ЦИКЛОФИЛИН А: СТРОЕНИЕ И ФУНКЦИИ

Cyclophilins belong to a large family of ancient conservative proteins with peptidyl-prolyl-cis-trans isomerase activity. The main member of this family – cyclophilin A – was discovered as an intracellular ligand for cyclosporine A. Further investigations revealed a wide range of functions of cyclophilin A. Cyclophilin A is involved in T-cell signaling, it takes part in folding, assembly and intracellular transport of proteins, as well as acts as an antioxidant. Different cell types secrete cyclophilin A under infection or oxidative stress. Cyclophilin A is one of the main factors involved in inflammation and pathogenesis of autoimmune, cardiovascular and other diseases. This protein is thought to take part in tumor progression. In this review we describe the structure of cyclophilin A and its main known functions in health and disease.Циклофилины – большое семейство консервативных, филогенетически очень древних белков, обладающих пептидил-пролил-цистранс-изомеразной активностью. Наиболее распространенным среди них является циклофилин А, который был обнаружен как внутриклеточный лиганд для связывания с циклоспорином А. Изучение механизма супрессии циклоспорина А, в основе которой лежит его взаимодействие с циклофилином А, послужило мощным толчком для исследований последнего. Было установлено, что циклофилин А принимает участие в проведении сигналов в Т-лимфоцитах, участвует в фолдинге, сборке и внутриклеточном транспорте белков, а также играет роль антиоксиданта. При инфекциях и оксидативном стрессе различные типы клеток способны секретировать циклофилин А. Он является одним из центральных факторов, участвующих в воспалении и патогенезе аутоиммунных, сердечно-сосудистых и других заболеваний. Предполагается, что циклофилин А может принимать участие в прогрессии опухолей. Настоящий обзор посвящен описанию строения и известных функций циклофилина А в норме и при различных патологических процессах

ОЦЕНКА ЭФФЕКТИВНОСТИ ПРИМЕНЕНИЯ ЗУБНОЙ ПАСТЫ НА ОСНОВЕ ЭФИРНОГО МАСЛА КЕДРА В ПРОФИЛАКТИКЕ ИСТИННОГО ПАТОЛОГИЧЕСКОГО ОРАЛЬНОГО ГАЛИТОЗА

