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Search Results: 1 - 10 of 461723 matches for " Vladislav A. Petyuk "
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Metabolic Reprogramming during Purine Stress in the Protozoan Pathogen Leishmania donovani
Jessica L. Martin equal contributor,Phillip A. Yates equal contributor,Radika Soysa,Joshua F. Alfaro,Feng Yang,Kristin E. Burnum-Johnson,Vladislav A. Petyuk,Karl K. Weitz,David G. Camp II,Richard D. Smith,Phillip A. Wilmarth,Larry L. David,Gowthaman Ramasamy,Peter J. Myler,Nicola S. Carter
PLOS Pathogens , 2014, DOI: doi/10.1371/journal.ppat.1003938
Abstract: The ability of Leishmania to survive in their insect or mammalian host is dependent upon an ability to sense and adapt to changes in the microenvironment. However, little is known about the molecular mechanisms underlying the parasite response to environmental changes, such as nutrient availability. To elucidate nutrient stress response pathways in Leishmania donovani, we have used purine starvation as the paradigm. The salvage of purines from the host milieu is obligatory for parasite replication; nevertheless, purine-starved parasites can persist in culture without supplementary purine for over three months, indicating that the response to purine starvation is robust and engenders parasite survival under conditions of extreme scarcity. To understand metabolic reprogramming during purine starvation we have employed global approaches. Whole proteome comparisons between purine-starved and purine-replete parasites over a 6–48 h span have revealed a temporal and coordinated response to purine starvation. Purine transporters and enzymes involved in acquisition at the cell surface are upregulated within a few hours of purine removal from the media, while other key purine salvage components are upregulated later in the time-course and more modestly. After 48 h, the proteome of purine-starved parasites is extensively remodeled and adaptations to purine stress appear tailored to deal with both purine deprivation and general stress. To probe the molecular mechanisms affecting proteome remodeling in response to purine starvation, comparative RNA-seq analyses, qRT-PCR, and luciferase reporter assays were performed on purine-starved versus purine-replete parasites. While the regulation of a minority of proteins tracked with changes at the mRNA level, for many regulated proteins it appears that proteome remodeling during purine stress occurs primarily via translational and/or post-translational mechanisms.
A Method to Determine Lysine Acetylation Stoichiometries
Ernesto S. Nakayasu,Si Wu,Michael A. Sydor,Anil K. Shukla,Karl K. Weitz,Ronald J. Moore,Kim K. Hixson,Jong-Seo Kim,Vladislav A. Petyuk,Matthew E. Monroe,Ljiljiana Pasa-Tolic,Wei-Jun Qian,Richard D. Smith,Joshua N. Adkins,Charles Ansong
International Journal of Proteomics , 2014, DOI: 10.1155/2014/730725
Abstract: Lysine acetylation is a common protein posttranslational modification that regulates a variety of biological processes. A major bottleneck to fully understanding the functional aspects of lysine acetylation is the difficulty in measuring the proportion of lysine residues that are acetylated. Here we describe a mass spectrometry method using a combination of isotope labeling and detection of a diagnostic fragment ion to determine the stoichiometry of protein lysine acetylation. Using this technique, we determined the modification occupancy for ~750 acetylated peptides from mammalian cell lysates. Furthermore, the acetylation on N-terminal tail of histone H4 was cross-validated by treating cells with sodium butyrate, a potent deacetylase inhibitor, and comparing changes in stoichiometry levels measured by our method with immunoblotting measurements. Of note we observe that acetylation stoichiometry is high in nuclear proteins, but very low in mitochondrial and cytosolic proteins. In summary, our method opens new opportunities to study in detail the relationship of lysine acetylation levels of proteins with their biological functions. 1. Introduction Lysine acetylation (KAc) of proteins is a ubiquitous posttranslational modification (PTM) that controls many cellular processes. The dynamic regulation of KAc by lysine acetyltransferases (KATs) and deacetylases (KDACs) modulates many important cellular functions, such as cell metabolism and gene expression [1, 2]. Recent advances in mass spectrometry combined with immunoaffinity purification are enabling the identification and relative quantification of thousands of acetylation sites in a single experiment [3–5]. These new data have boosted the discovery of regulatory functions of KAc for many proteins, including a variety of metabolic enzymes [2]. Although significant progress has been made, a major remaining hurdle in the field is the determination of acetylation stoichiometry on proteins. The knowledge of KAc stoichiometry is considered essential to better understand the mechanism and impact of this modification on the control protein functions, such as enzymatic activity [2, 6]. Indeed, this problem is not exclusive to KAc as there are almost no systematic determinations of the stoichiometry of PTMs. This has remained a challenge because methods to determine stoichiometry of PTMs are not compatible with enrichment procedures, since both modified and unmodified versions of polypeptides need to be present in the sample. Global studies have been successfully performed to determine the stoichiometries
