Контроль качества меченых FITC белков для интерактомных исследований методами капиллярного SDS гель-электрофореза и SPR биосенсором

The technology of dye-labeled proteins has many fields of application, especially in interactomics. The aim of this work was to adapt protocol of conjugation of low molecular weight (12 – 15 kDа) heme-containing proteins with fluorescein isothiocyanate, isomer I, (FITC) for subsequent protein-protein interaction studies. We have monitored the quality of FITC-labeling of the target protein and comparative assessment of its binding capacity. Using the cytochrome C (Mw 12 kDа) as an example, it has been shown that using the three step method approach including conventional spectrophotometry, capillary gel electrophoresis and SPR analysis it is possible to assess: (i) the capability of the FITC-labeled target protein to interact with its protein partner and protein material from tissue lysates, (ii) the fact of dye conjugation with the protein, and (iii) the quality of purification for final protein preparation from unreacted free dye moleculesТехнология меченых красителем белков имеет очень много областей использования, в том числе и для интерактомных исследований. Целью данной работы была оценка применимости протокола мечения белков флуоресцеин изотиоционатом (изомер I, (FITC)) для белков с небольшой молекулярной массой (12 –15 кДа) путем их ковалентной конъюгации с FITC, а также контроль качества включения метки в белок и сравнительная оценка его способности к белок-белковым взаимодействиям. На примере цитохрома с (12 кДа) было показано, что комбинированное использование методов традиционной спектрофотометрии, капиллярного гель-электрофореза и SPR-анализа позволяет сделать выводы о: а) сохранении способности меченого целевого белка взаимодействовать с белками-партнёрами и белковым материалом тканевых лизатов; б) факте включения метки в белок; в) качестве очистки финального белкового препарата от не прореагировавших с ним свободных молекул красителя

Высокопроизводительный скрининг с помощью оптического SPR-биосенсора низкомолекулярных соединений на взаимодействие с CYP51 Candida krusei

The opportunistic fungus Candida krusei is the causative agent of nosocomial infections characterized by high mortality and development of resistance to drugs of the azole class. Therefore, develjoment of non-azole antifungal agents against resistant fungal strains is extremly important. Lanosterol 14-alpha demethylase (CYP51) is a well-known antifungal target. The optical SPR biosensor is a universal tool for screening studies in search of new drug prototypes. This paper presents the methodological aspects of high-hroughput SPR based screening of a library of low molecular weight compounds of natural origin for their interaction with C. krusei CYP51. It has been shown that when performing high-throughput screening, a researcher should pay special attention to the degree of a sensorgram curvature in the association phase. The described approaches to the analysis of high throughput screening data can be useful for researchers working with SPR biosensors from various manufacturers.Условно-патогенный гриб Candida krusei (C. krusei) является возбудителем нозокомиальных инфекций, характеризующихся высокой летальностью. В последнее время наблюдается тенденция к увеличению доли штаммов дрожжевых грибов, резистентных к препаратам класса азолов. Поэтому поиск потенциальных противогрибковых соединений неазольной природы является актуальным направлением исследований при разработке новых эффективных терапевтических средств в отношении резистентных штаммов грибов. Ланостерол 14-альфа деметилаза (CYP51) является широко известной мишенью для противогрибковых средств. Оптические SPR-биосенсоры представляют собой универсальный инструмент для скрининговых исследований, целью которых является поиск прототипов новых лекарственных соединений. В данной работе представлены методические аспекты высокопроизводительного скрининга библиотеки низкомолекулярных соединений природного происхождения, направленного на установление их взаимодействия с CYP51 C. krusei с использованием SPR-биосенсора. Как показывают результаты, при проведении высокопроизводительного скрининга особое внимание следует обращать на степень выраженности наклона сенсограммы взаимодействия в фазе ассоциации. Описанные подходы к анализу данных высокопроизводительного скрининга могут быть полезны исследователям, работающим с SPR-биосенсорами различных моделей

SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species\u2013specific N.tabacum PGDB. The implementation of this strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species