Introduction. Given the mechanism of the development of halitosis and low efficiency of its self-elimination, means of oral hygiene with antiglycation characteristics should efficiently remove plaque and slow its formation, have antiseptic, antimicrobial and anti-inflammatory properties; have high deodorant quality, strengthen natural defense mechanisms and be safe to oral tissues and organism as a whole. Toothpastes and mouthwashes should consist of components that are able to mask and as well detoxify volatile sulphur and nitrogencontaining compounds produced by microorganisms of the oral cavity. The objective is to evaluate the dynamics of deodorant effect of the means of oral hygiene for identifying the effectiveness of preventive measures among the population.Materials and methods. At the department of preventive dentistry of the Federal State Budgetary Educational Institution of Higher Education «Pavlov First Saint Petersburg State Medical University” of the Ministry of Healthcare of the Russian Federation, we conducted the diagnostic assessment of halitosis based on the method of index determination of the deodorant effect by Ulitovsky S. B. This method allows to monitor the deodorant effect and in a single definition to determine the level of mouth breathing before using the means of hygiene.Results. The research revealed that the indicators of index determination of the deodorant effect by Ulitovsky S. B to the end of the study was 44.78±1.73 % in the 1st group and 26.92±1.61 % in the control group. Based on these data, which depended on the degree of antimicrobial activity of personal means of oral hygiene, the examined sample of prophylactic toothpaste showed the significant activity for such test cultures as Ps. aeruginosa, B. cereus and C. albicans.Conclusions. Based on the evaluating the dynamics of the deodorant effect of the means of oral hygiene throughout the study we identified the increasing of deodorant effect according to the index determination of the deodorant effect by Ulitovsky S. B. By the end of the study, the indicators in the main group were higher than in control group almost in 2 times. With the aim of identifying the most effective means of hygiene for the prevention of halitosis, we evaluated the antimicrobial effect of the prophylactic toothpaste with Cedar essential oil, silver ions, aminoftorid, Savory oil and leaves of the Saro tree. It showed the most pronounced activity against such test cultures as Ps. aeruginosa, B. cereus and C. albicans. The finding indicates high antiglycation effect and deodorant qualities of the examined prophylactic toothpaste.Введение. Учитывая механизм развития галитоза и низкую эффективность его самостоятельного устранения, средства гигиены рта с антигалитозными характеристиками должны качественно удалять зубной налет и замедлять его образование, обладать антисептическими, противомикробными и противовоспалительными свойствами; иметь высокие дезодорирующие качества, усиливать природные защитные механизмы и быть безопасными для тканей полости рта и организма в целом. В состав зубных паст и ополаскивателей должны входить компоненты, способные не маскировать, а нейтрализовывать летучие серо- и азотсодержащие соединения, продуцируемые микроорганизмами полости рта.Цель – оценка динамики дезодорирующего действия средств гигиены рта для выявления эффективности профилактических мероприятий у населения.Материал и методы. На базе кафедры стоматологии профилактической ФГБОУ ВО «ПСПбГМУ им. И. П. Павлова» проведена диагностическая оценка галитоза, основанная на методе индексного определения дезодорирующего действия С. Б. Улитовского, который позволяет провести мониторинг дезодорирующего действия, а при однократном определении до применения средств гигиены – определить уровень ротового дыхания.Результаты исследования. Установлено, что показатели эффективности индекса Дезодорирующего действия Улитовского к концу исследования в 1-й группе достигли 44,78±1,73 %, а в контрольной – 26,92±1,61 %. Исходя из полученных данных, которые зависят от степени антимикробной активности средств индивидуальной гигиены полости рта, исследованный образец профилактической зубной пасты проявляет наиболее выраженную активность в отношении таких тест-культур, как Ps. aeruginosa, B. cereus и C. albicans.Выводы. На основании оценки динамики дезодорирующего действия средств гигиены рта на протяжении всего исследования выявлено повышение эффективности дезодорирующего действия по индексу Дезодорирующего действия Улитовского. К концу исследования по показателям эффективности основная группа превышала контрольную почти в 2 раза. С целью выявления наиболее эффективных средств гигиены для профилактики галитоза проведенная оценка антимикробного действия профилактической зубной пасты на основе эфирного масла кедра, ионов серебра, аминофторида, масла чабера и листьев дерева саро показала наиболее выраженную активность в отношении таких тест-культур, как Ps. aeruginosa, B. cereus и C. albicans. Полученные данные свидетельствуют о высоком антигалитозном эффекте и дезодорирующих качествах исследуемой профилактической зубной пасты

Combining specificity determining and conserved residues improves functional site prediction

<p>Abstract</p> <p>Background</p> <p>Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core). Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities.</p> <p>Results</p> <p>Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs), as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples.</p> <p>Conclusion</p> <p>The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.</p

Ensemble approach to predict specificity determinants: benchmarking and validation

<p>Abstract</p> <p>Background</p> <p>It is extremely important and challenging to identify the sites that are responsible for functional specification or diversification in protein families. In this study, a rigorous comparative benchmarking protocol was employed to provide a reliable evaluation of methods which predict the specificity determining sites. Subsequently, three best performing methods were applied to identify new potential specificity determining sites through ensemble approach and common agreement of their prediction results.</p> <p>Results</p> <p>It was shown that the analysis of structural characteristics of predicted specificity determining sites might provide the means to validate their prediction accuracy. For example, we found that for smaller distances it holds true that the more reliable the prediction method is, the closer predicted specificity determining sites are to each other and to the ligand.</p> <p>Conclusion</p> <p>We observed certain similarities of structural features between predicted and actual subsites which might point to their functional relevance. We speculate that majority of the identified potential specificity determining sites might be indirectly involved in specific interactions and could be ideal target for mutagenesis experiments.</p