Comparative Analysis of Proteome and Transcriptome Variation in Mouse
Anatole Ghazalpour equal contributor ,Brian Bennett equal contributor,Vladislav A. Petyuk equal contributor,Luz Orozco equal contributor,Raffi Hagopian,Imran N. Mungrue,Charles R. Farber,Janet Sinsheimer,Hyun M. Kang,Nicholas Furlotte,Christopher C. Park,Ping-Zi Wen,Heather Brewer,Karl Weitz,David G. Camp II,Calvin Pan,Roumyana Yordanova,Isaac Neuhaus,Charles Tilford,Nathan Siemers,Peter Gargalovic,Eleazar Eskin,Todd Kirchgessner,Desmond J. Smith,Richard D. Smith,Aldons J. Lusis
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1001393
Abstract: The relationships between the levels of transcripts and the levels of the proteins they encode have not been examined comprehensively in mammals, although previous work in plants and yeast suggest a surprisingly modest correlation. We have examined this issue using a genetic approach in which natural variations were used to perturb both transcript levels and protein levels among inbred strains of mice. We quantified over 5,000 peptides and over 22,000 transcripts in livers of 97 inbred and recombinant inbred strains and focused on the 7,185 most heritable transcripts and 486 most reliable proteins. The transcript levels were quantified by microarray analysis in three replicates and the proteins were quantified by Liquid Chromatography–Mass Spectrometry using O(18)-reference-based isotope labeling approach. We show that the levels of transcripts and proteins correlate significantly for only about half of the genes tested, with an average correlation of 0.27, and the correlations of transcripts and proteins varied depending on the cellular location and biological function of the gene. We examined technical and biological factors that could contribute to the modest correlation. For example, differential splicing clearly affects the analyses for certain genes; but, based on deep sequencing, this does not substantially contribute to the overall estimate of the correlation. We also employed genome-wide association analyses to map loci controlling both transcript and protein levels. Surprisingly, little overlap was observed between the protein- and transcript-mapped loci. We have typed numerous clinically relevant traits among the strains, including adiposity, lipoprotein levels, and tissue parameters. Using correlation analysis, we found that a low number of clinical trait relationships are preserved between the protein and mRNA gene products and that the majority of such relationships are specific to either the protein levels or transcript levels. Surprisingly, transcript levels were more strongly correlated with clinical traits than protein levels. In light of the widespread use of high-throughput technologies in both clinical and basic research, the results presented have practical as well as basic implications.
Tolerance Pluralism and Criticism.
Vladislav A. Lektorsky
Philosophica , 2000,
Differential criterion of a bubble collapse in viscous liquids
Vladislav A. Bogoyavlenskiy
Physics , 1999, DOI: 10.1103/PhysRevE.60.504
Abstract: The present work is devoted to a model of bubble collapse in a Newtonian viscous liquid caused by an initial bubble wall motion. The obtained bubble dynamics described by an analytic solution significantly depends on the liquid and bubble parameters. The theory gives two types of bubble behavior: collapse and viscous damping. This results in a general collapse condition proposed as the sufficient differential criterion. The suggested criterion is discussed and successfully applied to the analysis of the void and gas bubble collapses.
Single-bubble sonoluminescence: Shape stability analysis of collapse dynamics in a semianalytical approach
Vladislav A. Bogoyavlenskiy
Physics , 2000, DOI: 10.1103/PhysRevE.62.2158
Abstract: This paper theoretically analyzes the hydrodynamic shape stability problem for sonoluminescing bubbles. We present a semianalytical approach to describe the evolution of shape perturbations in the strongly nonlinear regime of violent collapse. The proposed approximation estimating the damping rate produced by liquid viscosity is used to elucidate the influence of the collapse phase on subsequent evolution of the Rayleigh-Taylor instability. We demonstrate that time derivatives of shape perturbations grow significantly as the bubble radius vanishes, forming the dominant contribution to destabilization during the ensuing bounce phase. By this effect the Rayleigh-Taylor instability can be enhanced drastically, yielding a viable explanation of the upper threshold of driving pressure experimentally observed by Barber et al. [Phys. Rev. Lett. 72, 1380 (1994)].
