard deviation is associated with a decrease in the minimum value and the stability of the maximum in the studied period of time. The result of this process is the growth of the genetic potential in the breeding group, which is responsible for the high weight of the newborn individual. However, due to the small size of sows in comparison with commercial breeds (60-70 kg), this potential cannot be realized. Nevertheless, its redundancy ensures the stabilization of the maximum and average values of the trait - the mass of a newborn individual in minipigs of the ICG SB RAS. A possible way to increase the realization of the potential of large-copious breeding group is to reduce the multiple fertility of sows, which is quite solvable, but hardly advisable. Thus there is natural selection directed against individuals with a low birth weight in the herd. Natural and artificial selection for live weight of piglets at birth of 700 g or more, both help to stabilize the average value of the trait at the level optimal for the broodstock.Настоящая публикация представляет результаты анализа динамик изменения показателей крупноплодности селекционной группы мини-свиней ИЦиГ СО РАН. Анализ показал, что четыре показателя крупноплодности делятся на две пары. Первую пару составляют выборочные значения признака: среднее и максимальное. Для этих показателей характерна стабильность на протяжении изучаемого периода. Во вторую пару вошли выборочные минимальные значения и стандартные отклонения признака. Эти два показателя являются динамическими: для выборочных минимальных значений характерно снижение, а для выборочных стандартных отклонений равномерное повышение, описываемое уравнениями линейной регрессии. Показано, что динамические характеристики связаны друг с другом. Определено, что в данном комплексе ведущим является минимальное значение, а ведомым – стандартное отклонение. Объясняется это тем, что увеличение стандартного отклонения сопряжено с уменьшением минимального значения и стабильностью максимального в изучаемый промежуток времени. Результатом этого процесса является рост в селекционной группе генетического потенциала, отвечающего за высокую массу новорожденной особи. Однако из-за малых по сравнению с коммерческими породами размеров свиноматок (60–70 кг) этот потенциал не может быть реализован. Тем не менее его избыточность обеспечивает стабилизацию максимального и среднего значения признака – массы новорождённой особи у мини-свиней ИЦиГ СО РАН. Возможный путь повышения реализации потенциала крупноплодности селекционной группы – это снижение многоплодия свиноматок, что вполне решаемо, но вряд ли целесообразно. Таким образом, в стаде присутствует естественный отбор, направленный против особей с малой массой при рождении, который в совокупности с искусственным отбором на живую массу поросят при рождении 700 г и более способствует стабилизации среднего значения признака на оптимальном для маточного поголовья уровне

Оценка цитотоксической активности и токсичности производного трополонов с потенциальным противоопухолевым действием

