Time-domain chirally-sensitive three-pulse coherent probes of vibrational excitons in proteins

The third order optical response of bosonic excitons is calculated using the Green's function solution of the Nonlinear Exciton Equations (NEE) which establish a quasiparticle-scattering mechanism for optical nonlinearities. Both time ordered and non ordered forms of the response function which represent time and frequency domain techniques, respectively, are derived. New components of the response tensor are predicted for isotropic ensembles of periodic chiral structures to first order in the optical wavevector. The nonlocal nonlinear response function is calculated in momentum space, where the finite exciton-exciton interaction length greatly reduces the computational effort. Applications are made to coupled anharmonic vibrations in the amide I infrared band of peptides. Chirally-sensitive and non sensitive signals for alpha helices and antiparallel beta sheets are compared.Comment: 26 pages, 6 figure

Finding 3D motifs in ribosomal RNA structures

The identification of small structural motifs and their organization into larger subassemblies is of fundamental interest in the analysis, prediction and design of 3D structures of large RNAs. This problem has been studied only sparsely, as most of the existing work is limited to the characterization and discovery of motifs in RNA secondary structures. We present a novel geometric method for the characterization and identification of structural motifs in 3D rRNA molecules. This method enables the efficient recognition of known 3D motifs, such as tetraloops, E-loops, kink-turns and others. Furthermore, it provides a new way of characterizing complex 3D motifs, notably junctions, that have been defined and identified in the secondary structure but have not been analyzed and classified in three dimensions. We demonstrate the relevance and utility of our approach by applying it to the Haloarcula marismortui large ribosomal unit. Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author

Metabolic Flux Analysis of Mitochondrial Uncoupling in 3T3-L1 Adipocytes

BACKGROUND:Increasing energy expenditure at the cellular level offers an attractive option to limit adiposity and improve whole body energy balance. In vivo and in vitro observations have correlated mitochondrial uncoupling protein-1 (UCP1) expression with reduced white adipose tissue triglyceride (TG) content. The metabolic basis for this correlation remains unclear. METHODOLOGY/PRINCIPAL FINDINGS:This study tested the hypothesis that mitochondrial uncoupling requires the cell to compensate for the decreased oxidation phosphorylation efficiency by up-regulating lactate production, thus redirecting carbon flux away from TG synthesis. Metabolic flux analysis was used to characterize the effects of non-lethal, long-term mitochondrial uncoupling (up to 18 days) on the pathways of intermediary metabolism in differentiating 3T3-L1 adipocytes. Uncoupling was induced by forced expression of UCP1 and chemical (FCCP) treatment. Chemical uncoupling significantly decreased TG content by ca. 35%. A reduction in the ATP level suggested diminished oxidative phosphorylation efficiency in the uncoupled adipocytes. Flux analysis estimated significant up-regulation of glycolysis and down-regulation of fatty acid synthesis, with chemical uncoupling exerting quantitatively larger effects. CONCLUSIONS/SIGNIFICANCE:The results of this study support our hypothesis regarding uncoupling-induced redirection of carbon flux into glycolysis and lactate production, and suggest mitochondrial proton translocation as a potential target for controlling adipocyte lipid metabolism

Synergistic induction of lipid catabolism and anti-inflammatory lipids in white fat of dietary obese mice in response to calorie restriction and n-3 fatty acids

Calorie restriction is an essential component in the treatment of obesity and associated diseases. Long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFA) act as natural hypolipidaemics, reduce the risk of cardiovascular disease and could prevent the development of obesity and insulin resistance. We aimed to characterise the effectiveness and underlying mechanisms of the combination treatment with LC n-3 PUFA and 10% calorie restriction in the prevention of obesity and associated disorders in mice. Male mice (C57BL/6J) were habituated to a corn-oil-based high-fat diet (cHF) for 2 weeks and then randomly assigned to various dietary treatments for 5 weeks or 15 weeks: (1) cHF, ad libitum; (2) cHF with LC n-3 PUFA concentrate replacing 15% (wt/wt) of dietary lipids (cHF + F), ad libitum; (3) cHF with calorie restriction (CR; cHF + CR); and (4) cHF + F + CR. Mice fed a chow diet were also studied. We show that white adipose tissue plays an active role in the amelioration of obesity and the improvement of glucose homeostasis by combining LC n-3 PUFA intake and calorie restriction in cHF-fed mice. Specifically in the epididymal fat in the abdomen, but not in other fat depots, synergistic induction of mitochondrial oxidative capacity and lipid catabolism was observed, resulting in increased oxidation of metabolic fuels in the absence of mitochondrial uncoupling, while low-grade inflammation was suppressed, reflecting changes in tissue levels of anti-inflammatory lipid mediators, namely 15-deoxy-Delta(12,15)-prostaglandin J(2) and protectin D1. White adipose tissue metabolism linked to its inflammatory status in obesity could be modulated by combination treatment using calorie restriction and dietary LC n-3 PUFA to improve therapeutic strategies for metabolic syndrome

Structure of the dimeric N-glycosylated form of fungal β-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies

<p>Abstract</p> <p>Background</p> <p>Fungal β-<it>N</it>-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal β-<it>N</it>-acetylhexosaminidase. The fungal β-<it>N</it>-acetylhexosaminidases are robust enzymes commonly used in chemoenzymatic syntheses of oligosaccharides. The enzyme from <it>Aspergillus oryzae </it>was purified and its sequence was determined.</p> <p>Results</p> <p>The complete primary structure of the fungal β-<it>N</it>-acetylhexosaminidase from <it>Aspergillus oryzae </it>CCF1066 was used to construct molecular models of the catalytic subunit of the enzyme, the enzyme dimer, and the <it>N</it>-glycosylated dimer. Experimental data were obtained from infrared and Raman spectroscopy, and biochemical studies of the native and deglycosylated enzyme, and are in good agreement with the models. Enzyme deglycosylated under native conditions displays identical kinetic parameters but is significantly less stable in acidic conditions, consistent with model predictions. The molecular model of the deglycosylated enzyme was solvated and a molecular dynamics simulation was run over 20 ns. The molecular model is able to bind the natural substrate – chitobiose with a stable value of binding energy during the molecular dynamics simulation.</p> <p>Conclusion</p> <p>Whereas the intracellular bacterial β-<it>N</it>-acetylhexosaminidases are monomeric, the extracellular secreted enzymes of fungi and humans occur as dimers. Dimerization of the fungal β-<it>N</it>-acetylhexosaminidase appears to be a reversible process that is strictly pH dependent. Oligosaccharide moieties may also participate in the dimerization process that might represent a unique feature of the exclusively extracellular enzymes. Deglycosylation had only limited effect on enzyme activity, but it significantly affected enzyme stability in acidic conditions. Dimerization and <it>N</it>-glycosylation are the enzyme's strategy for catalytic subunit stabilization. The disulfide bridge that connects Cys⁴⁴⁸with Cys⁴⁸³stabilizes a hinge region in a flexible loop close to the active site, which is an exclusive feature of the fungal enzymes, neither present in bacterial nor mammalian structures. This loop may play the role of a substrate binding site lid, anchored by a disulphide bridge that prevents the substrate binding site from being influenced by the flexible motion of the loop.</p

Free banking and 'wild cat banking'

Zavedení jednotné evropské měny je další krok v procesu centralizace emise peněz a centralizace bankovnictví obecně. Není to ale proces nikterak přirozený, a ani jediný možný. Cílem této práce je představit teoretický koncept alternativy centralizovaného bankovnictví, tedy bankovnictví svobodné, které rozpracovali především zástupci rakouské školy. V analytické části se zaměřím na éru svobodného bankovnictví 19. století ve Spojených státech, označovanou dosti pejorativně jako bankovnictví divokých koček. Pokusím se dokázat, že toto období nebylo tak katastrofální, jak se tvrdí a že je neprávem považováno za selhání idejí svobodného bankovnictví v praxi

The Still evolving Principle of Universal Jurisdiction

The present study describes the nature, scope and application of universal jurisdiction as an important tool against impunity in international criminal law, in a straight forward manner, where inquiry into the recent developments of universal jurisdiction is undertaken. Forthwith, the formation of the principle of universal jurisdiction - especially its practical application - must be guided by international consensus, not through advocacy action of states with short term and narrow objectives. The thesis seeks to identify and observe how far the law of universal jurisdiction has actually evolved and how far we should expect it to evolve in the near future, considering its restrains and challenges. It is argued that the concept of state sovereignty, which constitutes the greatest impediment on the exercise of universal jurisdiction, has seen various changes to its fundamentals elements in the 21st Century. The aim is to look at the universality principle, not as an isolated part, but as part of a broader framework in modern international law and thus special attention is given to the relationship between universal jurisdiction and the principle of aut dedere aut judicare. These principles are interrelated, yet distinct, parallels in deterring commission of the most heinous offences of international..

Analysis of the pension systems with focus on the funded pillar

The diploma thesis deals with the privatization of the pay-as-you-go pension systems, and it aims to theoretically and empirically disconfirm the widely spread imaginary benefits of the transfer to the fully funded social security system. These so-called social security myths are inherently connected with the transformation of the implicit pension debt to the explicit debt which, as confirmed by the designed multiple regression model, has a negative influence on rating and therefore on financing expenses of certain states. The thesis also focuses on legislative modifications of pension funds in the Czech Republic which fundamentally add to almost zero real annual yield. After subtraction of deferred expenses and revaluation reserve held in equity of particular pension funds, the average real annual yield in recent fifteen years is actually negative

Strategic analysis of the surroundings of the Globus ČR company

Bakalářská práce se zabývá strategickou analýzou společnosti Globus ČR v.o.s., která se pohybuje v odvětví maloobchod s převahou potravin, nápojů a tabákových výrobků v nespecializovaných prodejnách a v detailnějším pohledu pak provozuje hypermarkety. Hlavním cílem této práce je vyhodnocení hrozeb a příležitostí vzniklých během pandemie COVID-19. Práce je rozdělena na dvě části, a to teoretickou a praktickou část. Teoretická část se věnuje výkladu vybraných metod strategické analýzy okolí a dále teorii z hlediska chování společností v dobách krize. V praktické části jsou použity a aplikovány na analyzovanou společnost následující metody strategické analýzy: PESTEL analýza, základní charakteristika odvětví, analýza konkurence, mapa konkurenčních skupin a Porterův model 5 sil. Poslední část práce je věnována závěru a následným doporučením.The bachelor thesis deals with a strategic analysis of Globus ČR v.o.s., which operates in the retail sector with a predominance of food, beverages, and tobacco products in non-specialized stores and in a more detailed look operate hypermarkets. The main aim of this thesis is to evaluate the threats and opportunities that arose during the COVID-19 pandemic. The thesis is divided into two parts, into a theoretical and a practical part. The theoretical part deals with the interpretation of selected methods of strategic analysis of the surroundings and the theory in terms of the behavior of companies in times of crisis. In the practical part, the following methods of strategic analysis are used and applied to the analyzed company: PESTEL analysis, basic characteristics of the industry, competition analysis, map of competing groups, and Porter's model of 5 forces. The last part of the work is devoted to the conclusion and subsequent recommendations