Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats

<p>Abstract</p> <p>Background</p> <p>Variability of the <it>VRN1 </it>promoter region of the unique collection of spring polyploid and wild diploid wheat species together with diploid goatgrasses (donor of B and D genomes of polyploid wheats) were investigated. Accessions of wild diploid (<it>T. boeoticum</it>, <it>T. urartu</it>) and tetraploid (<it>T. araraticum, T. timopheevii</it>) species were studied for the first time.</p> <p>Results</p> <p>Sequence analysis indicated great variability in the region from -62 to -221 nucleotide positions of the <it>VRN1 </it>promoter region. Different indels were found within this region in spring wheats. It was shown that <it>VRN1 </it>promoter region of B and G genome can also contain damages such as the insertion of the transposable element.</p> <p>Some transcription factor recognition sites including hybrid C/G-box for TaFDL2 protein known as the <it>VRN1 </it>gene upregulator were predicted inside the variable region. It was shown that deletions leading to promoter damage occurred in diploid and polyploid species independently. DNA transposon insertions first occurred in polyploid species. At the same time, the duplication of the promoter region was observed in A genomes of polyploid species.</p> <p>Conclusions</p> <p>We can conclude that supposed molecular mechanism of the <it>VRN1 </it>gene activating in cultivated diploid wheat species <it>T. monococcum </it>is common also for wild <it>T. boeoticum </it>and was inherited by <it>T. monococcum</it>. The spring polyploids are not related in their origin to spring diploids. The spring <it>T. urartu </it>and goatgrass accessions have another mechanism of flowering activation that is not connected with indels in <it>VRN1 </it>promoter region. All obtained data may be useful for detailed insight into origin of spring wheat forms in evolution and domestication process.</p

Rational in silico design of aptamers for organophosphates based on the example of paraoxon

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Poisoning by organophosphates (OPs) takes one of the leading places in the total number of exotoxicoses. Detoxication of OPs at the first stage of the poison entering the body could be achieved with the help of DNA- or RNA-aptamers, which are able to bind poisons in the bloodstream. The aim of the research was to develop an approach to rational in silico design of aptamers for OPs based on the example of paraoxon. From the published sequence of an aptamer binding organophosphorus pesticides, its threedimensional model has been constructed. The most probable binding site for paraoxon was determined by molecular docking and molecular dynamics (MD) methods. Then the nucleotides of the binding site were mutated consequently and the values of free binding energy have been calculated using MD trajectories and MM-PBSA approach. On the basis of the energy values, two sequences that bind paraoxon most efficiently have been selected. The value of free binding energy of paraoxon with peripheral anionic site of acetylcholinesterase (AChE) has been calculated as well. It has been revealed that the aptamers found bind paraoxon more effectively than AChE. The peculiarities of paraoxon interaction with the aptamers nucleotides have been analyzed. The possibility of improving in silico approach for aptamer selection is discussed

Reactive oxygen species in pathogenesis of atherosclerosis.

Co-author affiliations: - Sechenov Institute of Evolutionary Physiology and Biochemistry RAS, Saint Petersburg, Russia - Research Institute of Hygiene, Occupational Pathology and Human Ecology, Saint Petersburg, Russia - Koltzov Institute of Developmental Biology RAS, Moscow, Russia - Institute of Cell Biophysics RAS, Pushchino, Russia - Institute of General Pathology and Pathophysiology RAMS, Moscow, RussiaThe volume of publications on the role of reactive oxygen species (ROS) in biological processes has been increasing exponentially over the last decades. ROS in large amounts clearly have detrimental effects on cell physiology, whereas low concentrations of ROS are permanently produced in cells and play a role as signaling molecules. An imbalance in ROS production and defense mechanisms can lead to pathological vascular remodeling, atherosclerosis being among them. The aim of this review is to examine different sources of ROS from the point of view of their participation in pathogenesis of atherosclerosis and related cardiovascular risk. Among the possible sources of ROS discussed here are mitochondria, NADPH-oxidases, xanthine oxidase, peroxidases, NO-synthases, cytochrome P450, cyclooxygenases, lipoxygenases, and hemoglobin of red blood cells. A great challenge for future research is to establish interrelations, feedback and feed-forward regulation mechanisms of various sources of ROS in development of atherosclerosis and other vascular pathologies

