Induction of persistent double strand breaks following multiphoton irradiation of cycling and G1-arrested mammalian cells-replication-induced double strand breaks

DNA double strand breaks (DSBs) are amongst the most deleterious lesions induced within the cell following exposure to ionizing radiation. Mammalian cells repair these breaks predominantly via the nonhomologous end joining pathway which is active throughout the cell cycle and is error prone. The alternative pathway for repair of DSBs is homologous recombination (HR) which is error free and active during S- and G2/M-phases of the cell cycle. We have utilized near-infrared laser radiation to induce DNA damage in individual mammalian cells through multiphoton excitation processes to investigate the dynamics of single cell DNA damage processing. We have used immunofluorescent imaging of gamma-H2AX (a marker for DSBs) in mammalian cells and investigated the colocalization of this protein with ATM, p53 binding protein 1 and RAD51, an integral protein of the HR DNA repair pathway. We have observed persistent DSBs at later times postlaser irradiation which are indicative of DSBs arising at replication, presumably from UV photoproducts or clustered damage containing single strand breaks. Cell cycle studies have shown that in G1 cells, a significant fraction of multiphoton laser-induced prompt DSBs persists for > 4 h in addition to those induced at replication.     

cis-Delta(2,3)-double bond of phoslactomycins is generated by a post-PKS tailoring enzyme

The antifungal phoslactomycins (PLM A-F), produced by Streptomyces sp. HK803, are structurally unusual in that three of their four double bonds are in the cis form (Delta12,13, Delta14,15, Delta2,3). The PLM polyketide synthase (PKS) has the predicted dehydratase catalytic domain in modules 1, 2, and 5 required for establishing two of these cis double bonds (Delta12,13, Delta14,15), as well as the only trans Delta6,7 double bond. By contrast, the formation of the cis Delta2,3 in the unsaturated lactone moiety of PLMs has presented an enigma because the predicted dehydratase domain in module 7 is absent. Herein, we have demonstrated that the plmT2 gene product, with no homology to PKS dehydratase domains, is required for efficient formation of the cis Delta2,3 alkene. A series of new PLM products in which the C3 hydroxyl group is retained are made in plmT2 deletion mutants. In all of these cases, however, the hydroxyl group is esterified with malonic acid. These malonylated PLM products are converted to the corresponding cis Delta2,3 PLM products and acetic acid by a facile base-catalyzed decarboxylative elimination reaction. Complete or partial restoration of natural PLM production in a plmT2 deletion mutant can be accomplished by plasmid based expression of plmT2 or fos ORF4 (a homologous gene from the fostriecin biosynthetic gene cluster), respectively. The data indicate that dehydratase-independent pathways also function in establishment of unsaturated 6-membered lactone moieties in other PKS pathways and provide the first biosynthetic insights into the possible routes by which unusual malonylated polyketide products are generated.     

Flow injection determination of aluminium by spectrofluorimetric detection after complexation with N-o-vanillidine-2-amino-p-cresol: the application to natural waters

An on-line flow injection spectrofluorimetric method for the direct determination of aluminium in water samples is described. The method is based on the reaction of aluminium with N-o-vanillidine-2-amino-p-cresol (OVAC) in acidic medium at pH 4.0 to form a water-soluble complex. The excitation and emission wavelengths were 423.0 and 553.0 nm, respectively, at which the OVAC-Al complex gave the maximum fluorescence intensity at pH 4.0 in a 50% methanol-50% water medium at 50 °C. An interference from fluoride ions was minimised by the addition of Be²⁺. Other ions were found not to interfere at the concentrations likely to be found in natural waters. The proposed methods were validated in terms of linearity, repeatability, detection limit, accuracy and selectivity. Under these conditions, the calibration was linear up to 1000 μg L⁻¹ (r = 0.999). The limit of detection (3σ) for the determination of Al(III) was 0.057 μg L⁻¹ and the precision for multiple determinations of 3 ng mL⁻¹ Al(III) prepared in ultra-pure water was found to be 0.62% (n = 10).The Schiff base ligand could be used to determine ultra-trace aluminium from natural waters. Analysis of environmental certified reference materials showed good agreement with the certified values. The procedure was found to be equally applicable to both freshwater and saline solutions, including seawater.     

PAP inhibitor with in vivo efficacy identified by Candida albicans genetic profiling of natural products

Natural products provide an unparalleled source of chemical scaffolds with diverse biological activities and have profoundly impacted antimicrobial drug discovery. To further explore the full potential of their chemical diversity, we survey natural products for antifungal, target-specific inhibitors by using a chemical-genetic approach adapted to the human fungal pathogen Candida albicans and demonstrate that natural-product fermentation extracts can be mechanistically annotated according to heterozygote strain responses. Applying this approach, we report the discovery and characterization of a natural product, parnafungin, which we demonstrate, by both biochemical and genetic means, to inhibit poly(A) polymerase. Parnafungin displays potent and broad spectrum activity against diverse, clinically relevant fungal pathogens and reduces fungal burden in a murine model of disseminated candidiasis. Thus, mechanism-of-action determination of crude fermentation extracts by chemical-genetic profiling brings a powerful strategy to natural-product-based drug discovery.     

Assessing the role of polarization in docking

We describe a strategy for including ligand and protein polarization in docking that is based on the conversion of induced dipoles to induced charges. Induced charges have a distinct advantage in that they are readily implemented into a number of different computer programs, including many docking programs and hybrid QM/MM programs; induced charges are also more readily interpreted. In this study, the ligand was treated quantum mechanically to avoid parametrization issues and was polarized by the target protein, which was treated as a set of point charges. The induced dipole at a given target atom, due to polarization by the ligand and neighboring residues, was reformulated as induced charges at the given atom and its bonded neighbors, and these were allowed to repolarize the ligand in an iterative manner. The final set of polarized charges was evaluated in docking using AutoDock 4.0 on 12 protein-ligand systems against the default empirical Gasteiger charges, and against nonpolarized and partially polarized potential-derived charges. One advantage of AutoDock is that the best rmsd structure can be identified not only from the lowest energy pose but also from the largest cluster of poses. Inclusion of polarization does not always lead to the lowest energy pose having a lower rmsd, because docking is designed by necessity to be rapid rather than accurate. However, whenever an improvement in methodology, corresponding to a more thorough treatment of polarization, resulted in an increased cluster size, then there was also a corresponding decrease in the rmsd. The options for implementing polarization within a purely classical docking framework are discussed.     

Complexes pairing hypohalous acids with nitrosyl hydride. blue shift of a NH bond that is uninvolved in a H-bond

Correlated calculations are used to analyze the interaction between nitrosyl hydride (HNO) and hypohalous acids (HOF, HOCl, and HOBr). Two minima are located on the potential energy surface of each complex, in both of which HOX acts as proton donor. Donation to the N atom of HNO makes for a more strongly bound complex, as compared to the OH..O bond in the secondary minimum. Binding energies of the global minimum are about 22 kJ/mol, as compared to 18 kJ/mol for the secondary structure; there is little sensitivity to the identity of the halogen atom. Whereas the covalent OH bond of HOX stretches and shifts to the red upon complexation, the NH bond of HNO, whether involved in a H-bond or not, behaves in the opposite manner.     

Photovoltaic cells based on sequentially adsorbed multilayers of conjugated poly(p-phenylene ethynylene)s and a water-soluble fullerene derivative

We describe the layer-by-layer (LBL) fabrication of multilayer films and photovoltaic cells using poly(phenylene ethynylene)-based anionic conjugated polyelectrolytes as electron donors and water-soluble cationic fullerene C60 derivatives as acceptors. LBL film deposition was found to be linearly related to the number of bilayers as monitored by UV-vis absorption. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) of the multilayer films revealed an aggregated but relatively uniform morphology devoid of any long-range phase separation. The maximum incident monochromatic photon to current conversion efficiency (IPCE) of the photovoltaic cells was 5.5%, the highest efficiency reported to date for cells fabricated by using the LBL fabrication technique, and since the thin film cells do not provide complete absorption of the incident light, the current generation per photon absorbed may be as much as 10%. The cells exhibited open circuit voltages of 200-250 mV with highest measured short circuit currents up to 0.5 mA/cm2 and fill factors around 30%. The power conversion efficiencies measured at AM 1.5 solar conditions (100 mW/cm2) varied between 0.01 and 0.04%, and similar to the IPCE results, the efficiency is a function of the thickness of the PV active layer.     

Trace formulas and Borg-type theorems for matrix-valued Jacobi and Dirac finite difference operators

Borg-type uniqueness theorems for matrix-valued Jacobi operators H and supersymmetric Dirac difference operators D are proved. More precisely, assuming reflectionless matrix coefficients A,B in the self-adjoint Jacobi operator H=AS⁺+A^-S^-+B (with S^± the right/left shift operators on the lattice Z) and the spectrum of H to be a compact interval [E_-,E₊], E_-<E₊, we prove that A and B are certain multiples of the identity matrix. An analogous result which, however, displays a certain novel nonuniqueness feature, is proved for supersymmetric self-adjoint Dirac difference operators D with spectrum given by , 0?E_-<E₊.Our approach is based on trace formulas and matrix-valued (exponential) Herglotz representation theorems. As a by-product of our techniques we obtain the extension of Flaschka's Borg-type result for periodic scalar Jacobi operators to the class of reflectionless matrix-valued Jacobi operators.     

Large phase shifts in As2S3 waveguides for all-optical processing devices

A large phase shift of 4.7pi at 1.53 microm has been observed from a low-loss (0.2 dB/cm), small-core As2S3 waveguide fabricated by dry etching. The strength of the nonlinear response was limited by photosensitivity and photocrystallization of the As2S3 films at 1.53 microm, far below the material bandgap.     

String tensions for lattice gauge theories in 2 + 1 dimensions

Compact U(1) and SU(2) lattice gauge theories in 3 euclidean dimensions are studied by standard Monte Carlo techniques. The question of extracting reliable string tensions from these theories is examined in detail, including a comparison of the Monte Carlo Wilson loop data with weak coupling predictions and a careful error analysis: our conclusions are rather different from those of previous investigations of these theories. In the case of U(1) theory, we find that only a tiny range of β values can possibly be relevant for extracting a string tension and we are unable to convincingly demonstrate the expected exponential dependence of the string tension on β. For the SU(2) theory we are able to determine, albeit with rather large errors, a string tension from a study of Wilson loops.