Interaction of surfactants with DNA. Role of hydrophobicity and surface charge on intercalation and DNA melting

A probe, 9-(anthrylmethyl)trimethylammonium chloride, 1, was prepared. 1 binds to calf-thymus DNA or Escherichia coli genomic DNA with high affinity, as evidenced from the absorption titration. Strong hypochromism, spectral broadening and red-shifts in the absorption spectra were observed. Half-reciprocal plot constructed from this experiment gave binding constant of 5±0.5×104 M−1 in base molarity. We employed this anthryl probe-DNA complex for studying the effects of addition of various surfactant to DNA. Surfactants of different charge types and chain lengths were used in this study and the effects of surfactant addition to such probe-DNA complex were compared with that of small organic cations or salts. Addition of either salts or cationic surfactants led to structural changes in DNA and under these conditions, the probe from the DNA-bound complex appeared to get released. However, the cationic surfactants could induce such release of the probe from the probe-DNA complex at a much lower concentration than that of the small organic cations or salts. In contrast the anionic surfactants failed to promote any destabilization of such probe-DNA complexes. The effects of additives on the probe-DNA complexes were also examined by using a different technique (fluorescence spectroscopy) using a different probe ethidium bromide. The association complexes formed between the cationic surfactants and the plasmid DNA pTZ19R, were further examined under agarose gel electrophoresis and could not be visualized by ethidium bromide staining presumably due to cationic surfactant-induced condensation of DNA. Most of the DNA from such association complexes can be recovered by extraction of surfactants with phenol-chloroform. Inclusion of surfactants and other additives into the DNA generally enhanced the DNA melting temperatures by a few °C and at high [surfactant], the corresponding melting profiles got broadened.

Rice husk filtrate as a nutrient medium for the growth of Desulfotomaculum nigrificans: characterisation and sulfate reduction studies

The filtrate obtained by interacting a known amount of rice husk with deionised, Milli-Q water was assessed as a carbon source and nutrient medium for the growth of Desulfotomaculum nigrificans, a typical sulfate-reducing bacterium. The filtrate contained essential growth constituents such as magnesium, potassium, phosphorous apart from calcium, sodium, chloride and sulfate ions. Based on the 1H and 13C NMR characterization studies, the organic composition of the components dissolved from the rice husk, was found to be: (i) 66% lignocellulosic material, (ii) 24% xylose + arabinose and (iii) 10% galactose. The growth studies indicated a 15-fold increase in the bacterial cell number in about 20 days. Nearly 81% and 66% reduction in sulfate concentration could be achieved in about 28 days, from the solutions containing initial sulfate concentrations of 550 mg/l and 1200 mg/l respectively. In both the cases studied, the iron concentration could be reduced by over 85%.

Aspects of tautomerism. 8. Solvolysis of some pseudo and normal acid chlorides

Pseudo acid chlorides derived from levulinic acid ando-benzoyl-benzoic acid, solvolyse in aqueous acetone, aqueous dioxane and aqueous dimethylformamide by aS Nl process. Their reaction pattern is distinct from that of typical normal acid chlorides, viz.,p-benzoylbenzoyl chloride and fluorene-9-one-1-carboxylic acid chloride, which solvolyse by aS N2 pathway. No evidence for tautomerism could be obtained either between the normal and pseudo forms of the acid chlorides or the derived ion pairs.

Behaviour of natural zeolites used for the treatment of simulated and actual coal seam gas water

Coal seam gas operations produce significant quantities of associated water which often require demineralization. Ion exchange with natural zeolites has been proposed as a possible approach. The interaction of natural zeolites with solutions of sodium chloride and sodium bicarbonate in addition to coal seam gas water is not clear. Hence, we investigated ion exchange kinetics, equilibrium, and column behaviour of an Australian natural zeolite. Kinetic tests suggested that the pseudo first order equation best simulated the data. Intraparticle diffusion was part of the rate limiting step and more than one diffusion process controlled the overall rate of sodium ion uptake. Using a constant mass of zeolite and variable concentration of either sodium chloride or sodium bicarbonate resulted in a convex isotherm which was fitted by a Langmuir model. However, using a variable mass of zeolite and constant concentration of sodium ions revealed that the exchange of sodium ions with the zeolite surface sites was in fact unfavourable. Sodium ion exchange from bicarbonate solutions (10.3 g Na/kg zeolite) was preferred relative to exchange from sodium chloride solutions (6.4 g Na/kg zeolite). The formation of calcium carbonate species was proposed to explain the observed behaviour. Column studies of coal seam gas water showed that natural zeolite had limited ability to reduce the concentration of sodium ions (loading 2.1 g Na/kg zeolite) with rapid breakthrough observed. It was concluded that natural zeolites may not be suitable for the removal of cations from coal seam gas water without improvement of their physical properties.