Chemical pretreatment of cells for enhanced MALDI-TOF-MS discrimination of clinical staphylococci including MRSA

BACKGROUND: Limited success has been reported for matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) differentiation of staphylococci, including methicillin resistant Staphylococcus aureus (MRSA) strains. Chemical pretreatment of cells prior to MALDI-TOF-MS analysis has not been systematically investigated for enhanced discrimination of S.aureus strains. OBJECTIVES: To evaluate various chemical pretreatment of cells for MALDI-TOF-MS discrimination of clinical staphylococcal isolates, with a focus on differentiation of MRSA from methicillin sensitive S. aureus (MSSA) strains and from other staphylococcal species. METHOD: MALDI-TOF-MS of a well-characterised S. aureus strain(s) was optimised with respect to matrix chemical(s), matrix solvent and target plating method. Various chemical pretreatments (solvents, reductants, detergents) and pretreatment application methods were then evaluated for enhancement of spectral richness. The three most promising pretreatments were applied to MALDI-TOF-MS discrimination of three set of clinical isolates comprising non-S.aureus staphylococci (77 isolates ), MSSA (36) and MRSA (43), with analysis by total or set specific resolved peaks. RESULTS: The optimized MALDI-TOF-MS protocol involved α-cyano-4-hydroxycinnamic acid (CHCA) as matrix chemical (in 1:2 acetonitrile:H2O and 2% trifluoroacetic acid), with application as an overlay onto smeared cells (on-probe). On-probe application of chemical pretreatment was most effective at enhancing MALDI-TOF-MS spectral richness. Use of reductants and detergents as pretreatments were ineffective. The three most effective solvents/acid pretreatments - ethanol:formate, ethanol:acetate and formate:isopropanol - each generated reproducible and distinct spectra over the 2,000 -10,000 m/z range. For the combined sets of clinical isolates (114), all three of these pretreatments increased the total number of resolved peaks in comparison with no pretreatment controls. The ethanol:formate pretreatment gave 100% clustering of non-S. aureus staphylococci, based on total resolved peaks. The formate:isopropanol pretreatment generated the largest increase in number of MRSA set specific peaks (from 18 to 32; 78% increase) and clustered the majority (77%) of the MRSA strains together, although compete discrimination of the MSSA and MRSA was not achieved. CONCLUSION: MALDI-TOF-MS discrimination of clinical isolates of staphylococci is enhanced through chemical pretreatment of cells. Three chemical pretreatments, not previously applied to staphylococci, are highlighted for enhancing spectral richness and offering new opportunities for improved discrimination of staphylococci, including MRSA and MSSA strains

Chemical pretreatment of cells for enhanced MALDI-TOF-MS discrimination of clinical staphylococci including MRSA