Photoconductivity in macroporous silicon with regular structure of macropores

The effects of the increase of photoconductivity in periodic macroporous silicon structures depending on the size and period of cylindrical macropores are investigated. It is obtained that the ratio of macroporous silicon photoconductivity to bulk silicon photoconductivity achieves a maximum at the distance between macropores equal to two thicknesses of the Schottky layer, which corresponds to the experimental data. The increase of photoconductivity is due to both the large total surface area of macropores and the existence of Schottky layers in the near-surface region of cylindrical macropores

Out-of-plane optical transmittance of 2D photonic macroporous silicon structures

Optical transmission spectra of 2D photonic macroporous silicon structures are investigated. The absolute bandgap for high values of the out-of-plane component kz is situated between the second and third photonic bands. Essential reduction in the transmittance of electromagnetic radiation and the step formation are observed for wavelengths less than the optical period of structures due to directed and decay optical modes formed by macroporous silicon as a short waveguide. The absorption in the macroporous silicon structure is determined by a maximum of the longitudinal component of electromagnetic waves, its interaction with 2D surface oscillations, and the appearance of polaritonic resonances

ПУБЛИКАЦИОННАЯ АКТИВНОСТЬ РОССИЙСКОЙ МЕДИЦИНСКОЙ НАУКИ В ФОКУСЕ АКТУАЛЬНОЙ НАУЧНОЙ ПОЛИТИКИ: ОЦЕНКА ДОСТИЖИМОСТИ ЦЕЛЕВЫХ ПОКАЗАТЕЛЕЙ

A comprehensive review of National research policy papers issued over the past 6 years was carried out. A set of problems concerning the quality of predicted values of some bibliometric indicators reflecting the level of research performance and publication activity that were declared in governmental documents was discussed. Basic metrics of scientific performance that should be required to achieve the goals declared in the recent governmental policy papers including President’s Executive Order № 599 of May 7, 2012 (increasing the share of Russian researchers’ publications in the total number of publications in international scientific journals indexed in the Web of Science up to 2,44% in 2015). Taking into account the current structure of modern global science in which papers in biomedical subjects make up for approximately one third of the total world scientific output, it becomes obvious how difficult is the governmental task set up to the researchers — to double the number of journal publications indexed in Web of Science in the short-term period of the nearest three years. The priorities and reasonable goal-oriented efforts to meet the targets are proposed in the paper. Проведен анализ государственных программных документов по научной политике, в которых использовались индикаторы публикационной активности и прогнозные оценки роста результативности отечественных научных исследований. Рассчитаны основные показатели публикационной активности, которые должны быть достигнуты профессиональным медицинским сообществом, чтобы соответствовать целевым библиометрическим индикаторам, заявленным в Указе Президента № 599 от 7 мая 2012 г. (увеличение доли российских публикаций в Web of Science до 2,44% к 2015 г.), и в «Стратегии развития медицинской науки до 2025 г.» Показано, что глобальная наука, в сложившейся структуре которой на биомедицинские статьи приходится около 1/3 публикационного мирового потока, ставит перед российским медицинским сообществом очень сложную задачу: удвоить за 3 года число публикаций, индексируемых в Web of Science. Рассмотрены первоочередные и необходимые меры для выполнения этой задачи.

Signatures of the excitonic memory effects in four-wave mixing processes in cavity polaritons

We report the signatures of the exciton correlation effects with finite memory time in frequency domain degenerate four-wave mixing (DFWM) in semiconductor microcavity. By utilizing the polarization selection rules, we discriminate instantaneous, mean field interactions between excitons with the same spins, long-living correlation due to the formation of biexciton state by excitons with opposite spins, and short-memory correlation effects in the continuum of unbound two-exciton states. The DFWM spectra give us the relative contributions of these effects and the upper limit for the time of the exciton-exciton correlation in the unbound two-exciton continuum. The obtained results reveal the basis of the cavity polariton scattering model for the DFWM processes in high-Q GaAs microcavity.Comment: 11 pages, 1 figur

АНАЛИЗ ПУБЛИКАЦИОННОГО ПОТОКА РАМН ЗА 2011 Г. И ПЕРСПЕКТИВЫ УВЕЛИЧЕНИЯ ЕГО ОБЪЕМОВ И АВТОРИТЕТНОСТИ В СООТВЕТСТВИИ С ИНДИКАТОРАМИ «ПРОГРАММЫ ФУНДАМЕНТАЛЬНЫХ НАУЧНЫХ ИССЛЕДОВАНИЙ ГОСАКАДЕМИЙ НА 2013–2020 ГГ.»

The scope of bibliometric research is focused on academic output of the Russian Academy of Medical Sciences (RAMS) in 2011 by analyzing the data extracted from the Web of Science database and InCites application Research Performance Profile of RAMS. Using these analytical tools trends in dynamics of publications and citing of the RAMS researchers were calculated and the level of scientific output in some biomedical subject areas was estimated. Studies revealed the great importance of international collaboration and international coauthorship for RAMS in producing papers published in established scholarly journals. Basic metrics of scientific performance that should be required to achieve the goals declared in the recent governmental policy papers were measured for RAMS institutions as well. Another problem investigated in this research is the problem of low citedness of RAMS journal papers indexed in WoS. Factors and reasons influenced on low citedness were discovered In conclusion authors set out priorities and reasonable goal-oriented efforts to achieve better results in publication activity. В работе представлено библиометрическое исследование публикационного потока ученых Российской академии медицинских наук (РАМН) в международной аналитико-библиографической системе Web of Science за 2011 г. В рамках исследования был изучен профиль научной продуктивности РАМН в аналитическом приложении InCites. Выполнен анализ динамики публикационной активности и цитируемости публикаций сотрудников институтов РАМН, оценен уровень научной производительности и продуктивности отдельных исследовательских направлений, а также эффективность международного научного сотрудничества. Дана оценка соответствия реальных показателей результативности научной деятельности РАМН прогнозным значениям индикаторов публикационной активности, заявленным в ряде программных правительственных документов. Исследована проблема общей низкой цитируемости публикаций исследователей из РАМН и осуществленн анализ факторов, влияющих на уровень цитируемости отечественных работ в области биомедицины. В заключении даются рекомендации по росту публикационной и цитатной активности для публикаций РАМН. 

GG-Strands

A $G$-strand is a map $g(t,{s}):\,\mathbb{R}\times\mathbb{R}\to G$ for a Lie group $G$ that follows from Hamilton's principle for a certain class of $G$-invariant Lagrangians. The SO(3)-strand is the $G$-strand version of the rigid body equation and it may be regarded physically as a continuous spin chain. Here, $SO(3)_K$-strand dynamics for ellipsoidal rotations is derived as an Euler-Poincar\'e system for a certain class of variations and recast as a Lie-Poisson system for coadjoint flow with the same Hamiltonian structure as for a perfect complex fluid. For a special Hamiltonian, the $SO(3)_K$-strand is mapped into a completely integrable generalization of the classical chiral model for the SO(3)-strand. Analogous results are obtained for the $Sp(2)$-strand. The $Sp(2)$-strand is the $G$-strand version of the $Sp(2)$ Bloch-Iserles ordinary differential equation, whose solutions exhibit dynamical sorting. Numerical solutions show nonlinear interactions of coherent wave-like solutions in both cases. ${\rm Diff}(\mathbb{R})$-strand equations on the diffeomorphism group $G={\rm Diff}(\mathbb{R})$ are also introduced and shown to admit solutions with singular support (e.g., peakons).Comment: 35 pages, 5 figures, 3rd version. To appear in J Nonlin Sc

Non-Kaehler Heterotic String Compactifications with non-zero fluxes and constant dilaton

We construct new explicit compact supersymmetric valid solutions with non-zero field strength, non-flat instanton and constant dilaton to the heterotic equations of motion in dimension six. We present balanced Hermitian structures on compact nilmanifolds in dimension six satisfying the heterotic supersymmetry equations with non-zero flux, non-flat instanton and constant dilaton which obey the three-form Bianchi identity with curvature term taken with respect to either the Levi-Civita, the (+)-connection or the Chern connection. Among them, all our solutions with respect to the (+)-connection on the compact nilmanifold $M_3$ satisfy the heterotic equations of motion.Comment: LaTeX, 16 pp., no figures, new Theorem 1.1, references adde