Ion-regulatory proreins in neuronal development and communication

Brain function is critically dependent on the ionic homeostasis in both the extra- and intracellular compartment. The regulation of brain extracellular ionic composition mainly relies on active transport at blood brain and at blood cerebrospinal fluid interfaces whereas intracellular ion regulation is based on plasmalemmal transporters of neurons and glia. In addition, the latter mechanisms can generate physiologically as well as pathophysiologically significant extracellular ion transients. In this work I have studied molecular mechanisms and development of ion regulation and how these factors alter neuronal excitability and affect synaptic and non-synaptic transmission with a particular emphasis on intracellular pH and chloride (Cl-) regulation. Why is the regulation of acid-base equivalents (H+ and HCO3-) and Cl- of such interest and importance? First of all, GABAA-receptors are permeable to both HCO3- and Cl-. In the adult mammalian central nervous system (CNS) fast postsynaptic inhibition relies on GABAA-receptor mediated transmission. Today, excitatory effects of GABAA-receptors, both in mature neurons and during the early development, have been recognized and the significance of the dual actions of GABA on neuronal communication has become an interesting field of research. The transmembrane gradients of Cl- and HCO3- determine the reversal potential of GABAA-receptor mediated postsynaptic potentials and hence, the function of pH and Cl- regulatory proteins have profound consequences on GABAergic signaling and neuronal excitability. Secondly, perturbations in pH can cause a variety of changes in cellular function, many of them resulting from the interaction of protons with ionizable side chains of proteins. pH-mediated alterations of protein conformation in e.g. ion channels, transporters, and enzymes can powerfully modulate neurotransmission. In the context of pH homeostasis, the enzyme carbonic anhydrase (CA) needs to be taken into account in parallel with ion transporters: for CO2/HCO3- buffering to act in a fast manner, CO2 (de)hydration must be catalyzed by this enzyme. The acid-base equivalents that serve as substrates in the CO2 dehydration-hydration reaction are also engaged in many carrier and channel mediated ion movements. In such processes, CA activity is in key position to modulate transmembrane solute fluxes and their consequences. The bicarbonate transporters (BTs; SLC4) and the electroneutral cation-chloride cotransporters (CCCs; SLC12) belong the to large gene family of solute carriers (SLCs). In my work I have studied the physiological roles of the K+-Cl- cotransporter KCC2 (Slc12a5) and the Na+-driven Cl--HCO3- exchanger NCBE (Slc4a10) and the roles of these two ion transporters in the modualtion of neuronal communication and excitability in the rodent hippocampus. I have also examined the cellular localization and molecular basis of intracellular CA that has been shown to be essential for the generation of prolonged GABAergic excitation in the mature hippocampus. The results in my Thesis provide direct evidence for the view that the postnatal up-regulation of KCC2 accounts for the developmental shift from depolarizing to hyperpolarizing postsynaptic EGABA-A responses in rat hippocampal pyramidal neurons. The results also indicate that after KCC2 expression the developmental onset of excitatory GABAergic transmission upon intense GABAA-receptor stimulation depend on the expression of intrapyramidal CA, identified as the CA isoform VII. Studies on mice with targeted Slc4a10 gene disruption revealed an important role for NCBE in neuronal pH regulation and in pH-dependent modulation of neuronal excitability. Furthermore, this ion transporter is involved in the basolateral Na+ and HCO3- uptake in choroid plexus epithelial cells, and is thus likely to contribute to cerebrospinal fluid production.

Microwave absorption studies of iron encapsulating carbon-polymer nanocomposite films

Iron encapsulated carbon nanoparticle polyvinyl chloride composite films have been prepared by solvent mixing and drying method. The films were characterized by scanning electron microscope (SEM) and high resolution transmission electron microscope (HRTEM). A 5 nm thin graphitic carbon coating is observed on cubic Fe nanoparticles. The microwave absorption studies by wave guide technique in the Ka band range showed highest electromagnetic interference shielding efficiency of 18dB on a 300 micron thick film. The shielding efficiency depends on weight % of the filler in the composite. The data obtained for different films indicate that these lightweight materials are good candidates for potential electromagnetic interference shielding applications.