BACKGROUND: Limited success has been reported for matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) differentiation of staphylococci, including methicillin resistant Staphylococcus aureus (MRSA) strains. Chemical pretreatment of cells prior to MALDI-TOF-MS analysis has not been systematically investigated for enhanced discrimination of S.aureus strains. OBJECTIVES: To evaluate various chemical pretreatment of cells for MALDI-TOF-MS discrimination of clinical staphylococcal isolates, with a focus on differentiation of MRSA from methicillin sensitive S. aureus (MSSA) strains and from other staphylococcal species. METHOD: MALDI-TOF-MS of a well-characterised S. aureus strain(s) was optimised with respect to matrix chemical(s), matrix solvent and target plating method. Various chemical pretreatments (solvents, reductants, detergents) and pretreatment application methods were then evaluated for enhancement of spectral richness. The three most promising pretreatments were applied to MALDI-TOF-MS discrimination of three set of clinical isolates comprising non-S.aureus staphylococci (77 isolates ), MSSA (36) and MRSA (43), with analysis by total or set specific resolved peaks. RESULTS: The optimized MALDI-TOF-MS protocol involved α-cyano-4-hydroxycinnamic acid (CHCA) as matrix chemical (in 1:2 acetonitrile:H2O and 2% trifluoroacetic acid), with application as an overlay onto smeared cells (on-probe). On-probe application of chemical pretreatment was most effective at enhancing MALDI-TOF-MS spectral richness. Use of reductants and detergents as pretreatments were ineffective. The three most effective solvents/acid pretreatments - ethanol:formate, ethanol:acetate and formate:isopropanol - each generated reproducible and distinct spectra over the 2,000 -10,000 m/z range. For the combined sets of clinical isolates (114), all three of these pretreatments increased the total number of resolved peaks in comparison with no pretreatment controls. The ethanol:formate pretreatment gave 100% clustering of non-S. aureus staphylococci, based on total resolved peaks. The formate:isopropanol pretreatment generated the largest increase in number of MRSA set specific peaks (from 18 to 32; 78% increase) and clustered the majority (77%) of the MRSA strains together, although compete discrimination of the MSSA and MRSA was not achieved. CONCLUSION: MALDI-TOF-MS discrimination of clinical isolates of staphylococci is enhanced through chemical pretreatment of cells. Three chemical pretreatments, not previously applied to staphylococci, are highlighted for enhancing spectral richness and offering new opportunities for improved discrimination of staphylococci, including MRSA and MSSA strains

Inhibition of protein tyrosine phosphatases unmasks vasoconstriction and potentiates calcium signalling in rat aorta smooth muscle cells in response to an agonist of 5-HT2B receptors BW723C86

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.In blood vessels, serotonin 5-HT2B receptors mainly mediate relaxation, although their activation by the selective agonist BW723C86 is known to exert contraction of aorta in deoxycorticosterone acetate (DOCA)-salt and N(omega)-nitro-L-arginine (L-NAME) hypertensive rats [Russel et al., 2002; Banes et al., 2003] and in mice with type 2 diabetes [Nelson et al., 2012]. The unmasking effect on vasoconstriction can be caused by a shift in the balance of tyrosine phosphorylation in smooth muscle cells (SMC) due to oxidative stress induced inhibition of protein tyrosine phosphatases (PTP). We have demonstrated that BW723C86 which does not cause contraction of rat aorta and mesenteric artery rings, evoked a vasoconstrictor effect in the presence of PTP inhibitors sodium orthovanadate (Na3VO4) or BVT948. BW723C86 induced a weak rise of [Ca2+]i in the SMC isolated from rat aorta; however, after pre-incubation with Na3VO4 the response to BW723C86 increased more than 5-fold. This effect was diminished by protein tyrosine kinase (PTK) inhibitor genistein, inhibitor of Src-family kinases PP2, inhibitor of NADPH-oxidase VAS2870 and completely suppressed by N-acetylcysteine and 5-HT2B receptor antagonist RS127445. Using fluorescent probe DCFH-DA we have shown that Na3VO4 induces oxidative stress in SMC. In the presence of Na3VO4 BW723C86 considerably increased formation of reactive oxygen species while alone had no appreciable effect on DCFH oxidation. We suggest that oxidative stress causes inhibition of PTP and unmasking of 5-HT2B receptors functional activity

The General Transcription Repressor TaDr1 Is Co-expressed With TaVrn1 and TaFT1 in Bread Wheat Under Drought

