Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results. © 2014 Das et al

Молекулярный фенотип клеток крови, ассоциированный с прогрессированием трижды негативного рака молочной железы

Introduction. triple negative breast cancer is an aggressive clinical phenotype characterized by poor prognosis. immune system plays an important role in the development, treatment response, and progression of solid tumor. The search for immune-related markers associated with the prediction of treatment efficacy and disease prognosis, and based on the use of high-resolution molecular techniques, is a promising area of research, the results of which can be translated into clinical practice. Case description. The molecular profile of blood mononuclear cells in a 48-year-old female patient with histologically proven triple negative breast cancer (estrogen Receptor – 0; progesteron Receptor – 0; Her2/neu – 0; gata-3 – 0, androgen Receptor – 0 and Ki67 – 70 %) was described. The patient did not response to neoadjuvant chemotherapy with 4 cycles of paclitaxel + carboplatin followed by 2 cycles of adriamycin + cyclophosphamide. The patient underwent surgery. disease progression (pelvic bone metastases) occurred 2 months after surgery. The features of blood lymphocytes and monocytes associated with a lack of response to neoadjuvant chemotherapy and disease progression were described.Conclusion. This clinical case demonstrates that sequencing of peripheral blood mononuclear cells can be used as a method for identifying predictive markers of therapy efficacy and developing personalized treatments for patients with triple negative breast cancer.Актуальность. Трижды негативный подтип рака молочной железы характеризуется агрессивным течением и неблагоприятным прогнозом. Компоненты иммунной системы как непосредственные участники патогенеза играют роль в развитии, ответе на терапию и прогрессировании этой нозологии. Поиск маркеров иммунных клеток, ассоциированных с предсказанием эффективности лечения и прогнозом заболевания, основанный на применении молекулярных методов высокого разрешения, является перспективным направлением поискового исследования, результаты которого можно транслировать в клиническую практику. Описание клинического случая. Представлен первый опыт описания молекулярного профиля мононуклеарных клеток крови пациентки с трижды негативным раком молочной железы. Опухоль: инвазивная карцинома неспецифического типа с экспрессией: estrogen Receptor – 0; progesteron Receptor – 0; Her2/neu – 0; gata-3 – 0, androgen Receptor – 0, Ki67 – 70 % опухолевых клеток. Отмечено отсутствие ответа на неоадъювантную химиотерапию по схеме: 4 цикла «паклитаксел + + карбоплатин», с последующими 2 курсами АС (адриамицин + циклофосфан). Пациентке проведено оперативное лечение, через 2 мес после которого выявлены метастазы в кости таза. У пациентки описаны особенности лимфоцитов и моноцитов крови, которые могут быть ассоциированы с отсутствием ответа на неоадъювантную химиотерапию и прогрессированием заболевания.Заключение. Представленное клиническое наблюдение показывает, что метод секвенирования мононуклеарных клеток периферической крови можно использовать в качестве поискового для обнаружения предиктивных маркеров эффективности терапии и создания персонифицированной системы лечения пациенток с трижды негативным раком молочной железы

An international study evaluating elemental analysis

A statistical study on elemental analysis for 5 small organic compounds at 18 independent service providers across multiple countries demonstrates variation in the returned results that is outside journal guidelines (0.4%) in greater than 10% of measurements. The results indicate that a deviation of 0.4% is not a realistic journal requirement with the variability attributed to random error

Blood mononuclear cell molecular landscape associated with tumor progression in triple-negative breast cancer

Introduction. triple negative breast cancer is an aggressive clinical phenotype characterized by poor prognosis. immune system plays an important role in the development, treatment response, and progression of solid tumor. The search for immune-related markers associated with the prediction of treatment efficacy and disease prognosis, and based on the use of high-resolution molecular techniques, is a promising area of research, the results of which can be translated into clinical practice. Case description. The molecular profile of blood mononuclear cells in a 48-year-old female patient with histologically proven triple negative breast cancer (estrogen Receptor – 0; progesteron Receptor – 0; Her2/neu – 0; gata-3 – 0, androgen Receptor – 0 and Ki67 – 70 %) was described. The patient did not response to neoadjuvant chemotherapy with 4 cycles of paclitaxel + carboplatin followed by 2 cycles of adriamycin + cyclophosphamide. The patient underwent surgery. disease progression (pelvic bone metastases) occurred 2 months after surgery. The features of blood lymphocytes and monocytes associated with a lack of response to neoadjuvant chemotherapy and disease progression were described.Conclusion. This clinical case demonstrates that sequencing of peripheral blood mononuclear cells can be used as a method for identifying predictive markers of therapy efficacy and developing personalized treatments for patients with triple negative breast cancer

Reference Gene Selection for Quantitative Real-time PCR Normalization in Quercus suber

The use of reverse transcription quantitative PCR technology to assess gene expression levels requires an accurate normalization of data in order to avoid misinterpretation of experimental results and erroneous analyses. Despite being the focus of several transcriptomics projects, oaks, and particularly cork oak (Quercus suber), have not been investigated regarding the identification of reference genes suitable for the normalization of real-time quantitative PCR data. In this study, ten candidate reference genes (Act, CACs, EF-1α, GAPDH, His3, PsaH, Sand, PP2A, ß-Tub and Ubq) were evaluated to determine the most stable internal reference for quantitative PCR normalization in cork oak. The transcript abundance of these genes was analysed in several tissues of cork oak, including leaves, reproduction cork, and periderm from branches at different developmental stages (1-, 2-, and 3-year old) or collected in different dates (active growth period versus dormancy). The three statistical methods (geNorm, NormFinder, and CV method) used in the evaluation of the most suitable combination of reference genes identified Act and CACs as the most stable candidates when all the samples were analysed together, while ß-Tub and PsaH showed the lowest expression stability. However, when different tissues, developmental stages, and collection dates were analysed separately, the reference genes exhibited some variation in their expression levels. In this study, and for the first time, we have identified and validated reference genes in cork oak that can be used for quantification of target gene expression in different tissues and experimental conditions and will be useful as a starting point for gene expression studies in other oaks

Electrospinning of hydrogels for biomedical applications

The field of biomedical applications for hydrogels requires the development of nanostructures with specific controlled diameter and mechanical properties. Nanofibers are ideally candidates for these advanced requirements, and one of the easiest techniques that can produce one-dimensional nanostructured materials in fibrous form is the electrospinning. This technique provides extremely thin fibres with controlled diameter, highly porous microstructure with interconnected pores; extremely versatile allowing the use of various polymers for tailoring various applications requirements and it is a simple cost-effective method on preparation of scaffolds. In this section, we will discuss recent and specific applications with a focus on their mechanisms. As such, we conclude this section with a discussion on perspectives and future possibilities on this field.ye