Transcriptomic Studies in Non-Model Plants: Case of Pisum sativum L. and Medicago lupulina L.

Transcriptomics is a dynamically developing branch of biology highly important for geneticists and molecular ecologists alike. A large number of studies concerning differential gene expression, mapping of genes and quantitative trait loci (QTL), analysis of genotyping variations and so on has been conducted recently on several non‐model plants using next‐generation sequencing techniques. One example of non‐model legumes is garden pea (Pisum sativum L.), a valuable pulse crop capable of forming nitrogen‐fixing nodules and arbuscular mycorrhiza. Adaptation of standardised RNA‐seq approaches and data analysis developed for model plants to P. sativum should facilitate both studying of pea molecular genetics and breeding of new cultivars possessing agriculturally important traits. Another non‐model legume is black medick Medicago lupulina L. (a close relative of model legume plant barrel medick, Medicago truncatula Gaertn.), for which unique genetic lines almost obligatory dependent on arbuscular mycorrhiza symbiosis formation have been obtained. Such lines show promise as the perfect model for studying the genetic bases of arbuscular mycorrhiza development. In this chapter, we give a brief description of the current developments in the field of garden pea and black medick transcriptomics. Our aim is to provide a quick start guide to the non‐expert researchers for next‐generation sequencing (NGS)‐based transcriptome analysis

Экономика Грузии: хрупкая устойчивость роста

This paper is devoted to the analysis of the main factors of economic growth stability of Georgia persistent during the last 30 years of the country’s development. Exceptional gravity of the crisis in the beginning of market transformation of Georgia in 1980—1990 as well as the success of market reforms is discussed. The article also highlights the consequences of the transitional period both for the citizens of the country and for the whole economy, in particular for human capital development under conditions of persistent socio-economic imbalances. In addition, this research analyzes recent changes in the structure and the drivers of economic growth and the dependence of Georgian economy on external financing (both investments and personal remittances). Even though there has been a noticeable macroeconomic stability in the post-Soviet period which manifests itself in stable GDP growth rates, social development of Georgia is still characterized by a number of problems such as low natural population growth, high levels of poverty and social inequality

DNA cyclization and looping in the wormlike limit: normal modes and the validity of the harmonic approximation

For much of the last three decades Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, $J$, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last ten years, however, approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly dominated by anharmonic contributions. In the case of computed values of the J factor, deviations of the harmonic approximation from the exact value of $J$ as a function of DNA length have not been characterized. Using a recent, numerically exact method that accounts for both anharmonic and harmonic contributions to $J$ for wormlike chains of arbitrary size, we report here the apparent error that results from neglecting anharmonic behavior. For wormlike chains having contour lengths less than four times the persistence length the error in $J$ arising from the harmonic approximation is generally small, amounting to free energies less than the thermal energy, $k_B T$. For larger systems, however, the deviations between harmonic and exact $J$ values increase approximately linearly with size.Comment: 23 pages, 6 figures. Typos corrected. Manuscript improve

A randomized controlled trial of an intervention delivered by mobile phone app instant messaging to increase the acceptability of effective contraception among young people in Tajikistan.

BACKGROUND: Unintended pregnancy is associated with poorer health outcomes for women and their families. In Tajikistan, around 26% of married 15-24 year old women have an unmet need for contraception. There is some evidence that interventions delivered by mobile phone can affect contraceptive-related behaviour and knowledge. We developed an intervention delivered by mobile phone app instant messaging to improve acceptability of effective contraceptive methods among young people in Tajikistan. METHODS: This was a randomized controlled trial among Tajik people aged 16-24. Participants allocated to the intervention arm had access to an app plus intervention messages. Participants allocated to the control arm had access to the app plus control messages. The primary outcome was acceptability of at least one method of effective contraception at 4 months. Secondary outcomes were use of effective contraception at 4 months and during the study, acceptability of individual methods, service uptake, unintended pregnancy and induced abortion. Process outcomes were knowledge, perceived norms, personal agency and intention. Outcomes were analysed using logistic and linear regression. We conducted a pre-specified subgroup analysis and a post-hoc analysis of change in acceptability from baseline to follow-up. RESULTS: Five hundred and seventy-three participants were enrolled. Intervention content was included on the app, causing contamination. Four hundred and seventy-two (82%) completed follow-up for the primary outcome. There was no evidence of a difference in acceptability of effective contraception between the groups (66% in the intervention arm vs 64% in the control arm, adjusted OR 1.21, 95% CI .80-1.83, p = 0.36). There were no differences in the secondary or process outcomes between groups. There was some evidence that the effect of the intervention was greater among women compared to men (interaction test p = 0.03). There was an increase in acceptability of effective contraception from baseline to follow-up (2% to 65%, p < 0.001). CONCLUSIONS: The whole intervention delivered by instant messaging provided no additional benefit over a portion of the intervention delivered by app pages. The important increase in contraceptive acceptability from baseline to follow-up suggests that the intervention content included on the app may influence attitudes. Further research is needed to establish the effect of the intervention on attitudes towards and use of effective contraception among married/sexually active young people. TRIAL REGISTRATION: Clinicaltrial.gov NCT02905513 . Date of registration: 14 September 2016

