Raman and Computational Study on the Adsorption of Xanthine on Silver Nanocolloids

Xanthine is a nucleobase, deriving from adenine and guanine by deamination and oxidation processes, which may deposit in the human body causing diseases, similar to uric acid. Here, we have investigated the adsorption of xanthine on silver colloidal nanoparticles by means of surface-enhanced Raman scattering (SERS) with an exciting radiation in the near-infrared spectral region, where interference due to fluorescence does not occur, along with density functional theory calculations of molecule/metal model systems. By adopting a combined experimental and computational approach, we have identified the "marker" SERS bands of xanthine and the tautomer that preferentially binds the silver particles, as well as the molecular group involved in the interaction with metal. This investigation allows using the FT-SERS spectroscopy for biosensory and diagnostic purposes in body fluids, detecting abnormal levels of xanthine, and preventing metabolic diseases

Methods and codes for neutronic calculations of the MARIA research reactor.

The core of the MARIA high flux multipurpose research reactor is highly heterogeneous. It consists of beryllium blocks arranged in 6 x 8 matrix, tubular fuel assemblies, control rods and irradiation channels. The reflector is also heterogeneous and consists of graphite blocks clad with aluminum. Its structure is perturbed by the experimental beam tubes. This paper presents methods and codes used to calculate the MARIA reactor neutronics characteristics and experience gained thus far at IAE and ANL. At ANL the methods of MARIA calculations were developed in connection with the RERTR program. At IAE the package of programs was developed to help its operator in optimization of fuel utilization

Does participatory budgeting belong to democracy or bureaucracy? Case Study of Bialystok (Poland)

The paper presents the grounds for the wider project “Participatory budgeting - success or crisis of local democracy? Comparative legal study, aiming to explore what factors (dependent and independent from the policy makers) make from BP the instrument strengthening the local democracy and what are the barriers to fully exploit its potential. To this aim, we propose the theoretical model of the PB strengthening the local democracy. To test its validity, using the case of one of the Polish cities (Bialystok), we use the mix research method: the desk research, the qualitative and quantitative surveys and the qualitative interviews. The preliminary results have shown that PB do not imply the success of the democracy, but rather only its failure and the illusion of the citizens’ participation.Urszula K. Zawadzka-Pąk - Faculty of Law, University of Bialystok, PolandDominik Kościuk - Faculty of Law, University of Bialystok, PolandJustyna E. Kulikowska-Kulesza - Faculty of Law, University of Bialystok, PolandEwa Lotko - Faculty of Law, University of Bialystok, PolandAnna Brékine - University of Geneva, SwitzerlandAllegretti G., Paying Attention To The Participants’ Perceptions in Order to Trigger A Virtuous Circle, in: Hope For Democracy - 25 Years of Participatory Bugeting, Nelson Dias (org) 2014.Arnstein, S., A Ladder of Citizen Participation, “Journal of the American Planning Association” 1969, vol. 35.Damgaard B., Lewis J.M., Accountability and Citizen Participation, in: M. Bovens (ed.), Oxford Handbook of Public Accountability, Oxford 2014.De Tocqueville A., Democracy in America, Liberty Fund 2010.Huberts L., The Integrity of Governance, What it is, What We Know, What is Done, and Where to Go, Palgrave Macmillan 2014.Jensen M.C., Meckling W.H., Theory of the Firm: Managerial Behavior, Agency Costs and Ownership Structure, “Journal of Financial Economics” 1976, no. 4.Kennedy B., Unraveling Representative Bureaucracy: A Systematic. Analysis of the Literature, “Administration & Society” 2014, vol. 46 (4).Kingsly D.J., Representative Bureaucracy: An Interpretation of the British Civil Service, Yellow Springs, OH: Antioch Press 1944.Krislov S., Representative Bureaucracy, Ouid Pro Books, New Orleans, Louisiana 1974.Mosher F.C., Democracy and the Public Service, Oxford University Press, New York 1968.Murray C., The Tendrils of Community, in: D. Boaz (ed.), The Libertarian Reader, New York 1998.Senge P., The Fifth Discipline. The Art & Practice of the Learning Organization, Currency Doubleday, New York 1990.Wampler B., When Does Participatory Democracy Deepen the Quality of Democracy, “Comparative Politcs” 2008, no. 41 (1).36-428364

Use of molecular modelling to probe the mechanism of the nucleoside transporter NupG.

Nucleosides play key roles in biology as precursors for salvage pathways of nucleotide synthesis. Prokaryotes import nucleosides across the cytoplasmic membrane by proton- or sodium-driven transporters belonging to the Concentrative Nucleoside Transporter (CNT) family or the Nucleoside:H(+) Symporter (NHS) family of the Major Facilitator Superfamily. The high resolution structure of a CNT from Vibrio cholerae has recently been determined, but no similar structural information is available for the NHS family. To gain a better understanding of the molecular mechanism of nucleoside transport, in the present study the structures of two conformations of the archetypical NHS transporter NupG from Escherichia coli were modelled on the inward- and outward-facing conformations of the lactose transporter LacY from E. coli, a member of the Oligosaccharide:H(+) Symporter (OHS) family. Sequence alignment of these distantly related proteins (∼ 10% sequence identity), was facilitated by comparison of the patterns of residue conservation within the NHS and OHS families. Despite the low sequence similarity, the accessibilities of endogenous and introduced cysteine residues to thiol reagents were found to be consistent with the predictions of the models, supporting their validity. For example C358, located within the predicted nucleoside binding site, was shown to be responsible for the sensitivity of NupG to inhibition by p-chloromercuribenzene sulphonate. Functional analysis of mutants in residues predicted by the models to be involved in the translocation mechanism, including Q261, E264 and N228, supported the hypothesis that they play important roles, and suggested that the transport mechanisms of NupG and LacY, while different, share common features

A Novel Mechanism of Programmed Cell Death in Bacteria by Toxin–Antitoxin Systems Corrupts Peptidoglycan Synthesis

Most genomes of bacteria contain toxin–antitoxin (TA) systems. These gene systems encode a toxic protein and its cognate antitoxin. Upon antitoxin degradation, the toxin induces cell stasis or death. TA systems have been linked with numerous functions, including growth modulation, genome maintenance, and stress response. Members of the epsilon/zeta TA family are found throughout the genomes of pathogenic bacteria and were shown not only to stabilize resistance plasmids but also to promote virulence. The broad distribution of epsilon/zeta systems implies that zeta toxins utilize a ubiquitous bacteriotoxic mechanism. However, whereas all other TA families known to date poison macromolecules involved in translation or replication, the target of zeta toxins remained inscrutable. We used in vivo techniques such as microscropy and permeability assays to show that pneumococcal zeta toxin PezT impairs cell wall synthesis and triggers autolysis in Escherichia coli. Subsequently, we demonstrated in vitro that zeta toxins in general phosphorylate the ubiquitous peptidoglycan precursor uridine diphosphate-N-acetylglucosamine (UNAG) and that this activity is counteracted by binding of antitoxin. After identification of the product we verified the kinase activity in vivo by analyzing metabolite extracts of cells poisoned by PezT using high pressure liquid chromatograpy (HPLC). We further show that phosphorylated UNAG inhibitis MurA, the enzyme catalyzing the initial step in bacterial peptidoglycan biosynthesis. Additionally, we provide what is to our knowledge the first crystal structure of a zeta toxin bound to its substrate. We show that zeta toxins are novel kinases that poison bacteria through global inhibition of peptidoglycan synthesis. This provides a fundamental understanding of how epsilon/zeta TA systems stabilize mobile genetic elements. Additionally, our results imply a mechanism that connects activity of zeta toxin PezT to virulence of pneumococcal infections. Finally, we discuss how phosphorylated UNAG likely poisons additional pathways of bacterial cell wall synthesis, making it an attractive lead compound for development of new antibiotics

An ab initio and AIM investigation into the hydration of 2-thioxanthine

<p>Abstract</p> <p>Background</p> <p>Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX), a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an <it>ab initio </it>study of the hydration of 2TX, revealing water can form seven hydrated complexes.</p> <p>Results</p> <p>Hydrogen-bond (H-bond) interactions in 1:1 complexes of 2TX with water are studied at the MP2/6-311G(d, p) and B3LYP/6-311G(d, p) levels. Seven 2TX^...H₂O hydrogen bonded complexes have been theoretically identified and reported for the first time. The proton affinities (PAs) of the O, S, and N atoms and deprotonantion enthalpies (DPEs) of different N-H bonds in 2TX are calculated, factors surrounding why the seven complexes have different hydrogen bond energies are discussed. The theoretical infrared and NMR spectra of hydrated 2TX complexes are reported to probe the characteristics of the proposed H-bonds. An improper blue-shifting H-bond with a shortened C-H bond was found in one case. NBO and AIM analysis were carried out to explain the formation of improper blue-shifting H-bonds, and the H-bonding characteristics are discussed.</p> <p>Conclusion</p> <p>2TX can interact with water by five different H-bonding regimes, N-H^...O, O-H^...N, O-H^...O, O-H^...S and C-H^...O, all of which are medium strength hydrogen bonds. The most stable H-bond complex has a closed structure with two hydrogen bonds (N(7)-H^...O and O-H^...O), whereas the least stable one has an open structure with one H-bond. The interaction energies of the studied complexes are correlated to the PA and DPE involved in H-bond formation. After formation of H-bonds, the calculated IR and NMR spectra of the 2TX-water complexes change greatly, which serves to identify the hydration of 2TX.</p