Характеристика эффекторов адаптивного иммунитета, вовлеченных во вторичный ксеногенный иммунный ответ на клетки меланомы человека

Introduction. Current approaches are being developed for adoptive cancer therapy using T-cells genetically modified with T-cell receptors (TCRs) with specificity for tumor antigens. The complexities of identifying antigen-specific TCRs in a patient’s repertoire and selecting therapeutic  receptors necessitate the development of experimental strategies for generating tumor-specific T cells. One of such approaches could be the xenogeneic immunization of mice with human tumor cells. It seems plausible that the T cell repertoire stimulated by xenogeneic vaccination could be a source of TCRs suitable for adoptive cancer immunotherapy.Aim. To assess the prospects for using xenogeneic immunizations to generate tumor-specific memory T cells and identify their TCRs suitable for adoptive immunotherapy, we studied the dynamics of the secondary xenogeneic response in a model of induction of an immune response in mice to human melanoma cells.Materials and methods. Mice were immunized with human melanoma cells, and 45 days later, they were re-challenged with the immunizing tumor. The dynamics of the development of the secondary immune response in vivo and the composition of the involved effectors of adaptive immunity were analyzed by flow cytometry. The proliferation of lymphocytes from immune mice in response to human melanoma cells was evaluated in in vitro culture.Results. The secondary xenogeneic response was characterized by a more intense accumulation of T cells and the rapid development of the effector phase at the injection site of human melanoma. This correlated with an enhanced in vitro proliferative response of lymphocytes from immune animals to xenoantigens of the immunizing tumor. CD4+ and CD8+ memory  T cells contributed equally to the development of a secondary response to human melanoma cells expressing HLA class I and II molecules. When only HLA class I was expressed on the cells of the immunizing xenogeneic tumor, CD8+ memory cells were formed, which dominated the secondary immune response.Conclusion. Our findings confirmed the formation of a specific immunological memory for xenoantigens during xenogeneic immunization. This suggests the possibility of generating xenogeneic TCRs specific for human tumor antigens, which opens up opportunities to developing approaches for screening among them for receptor variants suited for adoptive immunotherapy of human cancers.Введение. В настоящее  время развиваются подходы адоптивной клеточной терапии онкологических заболеваний с использованием Т-клеток, генетически модифицированных Т-клеточными рецепторами (ТКР) со специфичностью к опухолевым антигенам. Трудоемкость идентификации антигенспецифических ТКР в репертуаре пациента и отбора терапевтических рецепторов делает актуальной разработку экспериментальных стратегий генерации опухолеспецифических Т-клеток. Одной из них может быть ксеногенная иммунизация модельных животных клетками опухоли человека. представляется привлекательной идея, что репертуар Т-клеток, стимулированный  ксеногенной иммунизацией, может стать источником для поиска ТКР, пригодных для адоптивной иммунотерапии опухолей человека.Цель исследования  – анализ динамики вторичного ксеногенного ответа в модели индукции иммунного ответа у мышей на клетки меланомы человека для оценки перспектив использования ксеногенных иммунизаций для генерации опухолеспецифических Т-клеток памяти и идентификации их ТКР, подходящих для адоптивной иммунотерапии.Материалы и методы. Мышей иммунизировали клетками меланомы человека; через 45 дней повторно вводили иммунизирующую опухоль. Динамику развития вторичного иммунного ответа in vivo и состав вовлеченных эффекторов адаптивного иммунитета анализировали методом проточной цитофлуориметрии. В культуре in vitro оценивали пролиферативный ответ лимфоцитов иммунных мышей на клетки иммунизирующей и сторонней меланом человека.Результаты. Вторичный ксеногенный ответ характеризовался более интенсивным накоплением Т-клеток и быстрым развитием эффекторной фазы в месте введения меланомы человека. это коррелировало с усиленным пролиферативным ответом in vitro лимфоцитов иммунных животных на ксеноантигены иммунизирующей опухоли. CD4+- и СD8+-Т-клетки памяти вносили  равный  вклад в развитие вторичного ответа на клетки меланомы человека, экспрессирующей молекулы антигенов гистосовместимости (human leukocyte antigens, HLA) классов I и II. При экспрессии только HLA класса I на клетках иммунизирующей ксеногенной опухоли формировались CD8+-клетки памяти, которые доминировали во вторичном иммунном ответе.Заключение. полученные нами данные подтвердили, что в ходе ксеногенной иммунизации формируется специфическая иммунологическая память к ксеноантигенам. Это указывает на возможность генерации ксеногенных ТКР, специфичных к антигенам опухоли человека, и открывает перспективы для разработки стратегий поиска среди них вариантов рецепторов, пригодных для адоптивной иммунотерапии опухолей человека