Computational modeling to elucidate molecular mechanisms of epigenetic memory

How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes differentiate reproducibly from a single fertilized egg? These are fundamental problems in developmental biology. Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. The complexity comes partly from the number of molecular species and the broad time scales involved. In recent years mathematical modeling has made significant contributions on elucidating the molecular mechanisms of DNA methylation and histone covalent modification inheritance. We will pedagogically introduce the typical procedure and some technical details of performing a mathematical modeling study, and discuss future developments.Comment: 36 pages, 4 figures, 2 tables, book chapte

Gut microbiota and carcinogenesis in various human organs

Scientific research in recent years has revealed a significant role of the human microbiome in carcinogenesis. These data served as a rationale for the inclusion of polymorphic microbiomes in the key characteristics of carcinogenesis as an important mechanistic determinant of cancer, in addition to other fundamental biological processes manifested during multi-stage carcinogenesis. The microbiome of the gastrointestinal tract is most actively involved in the pathogenesis of malignant neoplasms of the digestive system due to changes in the quantitative and qualitative composition of the microbiota, and increase in the production of genotoxic bacterial metabolites as factors of carcinogenesis. This review also addresses the changes in the microbiome in lung cancer, associated mainly with the production of short-chain fatty aicids, and in breast and endometrial cancers with specific changes in the composition of the bacterial community towar)ds species involved in the metabolism of estrogen precursors. The probable mechanisms of microorganisms participation in the development of prostate cancer (the effect of lipopolysaccharides, antibiotics and deconjugated estrogen) are considered. Data on the relationship between the composition and metabolic characteristics of the microbiome in various cancer sites open up perspectives for its use in the diagnosis, treatment and prevention of malignant neoplasms and justify the need for further research in this area

Clinical and microbiological study of the effectiveness of treatment of alveolitis of the tooth socket using a low-wave laser and a medicament based on gramicidin С

The authors obtained and analyzed the results of treatment of alveolitis with the use of light emitting diode radiation and a medical based on ’Gramicidin C' and the classical method of treatment of alveolitis by studying the microbiocinosis of the tooth socket before and after treatment and evaluation of pain in the dynamics using a visual-analog scale. The study included 70 people. Between the ages of 22 and 82. Depending on the method of treatment, the patients were divided into two groups. The main group consisted of 35 people, the treatment was carried out by the author's method (patent RU 2678199 C1). Treatment of patients of the comparison group (35 people) included abundant irrigation of the well of the previously removed tooth with an antiseptic solution -chlorhexidine 0.05%, followed by filling with iodoform gauze. The analysis of the data of microbiological study of the visual analog scale in the dynamics allows us to conclude that the use of a medical based on the antibiotic Gramicidin С has a significant antimicrobial activity on the pathogenic microflora of the tooth socket and is an alternative method for the treatment of alveolitis of the jaws. It is necessary to emphasize the advantages of complex application of light emitting diode radiation with red light with a wavelength ot 630 nm and the medical based on the antibiotic Gramicidin С for the treatment of alveolitis: as a result of the treatment in patients there is a relief of pain in the first two days of treatment due to the local action of HPA, as well as the cumulative analgesic effect of light emitting diode radiation.Цель исследования - оценить эффективность лечения альвеолита по авторской методике с помощью низковолнового лазера и лекарственного средства на основе антибиотика Грамицидина С. Авторами получены и проанализированы результаты лечения альвеолита с применением низковолнового лазерного излучения и лекарственного препарата на основе «Грамицидина С» и классической методики лечения альвеолита путем исследование микробиоциноза лунки зуба до и после лечения и оценки болевого синдрома в динамике при помощи визуально-аналоговой шкалы. В исследование вошли 70 человек. В возрасте от 22 до 82 лет. В зависимости от способа лечения больные были разделены на две группы. Основную группу составили 35 человек, лечение проводилось по авторской методике (патент RU 2678199 С1). Лечение пациентов группы сравнения (35 человек) включало обильное орошение лунки ранее удаленного зуба раствором антисептика - хлоргексидин 0,05%, с последующим заполнением йодоформной турундой. Анализ данных микробиологического исследования и визуально-аналоговой шкалы в динамике позволяет сделать вывод, что применение лекарственного средства на основе антибиотика Грамицидина С обладает значительной антимикробной активностью на патогенную микрофлору лунки зуба и является альтернативной методикой при лечении альвеолита челюстей. Необходимо особо отметить преимущества комплексного применения светодиодного излучения красным светом с длиной волны 630 нм и препарата на основе антибиотика Грамицидин С для лечения альвеолита: в результате проведенного лечения у пациентов происходит купирование болевого синдрома в первые двое суток лечения за счет местного действия ГПА, а также накопительного анальгезирующего действия низковолнового лазера