Sliding without slipping under Coulomb friction: opening waves and inversion of frictional force
Vladislav A. Yastrebov
Physics , 2015,
Abstract: An elastic layer slides on a rigid flat governed by Coulomb's friction law. We demonstrate that if the coefficient of friction is high enough, the sliding localizes within stick-slip pulses, which transform into opening waves propagating at intersonic speed in the direction of sliding or, for high Poisson's ratios, at supersonic speed in the opposite one. This sliding mode, characterized by small frictional dissipation, rapidly relaxes the shear elastic energy via stress waves and enables the contact surface slide ahead of the top one, resulting in inversion of the frictional force direction.
Georgy A. Ball,Vladislav A. Medintsev
Information Technologies and Learning Tools , 2011,
Abstract: The authors outline vital methodological questions which concern: (a) value guidelines of scientific cognition and scientific communication; b) theoretical bases (corresponding to task approach) of building of scientific activity; c) rational using of modern information and communication technologies in that activity. Among the most important steps towards the improvement of scientific communication the following were stressed: a) awareness by scientists of their responsibility not only for adequate knowledge of the objects, but also for creating backgrounds so that the results of this knowledge might become the property of the consumers of scientific products, b) development, to form such backgrounds, the ways based on adequate theoretical tools (in particular, on the task theory) and on modern information and communication technologies, c) coverage and discussion of the results of such development. Окреслюються актуальн методолог чн питання, що стосуються: а) ц нн сних ор нтир в наукового п знання й науково комун кац ; б) теоретичних засад (в дпов дних задачному п дходов ) побудови науково д яльност ; в) рац онального використання у н й сучасних нформац йно-комун кац йних технолог й. Серед важливих крок в на шляху вдосконалення науково комун кац вид лено так : а) усв домлення вченими сво в дпов дальност не т льки за адекватне п знання досл джуваних об’ кт в, але й за створення залежних в д них передумов для того, щоб результати цього п знання стали надбанням споживач в науково продукц ; б) розробка, з спиранням на доречн теоретичн засоби (зокрема, на теор ю задач) на сучасн нформац йно-комун кац йн технолог , шлях в формування зазначених передумов; в) широке висв тлення й обговорення результат в тако розробки.
Assessment of Economic Inclination of Norms of Capital, Liquidity and Bank Risks Оценка экономического тяготения нормативов капитала, ликвидности и риска банков
Papaika Aleksandr A.,Kosogov Vladislav A.
Business Inform , 2013,
Abstract: The article gives definition of economic inclination of norms of capital, liquidity and bank risks. It provides statistical assessment of the force of economic inclination on the materials of banks, which represent all groups, on the basis of correlation and regression analysis. It states methodical approaches to calculation of regulatory capital, norms of sufficiency (adequacy) of regulatory capital, immediate and current liquidity, maximal size of the credit risk per one counteragent, studies the character and closeness of their interdependence. It shows a linear bar chart of the specific weight of frequencies of the indicator of statistically important ratios of correlation of pairs of economic indicators. It builds correlation and regression models, which allow determination of the force of economic inclination of indicators and could be used for forecasting and planning banking activity and for making decisions with respect to management of capital, liquidity and bank risks. Дана дефиниция экономического тяготения нормативов капитала, ликвидности и риска банков. Статистическая оценка силы экономического тяготения проведена на материалах банков, которые представляют все группы, на основе корреляционно-регрессионного анализа. Изложены методические подходы к расчету регулятивного капитала, нормативов достаточности (адекватности) регулятивного капитала, мгновенной и текущей ликвидности, максимального размера кредитного риска на одного контрагента, исследованы характер и теснота их взаимозависимости. Приведена линейчатая гистограмма удельного веса частот признака статистически значимых коэффициентов корреляции пар экономических показателей. Построены корреляционно-регрессионные модели, которые позволяют определить силу экономического тяготения показателей и могут использоваться для прогнозирования и планирования банковской деятельности, для принятия решений относительно управления капиталом, ликвидностью, рисками банка.
Diffusion-limited aggregation: A relationship between surface thermodynamics and crystal morphology
Vladislav A. Bogoyavlenskiy,Natasha A. Chernova
Physics , 2000, DOI: 10.1103/PhysRevE.61.1629
Abstract: We have combined the original diffusion-limited aggregation model introduced by Witten and Sander with the surface thermodynamics of the growing solid aggregate. The theory is based on the consideration of the surface chemical potential as a thermodynamic function of the temperature and nearest-neighbor configuration. The Monte Carlo simulations on a two-dimensional square lattice produce the broad range of shapes such as fractal dendritic structures, densely branching patterns, and compact aggregates. The morphology diagram illustrating the relationship between the model parameters and cluster geometry is presented and discussed.
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