Gene Flow in Genetically Modified Wheat

Understanding gene flow in genetically modified (GM) crops is critical to answering questions regarding risk-assessment and the coexistence of GM and non-GM crops. In two field experiments, we tested whether rates of cross-pollination differed between GM and non-GM lines of the predominantly self-pollinating wheat Triticum aestivum. In the first experiment, outcrossing was studied within the field by planting “phytometers” of one line into stands of another line. In the second experiment, outcrossing was studied over distances of 0.5–2.5 m from a central patch of pollen donors to adjacent patches of pollen recipients. Cross-pollination and outcrossing was detected when offspring of a pollen recipient without a particular transgene contained this transgene in heterozygous condition. The GM lines had been produced from the varieties Bobwhite or Frisal and contained Pm3b or chitinase/glucanase transgenes, respectively, in homozygous condition. These transgenes increase plant resistance against pathogenic fungi. Although the overall outcrossing rate in the first experiment was only 3.4%, Bobwhite GM lines containing the Pm3b transgene were six times more likely than non-GM control lines to produce outcrossed offspring. There was additional variation in outcrossing rate among the four GM-lines, presumably due to the different transgene insertion events. Among the pollen donors, the Frisal GM line expressing a chitinase transgene caused more outcrossing than the GM line expressing both a chitinase and a glucanase transgene. In the second experiment, outcrossing after cross-pollination declined from 0.7–0.03% over the test distances of 0.5–2.5 m. Our results suggest that pollen-mediated gene flow between GM and non-GM wheat might only be a concern if it occurs within fields, e.g. due to seed contamination. Methodologically our study demonstrates that outcrossing rates between transgenic and other lines within crops can be assessed using a phytometer approach and that gene-flow distances can be efficiently estimated with population-level PCR analyses

Comparative efficacy of two microdoses of a potentized homoeopathic drug, Cadmium Sulphoricum, in reducing genotoxic effects produced by cadmium chloride in mice: a time course study

BACKGROUND: Cadmium poisoning in the environment has assumed an alarming problem in recent years. Effective antimutagenic agents which can reverse or combat cadmium induced genotoxicity in mice have not yet been reported. Therefore, in the present study, following the homeopathic principle of "like cures like", we tested the efficacy of two potencies of a homeopathic drug, Cadmium Sulphoricum (Cad Sulph), in reducing the genotoxic effects of Cadmium chloride in mice. Another objective was to determine the relative efficacy of three administrative modes, i.e. pre-, post- and combined pre and post-feeding of the homeopathic drugs. For this, healthy mice, Mus musculus, were intraperitoneally injected with 0.008% solution of CdCl(2) @ 1 ml/100 gm of body wt (i.e. 0.8 mcg/gm of bw), and assessed for the genotoxic effects through such studies as chromosome aberrations (CA), micronucleated erythrocytes (MNE), mitotic index (MI) and sperm head anomaly (SHA), keeping suitable succussed alcohol fed (positive) and CdCl(2) untreated normal (negative) controls. The CdCl(2) treated mice were divided into 3 subgroups, which were orally administered with the drug prior to, after and both prior to and after injection of CdCl(2) at specific fixation intervals and their genotoxic effects were analyzed. RESULTS: While the CA, MNE and SHA were reduced in the drug fed series as compared to their respective controls, the MI showed an apparent increase. The combined pre- and post-feeding of Cad Sulph showed maximum reduction of the genotoxic effects. CONCLUSIONS: Both Cad Sulph-30 and 200 were able to combat cadmium induced genotoxic effects in mice and that combined pre- and post-feeding mode of administration was found to be most effective in reducing the genotoxic effect of CdCl(2) followed by the post-feeding mode