The general transcription repressor, TaDr1 gene, was identified during screening of a wheat SNP database using the Amplifluor-like SNP marker KATU-W62. Together with two genes described earlier, TaDr1A and TaDr1B, they represent a set of three homeologous genes in the wheat genome. Under drought, the total expression profiles of all three genes varied between different bread wheat cultivars. Plants of four high-yielding cultivars exposed to drought showed a 2.0–2.4-fold increase in TaDr1 expression compared to controls. Less strong, but significant 1.3–1.8-fold up-regulation of the TaDr1 transcript levels was observed in four low-yielding cultivars. TaVrn1 and TaFT1, which controls the transition to flowering, revealed similar profiles of expression as TaDr1. Expression levels of all three genes were in good correlation with grain yields of evaluated cultivars growing in the field under water-limited conditions. The results could indicate the involvement of all three genes in the same regulatory pathway, where the general transcription repressor TaDr1 may control expression of TaVrn1 and TaFT1 and, consequently, flowering time. The strength of these genes expression can lead to phenological changes that affect plant productivity and hence explain differences in the adaptation of the examined wheat cultivars to the dry environment of Northern and Central Kazakhstan. The Amplifluor-like SNP marker KATU-W62 used in this work can be applied to the identification of wheat cultivars differing in alleles at the TaDr1 locus and in screening hybrids

Разработка алгоритмов и программного обеспечения систем управления движением роботизированного почвообрабатывающего агрегата

Abstract. Automation of agricultural machinery is aimed at solving specific practical tasks: control and maintenance of the technological process quality, increasing labor productivity as well as crop yields. The method of "precision farming" is economically expedient, since it is a direct saving of technological material, as well as it helps reducing the negative impact on the environment and farm produce. (Research purpose) The research purpose is to review and analyze the main aspects required to develop the algorithms and software for motion control systems for a robotic tillage unit. (Materials and methods) To implement process control, it is necessary to control the direction of travel along a specified path, change the speed of movement depending on the engine load, switching the transmission gears. Physical-and-mechanical characteristics of the unit are rather heterogeneous and depend on weather conditions. Therefore, the algorithm for controlling the power of the robotic mobile unit must take into account, as much as possible, variations in the external effects of drawbar properties and the motion resistance, as a random factor. (Results and discussion) The authors have developed an imitation model representing the movement of a robotic unit. For the simulation, use has been made of a cyclic trajectory of the unit movement, consisting of two types of sections: the rectilinear ones reflecting the soil tillage pattern, and the turn areas where the unit makes a turn along a curvilinear trajectory around a certain center. (Conclusions) The implementation of robotic technologies in agricultural production result in increased technical, technological, production and economic indicators of agricultural units in field work, increased labor productivity, reduced time required for fieldworks, more rational use of bioenergy resources, increased yields of agricultural crops and reduced environmental impacts.Реферат. Автоматизация сельскохозяйственной техники призвана решать конкретные практические задачи: контроль и поддержание качества выполнения технологического процесса, повышение производительности труда, увеличение урожайности сельскохозяйственных культур. Метод «точного земледелия» экономически целесообразен, так как способствует экономии технологического материала, снижению отрицательного воздействия на окружающую среду и производимую продукцию. (Цель исследования) Рассмотреть и проанализировать основные аспекты, необходимые при разработке алгоритмов и программного обеспечения систем управления движением роботизированного агрегата для пахотных работ. (Материалы и методы) Управление технологическим процессом включает руководство движением по заданной траектории, возможность изменения скорости движения в зависимости от загрузки двигателя, переключая передачу в трансмиссии. Физико-механические свойства агрегата существенно отличаются неоднородностью и зависят от погодных условий; алгоритм управления роботизированным мобильным агрегатом должен в максимальной степени учитывать вариации внешних воздействий сцепных свойств и сопротивлений движению в статусе случайных величин. (Результаты и обсуждение) Разработали имитационную модель, представляющую движение роботизированного агрегата. Выбрали цикличную траекторию перемещения агрегата, состоящую из двух видов участков: прямолинейных, на которых происходит обработка почвы, и участков разворота, где агрегат совершает разворот по криволинейной траектории вокруг некоторого центра. (Выводы) Внедрение роботизированных технологий в земледелие повышает технические, технологические, производственно-экономические показатели сельскохозяйственных агрегатов при проведении полевых работ, увеличивает производительность труда, сокращает сроки проведения работ, способствует рациональному использованию биоэнергетических ресурсов, повышает урожайность и снижает экологическую нагрузку на окружающую среду

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis