A DNA Damage-Induced, SOS-Independent Checkpoint Regulates Cell Division in Caulobacter crescentus

Cells must coordinate DNA replication with cell division, especially during episodes of DNA damage. The paradigm for cell division control following DNA damage in bacteria involves the SOS response where cleavage of the transcriptional repressor LexA induces a division inhibitor. However, in Caulobacter crescentus, cells lacking the primary SOS-regulated inhibitor, sidA, can often still delay division post-damage. Here we identify didA, a second cell division inhibitor that is induced by DNA damage, but in an SOS-independent manner. Together, DidA and SidA inhibit division, such that cells lacking both inhibitors divide prematurely following DNA damage, with lethal consequences. We show that DidA does not disrupt assembly of the division machinery and instead binds the essential division protein FtsN to block cytokinesis. Intriguingly, mutations in FtsW and FtsI, which drive the synthesis of septal cell wall material, can suppress the activity of both SidA and DidA, likely by causing the FtsW/I/N complex to hyperactively initiate cell division. Finally, we identify a transcription factor, DriD, that drives the SOS-independent transcription of didA following DNA damage.National Institutes of Health (U.S.) (Grant R01GM082899)National Science Foundation (U.S.). Graduate Research Fellowship Progra

Semi-empirical Gibbs free energy formulations for minerals and fluids for use in thermodynamic databases of petrological interest

The P-T partition function in statistical thermodynamics can be used to derive semi-empirical formulations of the Gibbs free energy G for minerals and fluids. Parameterization of these equations includes simultaneous regression of experimental heat capacity and molar volume data, allowing fitting, appraisal and optimization of various data sources, as required in the construction of internally consistent petrological data bases. This approach can also be extended to minerals with λ-transitions and to fluids by considering the Gibbs free energy as a function of pressure P, temperature T and an ordering parameter Xα, so that accurate modelled representation and extrapolation of the thermodynamic properties of large numbers of petrologically significant minerals and coexisting fluids can be attained. The ordering parameter is chosen to denote the equilibrium mole fraction (thermodynamic probability) of ordered clusters (structural units) in a substance when G(T,P, Xα)=min. The procedure is tested on existing experimental data for the system MgO-SiO2-H2O. The proposed Gibbs free energy formulation permits thermodynamic properties of minerals, fluids and phase equilibria to be described and extrapolated over a wide range of pressure (0-800 kbar) and temperature (20-3000 K), thus allowing effective use in thermodynamic data bases of petrological interes

Dynamics of two phosphorelays controlling cell cycle progression in 1 Caulobacter crescentus

In Caulobacter crescentus, progression through the cell cycle is governed by the periodic activation and inactivation of the master regulator CtrA. Two phosphorelays, each initiating with the histidine kinase CckA, promote CtrA activation by driving its phosphorylation and by inactivating its proteolysis. Here, we examined whether the CckA phosphorelays also influence the downregulation of CtrA. We demonstrate that CckA is bifunctional, capable of acting as either a kinase or phosphatase to drive the activation or inactivation, respectively, of CtrA. By identifying mutations that uncouple these two activities, we show that CckA's phosphatase activity is important for downregulating CtrA prior to DNA replication initiation in vivo but that other phosphatases may exist. Our results demonstrate that cell cycle transitions in Caulobacter require and are likely driven by the toggling of CckA between its kinase and phosphatase states. More generally, our results emphasize how the bifunctional nature of histidine kinases can help switch cells between mutually exclusive states

Spatial tethering of kinases to their substrates relaxes evolutionary constraints on specificity

Signal transduction proteins are often multi-domain proteins that arose through the fusion of previously independent proteins. How such a change in the spatial arrangement of proteins impacts their evolution and the selective pressures acting on individual residues is largely unknown. We explored this problem in the context of bacterial two-component signalling pathways, which typically involve a sensor histidine kinase that specifically phosphorylates a single cognate response regulator. Although usually found as separate proteins, these proteins are sometimes fused into a so-called hybrid histidine kinase. Here, we demonstrate that the isolated kinase domains of hybrid kinases exhibit a dramatic reduction in phosphotransfer specificity in vitro relative to canonical histidine kinases. However, hybrid kinases phosphotransfer almost exclusively to their covalently attached response regulator domain, whose effective concentration exceeds that of all soluble response regulators. These findings indicate that the fused response regulator in a hybrid kinase normally prevents detrimental cross-talk between pathways. More generally, our results shed light on how the spatial properties of signalling pathways can significantly affect their evolution, with additional implications for the design of synthetic signalling systems.National Science Foundation (U.S.) (CAREER Award)National Science Foundation (U.S.). Graduate Research Fellowship Progra

Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks

Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because ADAGE models, like many neural networks, are over-parameterized, different ADAGE models perform equally well. To enhance model robustness and better build signatures consistent with biological pathways, we developed an ensemble ADAGE (eADAGE) that integrated stable signatures across models. We applied eADAGE to a compendium of Pseudomonas aeruginosa gene expression profiling experiments performed in 78 media. eADAGE revealed a phosphate starvation response controlled by PhoB in media with moderate phosphate and predicted that a second stimulus provided by the sensor kinase, KinB, is required for this PhoB activation. We validated this relationship using both targeted and unbiased genetic approaches. eADAGE, which captures stable biological patterns, enables cross-experiment comparisons that can highlight measured but undiscovered relationships.Gordon and Betty Moore Foundation (GBMF 4552)National Institutes of Health (U.S.) (grant R01-AI091702)Cystic Fibrosis Foundation (STANTO15R0

СУЧАСНИЙ СТАН І НАПРЯМИ ПОКРАЩЕННЯ БОРГОВОЇ БЕЗПЕКИ УКРАЇНИ

The article examines the debt safety as a priority trend to ensure financial safety of Ukraine and its main component. It considers modern scientific views of defining the nature of the debt safety and effects of the debt burden on the economy of Ukraine. In order to reveal the factors that affect the assessment of the debt safety of Ukraine, we have analyzed the dynamics of the state safety debt by means of a system of indicators. It researches on the main indicators of debt safety state reflecting the content and effectiveness of public debt management through taking into account some boundary values which allowed us to specify the main factors that caused some negative tendencies in the calculated indicators. The study has identified the most dangerous values of the indicators directly affecting the state of the debt safety in Ukraine. In particular, this is a ratio of the total public debt to GDP and the external debt per person in the US dollars. This study also conducted a detailed economic assessment of the state of the debt safety in Ukraine during 2013–2016. It provides some estimates of the public debt, internal and external public debt which is based on the cost of its maintenance, the ratio of total public and publicly guaranteed debt to GDP. We suggest some ways of increasing the debt safety of Ukraine, taking in account political instability and military conflict in the East of the country.В статье раскрыта долговая безопасность, как приоритетное направление обеспечения финансовой безопасности Украины. Исследованы современные научные взгляды относительно определения сущности долговой безопасности и проблем долговой нагрузки на экономику Украины. Произведена оценка долговой безопасности Украины с помощью системы показателей, что дало возможность раскрыть факторы, которые имеют влияние на состояние долговой безопасности Украины. Рассчитаны основные индикаторы состояния долговой безопасности, которые отображают результативность управления государственным долгом с учетом предельных значений, что дало возможность установить основные факторы, которые повлекли негативные тенденции рассчитанных показателей. Предложены направления относительно повышения уровня долговой безопасности Украины. У статті розкрито боргову безпеку, як пріоритетний напрям забезпечення фінансової безпеки України. Досліджено сучасні наукові погляди щодо визначення сутності боргової безпеки та проблем боргового навантаження на економіку України. Дано оцінку боргової безпеки України за допомогою системи показників, що дало змогу розкрити чинники, які мають вплив на стан боргової безпеки України. Розраховано основні індикатори стану боргової безпеки, які відображають зміст і результативність управління державним боргом з урахуванням граничних значень, що дало змогу встановити основні фактори, які спричинили негативні тенденції розрахованих показників. Запропоновано напрями щодо підвищення рівня боргової безпеки України

ПЕРСПЕКТИВИ ВИКОРИСТАННЯ КРИПТОВАЛЮТИ БІТКОЇН ЯК ФІНАНСОВОЇ ІННОВАЦІЇ В ІНФОРМАЦІЙНІЙ ЕКОНОМІЦІ УКРАЇНИ

We have established that a relatively new market of cryptocurrency is the subject of great interest for research under the current conditions of financial innovations in payment services. Our findings have revealed objective prerequisites for creating cryptocurrency as an innovative means of information-based payment. Cryptocurrency poses a challenge to the financial system of Ukraine since both the central bank and other state regulators can not control its emission and circulation. They show the growth dynamics in cryptocurrency market capitalization where Bitcoin predominates. Although cryptocurrency is not included in the National Register of payment systems and it is officially prohibited for circulation in Ukraine, our country ranks among the world’s top five countries by number of users of different bitcoin-wallets. We have examined the strengths of Bitcoin that have made this cryptocurrency a convenient means of international payment with a high investment potential. The results show disadvantages to using cryptocurrency for both the whole country in general and ordinary consumers in particular. We have defined main threats that national governments can face in case of an unregulated spread of cryptocurrency. Also this study, based on the works of leading foreign scientists and financial market experts, systematizes factors that influence the price of Bitcoin. It substantiates opportunities and prospects for the cryptocurrency market development in Ukraine. The study has shown that cryptocurrencies have their own niche in payment systems; they are quite competitive and reliable financial instruments. The growth dynamics of cryptocurrency market capitalization in the world makes Bitcoin the most successful example of the use of virtual currency in the information economy. As the modern society is being inevitably virtualized, our country’s economy should follow the path of innovations by finding solutions to a number of technical, economic and legal issues on the cryptocurrency market development in Ukraine through involving the experience of the leading European countries.Встановлено, що у сучасних умовах розвитку фінансових інновацій у сфері платіжних послуг предметом наукових дискусій є відносно новий і малодосліджений ринок криптовалюти. Розкрито об’єктивні передумови створення криптовалюти як інноваційного платіжного засобу заснованого на інформації. Криптовалюта стала викликом для фінансової системи України, оскільки її емісію та обіг не може контролювати центральний банк та інші державні регулюючі органи. Показано динаміку зростання капіталізації ринку криптовалют із домінуючою часткою біткоїна. І хоча криптовалюта не внесена до національного Реєстру платіжних систем, і є офіційно забороненою для обігу на території України, наша держава ввійшла до п’ятірки країн світу за кількістю користувачів різних біткоїн-гаманців. Визначено сильні сторони біткоїна, які зробили цю криптовалюту зручним міжнародним платіжним засобом з високим інвестиційним потенціалом. Висвітлено недоліки обігу криптовалюти як для пересічних споживачів, так і держави в цілому. Виокремлено основні загрози нерегульованого поширення криптовалюти для національних урядів. Ґрунтуючись на працях провідних зарубіжних науковців і експертів фінансового ринку, систематизовано фактори впливу на ціну біткоїна. Обґрунтовано можливості та перспективи розвитку ринку криптовалюти в Україні. У результаті дослідження встановлено, що криптовалюти зайняли свою нішу в платіжних системах і є конкурентоспроможними та надійними фінансовими інструментами. Зважаючи на динаміку росту капіталізації ринку криптовалют у світі, біткоїн є поки що найуспішнішим прикладом використання віртуальної валюти в інформаційній економіці. Оскільки процес віртуалізації сучасного суспільства невідворотний, економіка нашої держави має підтримувати курс на інноваційність шляхом вирішення низки технічних, економічних та правових питань щодо розвитку ринку криптовалют в Україні, спираючись на досвід провідних європейських країн

Order/disorder phase transition in cordierite and its possible relationship to the development of symplectite reaction textures in granulites

Based on a consistent set of empirical interatomic potentials, static structure energy calculations of various Al/Si configurations in the supercell of Mg-cordierite and Monte Carlo simulations the phase transition between the orthorhombic and hexagonal modifications of cordierite (Crd) is predicted at 1623 K. The temperature dependences of the enthalpy, entropy, and free energy of the Al/Si disorder were calculated using the method of thermodynamic integration. The simulations suggest that the commonly observed crystallization of cordierite in the disordered hexagonal form could be related to a tendency of Al to occupy T1 site, which is driven by local charge balance. The increase in the Al fraction in the T1 site over the ratio of 2/3(T1): 1/3(T2), that characterizes the ordered state, precludes formation of the domains of the orthorhombic phase. This intrinsic tendency to the crystallization of the metastable hexagonal phase could have significantly postponed the formation of the association of orthorhombic cordierite and orthopyroxene over the association of quartz and garnet in metapelites subjected to granulite facies metamorphism. The textures of local metasomatic replacement (the formation of Crd + Opx or Spr + Crd symplectites between the grains of garnet and quartz) indicate the thermodynamic instability of the association of Qtz + Grt at the moment of the metasomatic reaction. This instability could have been caused by the difficulty of equilibrium nucleation of orthorhombic cordierite