Crowdsourcing Fungal Biodiversity : Revision of Inaturalist Observations in Northwestern Siberia

The paper presents the first analysis of crowdsourcing data of all observations of fungi (including lichens) and myxomycetes in Northwestern Siberia uploaded to iNaturalist.org to date (24.02.2022). The Introduction presents an analysis of fungal diversity crowdsourcing globally, in Russia, and in the region of interest. Materials and methods describe the protocol of uploading data to iNaturalist.org, the structure of the crowdsourcing community. initiative to revise the accumulated data. procedures of data analysis, and compilation of a dataset of revised crowdsourced data. The Results present the analysis of accumulated data by several parameters: temporal, geographical and taxonomical scope, observation and identification efforts, identifiability of various taxa, species novelty and Red Data Book categories and the protection status of registered observations. The Discussion provides data on usability of crowdsourcing data for biodiversity research and conservation of fungi, including pros and contras. The Electronic Supplements to the paper include an annotated checklist of observations of protected species with information on Red Data Book categories and the protection status, and an annotated checklist of regional records of new taxa. The paper is supplemented with a dataset of about 15 000 revised and annotated records available through Global Biodiversity Information Facility (GBIF). The tradition of crowdsourcing is rooted in mycological societies around the world, including Russia. In Northwestern Siberia, a regional mycological club was established in 2018, encouraging its members to contribute observations of fungi on iNaturalist.org. A total of about 15 000 observations of fungi and myxomycetes were uploaded so far, by about 200 observers, from three administrative regions (Yamalo-Nenetsky Autonomous Okrug, Khanty-Mansi Autonomous Okrug, and Tyumen Region). The geographical coverage of crowdsourcing observations remains low. However. the observation activity has increased in the last four years. The goal of this study consisted of a collaborative effort of professional mycologists invited to help with the identification of these observations and analysis of the accumulated data. As a result, all observations were reviewed by at least one expert. About half of all the observations have been identified reliably to the species level and received Research Grade status. Of those, 90 species (195 records) represented records of taxa new to their respective regions: 876 records of 53 species of protected species provide important data for conservation programmes. The other half of the observations consists of records still under-identified for various reasons: poor quality photographs, complex taxa (impossible to identify without microscopic or molecular study). or lack of experts in a particular taxonomic group. The Discussion section summarises the pros and cons of the use of crowdsourcing for the study and conservation of regional fungal diversity, and summarises the dispute on this subject among mycologists. Further research initiatives involving crowdsourcing data must focus on an increase in the quality of observations and strive to introduce the habit of collecting voucher specimens among the community of amateurs. The timely feedback from experts is also important to provide quality and the increase of personal involvement.Peer reviewe

Transgene × Environment Interactions in Genetically Modified Wheat

BACKGROUND: The introduction of transgenes into plants may cause unintended phenotypic effects which could have an impact on the plant itself and the environment. Little is published in the scientific literature about the interrelation of environmental factors and possible unintended effects in genetically modified (GM) plants. METHODS AND FINDINGS: We studied transgenic bread wheat Triticum aestivum lines expressing the wheat Pm3b gene against the fungus powdery mildew Blumeria graminis f.sp. tritici. Four independent offspring pairs, each consisting of a GM line and its corresponding non-GM control line, were grown under different soil nutrient conditions and with and without fungicide treatment in the glasshouse. Furthermore, we performed a field experiment with a similar design to validate our glasshouse results. The transgene increased the resistance to powdery mildew in all environments. However, GM plants reacted sensitive to fungicide spraying in the glasshouse. Without fungicide treatment, in the glasshouse GM lines had increased vegetative biomass and seed number and a twofold yield compared with control lines. In the field these results were reversed. Fertilization generally increased GM/control differences in the glasshouse but not in the field. Two of four GM lines showed up to 56% yield reduction and a 40-fold increase of infection with ergot disease Claviceps purpurea compared with their control lines in the field experiment; one GM line was very similar to its control. CONCLUSIONS: Our results demonstrate that, depending on the insertion event, a particular transgene can have large effects on the entire phenotype of a plant and that these effects can sometimes be reversed when plants are moved from the glasshouse to the field. However, it remains unclear which mechanisms underlie these effects and how they may affect concepts in molecular plant breeding and plant evolutionary ecology

ФУНКЦИОНАЛЬНЫЙ ПОТЕНЦИАЛ КЛЕТОК ПАМЯТИ CD8+ В УСЛОВИЯХ ЛИМФОПЕНИИ, ВЫЗВАННОЙ ВВЕДЕНИЕМ ГИДРОКОРТИЗОНА

Background. Wide use of glucocorticoids therapy for neoplasms, autoimmune diseases and allergies is associated with suppression of adaptive immunity that requires profound study of their immunoregulatory properties and immunotoxicity.Results. In this work, using our model of selective activation of mouse CD8+ memory cells in the mixed lymphocyte reaction (MLR) in vitro, we show for the first time that intraperitoneal injection of high dose hydrocortisone (2.5 mg per animal) allows to detect memory cells in the thymus of animals immunized with allogeneic tumor cells. Similar to memory cells from other lymphoid organs, hydrocortisone-resistant thymic lymphocytes from immune animals respond on allogeneic stimulators subjected to severe heat shock and are immunologically specific to immunizing alloantigen. Thus, cortisone-resistant thymocytes are partially or completely represented by memory cells. We also show here that memory responses of heterozygotes on TCR a-chain knock-out (genetically incapable to secondary rearrangement of TCR achains) are significantly enhanced as compared with the ones of wild type mice.Conclusion. These findings allows to suggest the hypothesis according to which memory T cell clones proliferating in primary immune response migrate into thymus providing necessary microenvironment for reexpression of recombinases. After editing of genes encoding TCR achains, such T lymphocytes can return to peripheral repertoire maintaining its wideness.Введение. Широкое применение глюкокортикоидов в терапии онкологических, аутоиммунных и аллергических заболеваний сопряжено с подавлением функций адаптивного иммунитета и ставит задачу углубленного исследования их иммунорегуляторных свойств и иммунотоксичности.Результаты. Используя разработанную нами модель селективной активации мышиных клеток памяти CD8+ в смешанной культуре лимфоцитов (mixedlymphocytereaction, MLR) invitro, в этой работе мы впервые показали, что внутрибрюшинное введение мышам гидрокортизона в высокой дозе (2,5 мг на 1 животное) позволяет обнаружить Т-клетки памяти в тимусе животных, иммунизированных клетками  аллогенной опухоли. Как и клетки  памяти из других лимфоидных органов, лимфоциты тимуса иммунных животных, резистентные к гидрокортизону, отвечают пролиферацией на аллогенные стимуляторы, подвергнутые острому тепловому шоку и иммунологически специфичны к иммунизирующему аллоантигену. Таким образом, кортизонрезистентные тимоциты частично или полностью представлены клетками памяти. Также мы показали, что у гетерозигот по нокауту α-цепи TCR (генетически неспособных ко вторичной реаранжировке α-цепей) ответы клеток памяти значительно усилены по сравнению с ответами клеток памяти мышей дикого типа.Заключение. Полученные данные позволяют выдвинуть гипотезу, согласно которой клоны Т-клеток памяти, размножившиеся в первичном иммунном ответе, мигрируют в тимус, обеспечивающий микроокружение, необходимое для реэкспрессии ими рекомбиназ. После завершения редактирования α-цепей TCR такие Т-лимфоциты могут вернуться в периферический репертуар, поддерживая его широту