The aim. To study the toxicity of 2-(6,8-dimethyl-5-nitro-4-chloroquinoline-2-yl)-5,6,7-trichloro-1,3-tropolone in vitro and in vivo.Materials and methods. 2-(6,8-dimethyl-5-nitro-4-chloroquinoline-2-yl)-5,6,7-trichloro-1,3-tropolone was synthesized using a method for expanding the o-quinone cycle during the reaction between 5-nitro-2,6,8-trimethyl4-chloroquinoline and 3,4,5,6-tetrachloro-1,2-benzoquinone while boiled in dioxane. An in vitro experiment was carried out in the human A549 cell line. Cell viability was assessed using the MTT colorimetric assay by reducing the optical density of the experimental samples compared with the control ones. Acute toxicity was studied on 20 BALB/c Nude male mice. The test compound was administered once orally as a suspension in 1% starch gel at three doses: 0.0055 (group 1), 0.055 (group 2) and 0.55 mg / g (group 3). The control group (group 4) received a placebo.Results. We synthesized a new compound, 2-(6,8-dimethyl-5-nitro-4-chloroquinoline-2-yl)-5,6,7-trichloro-1,3-tropolone. Its structure was established by 1 H nuclear magnetic resonance (NMR), infrared (IR) spectroscopy, and mass spectrometry. The yield was 19.8 g (52%), the melting point was 205–207 ºС, bright yellow crystals (benzene) were observed. The half-maximal inhibitory concentration (IC50) of 2-(6,8-dimethyl-5-nitro-4-chloroquinoline-2-yl)-5,6,7-trichloro-1,3-tropolone was 0.21 ± 0.01 μM, which was significantly lower (р < 0.05) than the IC50 of cisplatin (3.84 ± 0.23). Following the in vivo experiment, no toxic effect of tropolone was detected when administered once at a dose of 0.0055, 0.055, and 0.55 mg / g. Conclusion. 2-(6,8-dimethyl-5-nitro-4-chloroquinoline-2-yl)-5,6,7-trichloro-1,3-tropolone demonstrated cytotoxic effects on the A549 cell line at a lower IC50 than cisplatin which is widely used in treatment of cancers, including lung cancer. Insolubility of 2-(6,8-dimethyl-5-nitro-4-chloroquinoline-2-yl)-5,6,7-trichloro-1,3-tropolone in water and the absence of its toxic effect in the studied modes determine the scope of its application for further study of cumulative and antitumor effects. Цель – исследование токсичности 2-(6,8-диметил-5-нитро-4-хлорхинолин-2-ил)-5,6,7-трихлор-1,3-трополона in vitro и in vivo.Материалы и методы. Для синтеза 2-(6,8-диметил-5-нитро-4-хлорхинолин-2-ил)-5,6,7-трихлор-1,3-трополона использован метод расширения о-хинонового цикла в процессе реакции между 5-нитро-2,6,8-триметил-4-хлорхинолином и 3,4,5,6-тетрахлор-1,2-бензохиноном при кипячении в диоксане. Эксперимент in vitro проведен на клеточной линии рака легкого человека A549. Оценку жизнеспособности клеток проводили при помощи МТТ-колориметрического теста по уменьшению оптической плотности опытных проб по сравнению с контрольными. Исследование острой токсичности проведено на 20 самках мышей линии Balb/c Nude. Исследуемое соединение вводили однократно перорально в форме суспензии в 1%-м крахмальном геле в трех дозах: 0,0055 (1-я группа), 0,055 (2-я группа) и 0,55 мг/г (3-я группа). Контрольная группа (4-я) получала плацебо.Результаты. Получен 2-(6,8-диметил-5-нитро-4-хлорхинолин-2-ил)-5,6,7-трихлор-1,3-трополон по ранее разработанному методу, его строение установлено данными ядерно-магнитного резонанса 1 Н и инфракрасной и масс-спектрометрии. Выход составил 19,8 г (52%), температура плавления 205–207 º С, ярко-желтые кристаллы (бензол). Ингибирующая концентрация IC50 2-(6,8-диметил-5-нитро-4-хлорхинолин-2-ил)-5,6,7- трихлор-1,3-трополона была равна 0,21 ± 0,01 мкМ, что оказалось статистически значимо меньше (р < 0,05) ингибирующей концентрации IC50 цисплатина равной 3,84 ± 0,23 мкМ. В результате исследования in vivo не выявлено токсического действия трополона при однократном введении в дозах 0,0055; 0,055 и 0,55 мг/г.Заключение. Показано, что 2-(6,8-диметил-5-нитро-4-хлорхинолин-2-ил)-5,6,7-трихлор-1,3-трополон проявляет цитотоксическую активность в отношении клеточной линии A549 в более низкой ингибирующей концентрации IC50, чем цисплатин, широко применяющийся в лечении злокачественных новообразований, в том числе рака легкого. Нерастворимость в воде 2-(6,8-диметил-5-нитро-4-хлорхинолин-2-ил)-5,6,7- трихлор-1,3-трополона и отсутствие его токсического действия в исследованных нами режимах определяют границы его использования для дальнейшего изучения кумулятивных и противоопухолевых эффектов.

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Data for master's thesi

Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics

Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA

Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.The authors kindly acknowledge the Australian Research Council Future Fellowship Fund (Grant No. FT130100211) for funding

Toehold-Mediated Nonenzymatic DNA Strand Displacement As a Platform for DNA Genotyping

Toehold-mediated DNA strand displacement provides unique advantages in the construction and manipulation of multidimensional DNA nanostructures as well as nucleic acid sequence analysis. We demonstrate a step change in the use of toehold-mediated DNA strand displacement reactions, where a double-stranded DNA duplex, containing a single-stranded toehold domain, enzymatically generated and then treated as a molecular target for analysis. The approach was successfully implemented for human DNA genotyping, such as gender identification where the amelogenin gene was used as a model target system, and detecting single nucleotide polymorphisms of human mitochondrial DNA. Kinetics of the strand displacement was monitored by the quenched Förster resonance energy transfer effect