Two-Component Signal Transduction Pathways Regulating Growth and Cell Cycle Progression in a Bacterium: A System-Level Analysis

Two-component signal transduction systems, comprised of histidine kinases and their response regulator substrates, are the predominant means by which bacteria sense and respond to extracellular signals. These systems allow cells to adapt to prevailing conditions by modifying cellular physiology, including initiating programs of gene expression, catalyzing reactions, or modifying protein–protein interactions. These signaling pathways have also been demonstrated to play a role in coordinating bacterial cell cycle progression and development. Here we report a system-level investigation of two-component pathways in the model organism Caulobacter crescentus. First, by a comprehensive deletion analysis we show that at least 39 of the 106 two-component genes are required for cell cycle progression, growth, or morphogenesis. These include nine genes essential for growth or viability of the organism. We then use a systematic biochemical approach, called phosphotransfer profiling, to map the connectivity of histidine kinases and response regulators. Combining these genetic and biochemical approaches, we identify a new, highly conserved essential signaling pathway from the histidine kinase CenK to the response regulator CenR, which plays a critical role in controlling cell envelope biogenesis and structure. Depletion of either cenK or cenR leads to an unusual, severe blebbing of cell envelope material, whereas constitutive activation of the pathway compromises cell envelope integrity, resulting in cell lysis and death. We propose that the CenK–CenR pathway may be a suitable target for new antibiotic development, given previous successes in targeting the bacterial cell wall. Finally, the ability of our in vitro phosphotransfer profiling method to identify signaling pathways that operate in vivo takes advantage of an observation that histidine kinases are endowed with a global kinetic preference for their cognate response regulators. We propose that this system-wide selectivity insulates two-component pathways from one another, preventing unwanted cross-talk

A gravimetric method for the quantitative determination of soluble β-glucan content in oat grain

Background. Oat (Avena sativa L.) is one of the most important sources of protein, oil, starch and dietary fibers, in particular β-glucans. Dietary fiber serves as a source of nutrition for the intestinal microflora and significantly affects not only its composition, but also the normal functioning of the intestine as a whole. In connection with the increased interest in β-glucans as a food component and dietary supplement, there is a need in a convenient and inexpensive method for determination of β-glucans content in grain. The article provides an overview of the existing methods for the isolation and determination of soluble β-glucans in cereals: enzymatic, alkaline, alkaline-enzymatic, colorimetric; their advantages and disadvantages are noted. The main disadvantages of some methods are the complexity and duration of execution, significant cost of the required reagents, and the inability to determine the exact content of β-glucans due to their insufficient purification from various impurities.Results. This study used the example of naked and covered oat cultivars to demonstrate applicability of the gravimetric method that we developed by modifying the alkaline method. Whole grain oat flour was pretreated with a 50% ethanol solution to inactivate β-glucanase and remove free sugars, some lipids, proteins, and other substances. β-glucans were released from the aleurone layer and the endosperm with a 5% sodium hydroxide solution, and finally extracted with a 70% ethanol solution. Β-glucans floated to the surface in the form of a bunch of fibers, which was then dried at a temperature about 100-102°C to constant weight and weighed. The content of β-glucans was calculated from the dry weight (%). The isolated β-glucans were checked for the presence of accompanying substances: the content of nitrogenous substances was determined by the Kjeldahl method, and the presence of starch was determined by a qualitative reaction with Lugolʼs reagent.Conclusions. The content of β-glucans in the grain of the studied samples ranged from 3.12±0.18 up to 4.65±0.17% of the dry weight. As a result of the study, the optimal conditions of β-glucans isolation were selected: the extraction mixtures ratios, as well as the modes of centrifugation, sedimentation and drying were established. It has been shown that this method makes it possible to isolate β-glucans with a minimum impurity of nitrogenous substances (0.07-0.12%) and no traces of starch. One of the advantages of the described method is its availability for mass analysis when studying a collection of grain crops