Cytotoxicity of half sandwich ruthenium(II) complexes with strong hydrogen bond acceptor ligands and their mechanism of action

Neutral and cationic organometallic ruthenium(II) piano stool complexes of the type [(eta(6)-cymene)R-uCl(X)(Y)] (complexes R1-R8) has been synthesized and characterized. In cationic complexes, X, Y is either a eta(2) phosphorus ligand such as 1,1-bis(diphenylphosphino)methane (DPPM) and 1,2-bis(diphenylphosphino)ethane (DPPE) or partially oxidized ligands such as 1,2-bis(diphenylphosphino)methane monooxide (DPPMO) and 1,2-bis(diphenylphosphino)ethane monooxide (DPPEO) which are strong hydrogen bond acceptors. In neutral complexes. X is chloride and Y is a monodentate phosphorous donor. Complexes with DPPM and DPPMO ligands ([(eta(6)-cymene)Ru(eta(2)-DPPM)Cl]PF6 (R2), [(eta(6)-cymene)Ru(eta(2)-DPPMO)Cl]PF6 (R3), [(eta(6)-cymene)Ru(eta(1)-DPPM)Cl-2] (R5) and [(eta(6)-cymene)Ru(eta(1)-DPPMO)Cl-2] (R6) show good cytotoxicity. Growth inhibition study of several human cancer cell lines by these complexes has been carried out. Mechanistic studies for R5 and R6 show that inhibition of cancer cell growth involves both cell cycle arrest and apoptosis induction. Using an apoptosis PCR array, we identified the sets of antiapoptotic genes that were down regulated and pro-apoptotic genes that were up regulated. These complexes were also found to be potent metastasis inhibitors as they prevented cell invasion through matrigel. The complexes were shown to bind DNA in a non intercalative fashion and cause unwinding of plasmid DNA in cell-free medium by competitive ethidium bromide binding, viscosity measurements, thermal denaturation and gel mobility shift assays.

Processing of Mycobacterium tuberculosis bacilli by human monocytes for CD4+ alphabeta and gammadelta T cells: role of particulate antigen.

Mycobacterium tuberculosis readily activates both CD4+ and Vdelta2+ gammadelta T cells. Despite similarity in function, these T-cell subsets differ in the antigens they recognize and the manners in which these antigens are presented by M. tuberculosis-infected monocytes. We investigated mechanisms of antigen processing of M. tuberculosis antigens to human CD4 and gammadelta T cells by monocytes. Initial uptake of M. tuberculosis bacilli and subsequent processing were required for efficient presentation not only to CD4 T cells but also to Vdelta2+ gammadelta T cells. For gammadelta T cells, recognition of M. tuberculosis-infected monocytes was dependent on Vdelta2+ T-cell-receptor expression. Recognition of M. tuberculosis antigens by CD4+ T cells was restricted by the class II major histocompatibility complex molecule HLA-DR. Processing of M. tuberculosis bacilli for Vdelta2+ gammadelta T cells was inhibitable by Brefeldin A, whereas processing of soluble mycobacterial antigens for gammadelta T cells was not sensitive to Brefeldin A. Processing of M. tuberculosis bacilli for CD4+ T cells was unaffected by Brefeldin A. Lysosomotropic agents such as chloroquine and ammonium chloride did not affect the processing of M. tuberculosis bacilli for CD4+ and gammadelta T cells. In contrast, both inhibitors blocked processing of soluble mycobacterial antigens for CD4+ T cells. Chloroquine and ammonium chloride insensitivity of processing of M. tuberculosis bacilli was not dependent on the viability of the bacteria, since processing of both formaldehyde-fixed dead bacteria and mycobacterial antigens covalently coupled to latex beads was chloroquine insensitive. Thus, the manner in which mycobacterial antigens were taken up by monocytes (particulate versus soluble) influenced the antigen processing pathway for CD4+ and gammadelta T cells.

Microsphere Bouquets of Bismuth Telluride Nanoplates: Room-Temperature Synthesis and Thermoelectric Properties

We report the synthesis and properties of sphere-shaped microscale aggregates of bismuth telluride nanoplates. We obtain porous microspheres by reducing bismuth chloride and orthotelluric acid with hydrazine in the presence of thioglycolic acid-which serves as the shape-and size-directing agent-followed by room-temperature aging-which promotes nanoplate aggregation. Thin film assemblies of the nanoplate microspheres exhibit n-type behavior due to sulfur doping and a Seebeck coefficient higher than that reported for assemblies of chalcogenide nanostructures. Adaptation of our scalable approach to synthesize and hierarchically assemble nanostructures with controlled doping could be attractive for tailoring novel thermoelectric materials for applications in high-efficiency refrigeration and harvesting electricity from heat.

Oxovanadium(IV) complexes of phenanthroline bases: the dipyridophenazine complex as a near-IR photocytotoxic agent

Oxovanadium(IV) complexes [VOCl(B)(2)]Cl (1-3) of phenanthroline bases (B), viz. 1,10-phenanthroline (phen in 1), dipyrido[3,2-d: 2', 3'-f] quinoxaline (dpq in 2) and dipyrido[3,2-a: 2', 3'-c] phenazine (dppz in 3), have been prepared, characterized and their DNA and protein binding, photo-induced DNA and protein cleavage activity andm photocytotoxicity have been studied. Complex 2, structurally characterized by X-ray crystallography, shows the presence of a vanadyl group in VOClN4 coordination geometry. The dpq ligand displays a chelating mode of binding with a N-donor site trans to the oxo-group. The chloride ligand is cis to the oxo-group. The one-electron paramagnetic complexes show a d-d band near 715 nm in 15% DMF-Tris-HCl buffer. The complexes are redox active exhibiting a V(IV)/V(III) redox couple within -0.5 to -0.7 V vs. SCE in 20% DMF-Tris-HCl/0.1 M KCl. The complexes bind to calf thymus (CT) DNA in the order: 3 (dppz) > 2 (dpq) > 1 (phen). The binding data reveal the groove and/or partial intercalative DNA binding nature of the complexes. The complexes show chemical nuclease'' activity in the dark in the presence of 3-mercaptopropionic acid or hydrogen peroxide via a hydroxyl radical pathway. The dpq and dppz complexes are efficient photocleavers of DNA in UV-A light of 365 nm forming reactive singlet oxygen (O-1(2)) and hydroxyl radical ((OH)-O-center dot) species. Complexes 2 and 3 also show DNA cleavage activity in red light (> 750 nm) by an exclusive (OH)-O-center dot pathway. The complexes display a binding propensity to bovine serum albumin (BSA) protein giving K-BSA values in the range of 7.1 x 10(4)-1.8 x 10(5) M-1. The dppz complex 3 shows BSA and lysozyme protein cleavage activity in UV-A light of 365 nm via (OH)-O-center dot pathway. The dppz complex 3 exhibits significant PDT effect in human cervical cancer HeLa cells giving IC50 values of 1.0 mu M and 12.0 mu M in UV-A and visible light, respectively (IC50 = > 100 mu M in the dark).

Numerical studies on channel formation and growth during solidification: Effect of process parameters

In the present work, solidification of a hyper-eutectic ammonium chloride solution in a bottom-cooled cavity (i.e. with stable thermal gradient) is numerically studied. A Rayleigh number based criterion is developed, which determines the conditions favorable for freckles formation. This criterion, when expressed in terms of physical properties and process parameters, yields the condition for plume formation as a function of concentration, liquid fraction, permeability, growth rate of a mushy layer and thermophysical properties. Subsequently, numerical simulations are performed for cases with initial and boundary conditions favoring freckle formation. The effects of parameters, such as cooling rate and initial concentration, on the formation and growth of freckles are investigated. It was found that a high cooling rate produced larger and more defined channels which are retained for a longer durations. Similarly, a lower initial concentration of solute resulted in fewer but more pronounced channels. The number and size of channels are also found to be related to the mushy zone thickness. The trends predicted with regard to the variation of number of channels with time under different process conditions are in accordance with the experimental observations reported in the literature.

Tendency toward crossover of the effective susceptibility exponent from its doubled Ising value to its doubled mean-field value near a double critical point

The critical behavior of osmotic susceptibility in an aqueous electrolyte mixture 1-propanol (1P)+water (W)+potassium chloride is reported. This mixture exhibits re-entrant phase transitions and has a nearly parabolic critical line with its apex representing a double critical point (DCP). The behavior of the susceptibility exponent is deduced from static light-scattering measurements, on approaching the lower critical solution temperatures (TL’s) along different experimental paths (by varying t) in the one-phase region. The light-scattering data analysis substantiates the existence of a nonmonotonic crossover behavior of the susceptibility exponent in this mixture. For the TL far away from the DCP, the effective susceptibility exponent γeff as a function of t displays a nonmonotonic crossover from its single limit three-dimensional (3D)-Ising value ( ∼ 1.24) toward its mean-field value with increase in t. While for that closest to the DCP, γeff displays a sharp, nonmonotonic crossover from its nearly doubled 3D-Ising value toward its nearly doubled mean-field value with increase in t. The renormalized Ising regime extends over a relatively larger t range for the TL closest to the DCP, and a trend toward shrinkage in the renormalized Ising regime is observed as TL shifts away from the DCP. Nevertheless, the crossover to the mean-field limit extends well beyond t>10−2 for the TL’s studied. The observed crossover behavior is attributed to the presence of strong ion-induced clustering in this mixture, as revealed by various structure probing techniques. As far as the critical behavior in complex or associating mixtures with special critical points (like the DCP) is concerned, our results indicate that the influence of the DCP on the critical behavior must be taken into account not only on the renormalization of the critical exponent but also on the range of the Ising regime, which can shrink with decrease in the influence of the DCP and with the extent of structuring in the system. The utility of the field variable tUL in analyzing re-entrant phase transitions is demonstrated. The effective susceptibility exponent as a function of tUL displays a nonmonotonic crossover from its asymptotic 3D-Ising value toward a value slightly lower than its nonasymptotic mean-field value of 1. This behavior in the nonasymptotic, high tUL region is interpreted in terms of the possibility of a nonmonotonic crossover to the mean-field value from lower values, as foreseen earlier in micellar systems.

Dimethyl sulfide and other biogenic volatile organic compound emissions from branching coral and reef seawater: Potential sources of secondary aerosol over the Great Barrier Reef

Volatile organic compounds (VOCs) in the headspace of bubble chambers containing branches of live coral in filtered reef seawater were analysed using gas chromatography with mass spectrometry (GC-MS). When the coral released mucus it was a source of dimethyl sulfide (DMS) and isoprene; however, these VOCs were not emitted to the chamber headspace from mucus-free coral. This finding, which suggests that coral is an intermittent source of DMS and isoprene, was supported by the observation of occasional large pulses of atmospheric DMS (DMSa) over Heron Island reef on the southern Great Barrier Reef (GBR), Australia, in the austral winter. The highest DMSa pulse (320 ppt) was three orders of magnitude less than the DMS mixing ratio (460 ppb) measured in the headspace of a dynamically purged bubble chamber containing a mucus-coated branch of Acropora aspera indicating that coral reefs can be strong point sources of DMSa. Static headspace GC-MS analysis of coral fragments identified mainly DMS and seven other minor reduced sulfur compounds including dimethyl disulfide, methyl mercaptan, and carbon disulfide, while coral reef seawater was an indicated source of methylene chloride, acetone, and methyl ethyl ketone. The VOCs emitted by coral and reef seawater are capable of producing new atmospheric particles < 15 nm diameter as observed at Heron Island reef. DMS and isoprene are known to play a role in low-level cloud formation, so aerosol precursors such as these could influence regional climate through a sea surface temperature regulation mechanism hypothesized to operate over the GBR.

The generalized anomeric effect in the 1,3-thiazolidines: Evidence forboth sulphur and nitrogen as electron donors. Crystal structures of various N-acylthiazolidines including mercury(II) complexes. Possible relevance to penicillin action

Evidence for the generalized anomeric effect (GAE) in the N-acyl-1,3-thiazolidines, an important structural motif in the penicillins, was sought in the crystal structures of N-(4-nitrobenzoyl)-1,3-thiazolidine and its (2:1) complex with mercuric chloride, N-acetyl-2-phenyl-1,3-thiazolidine, and the (2:1) complex of N-benzoyl-1,3-thiazolidine with mercuric bromide. An inverse relationship was generally observed between the. C-2-N and C-2-S bond lengths of the thiazolidine ring, supporting the existence of the GAE. (Maximal bond length changes were similar to 0.04 angstrom for C-2-N-3, S-1-C-2, and similar to 0.08 angstrom for N-3-C-6.) Comparison with N-acylpyrrolidines and tetrahydrothiophenes indicates that both the nitrogen-to-sulphur and sulphur-to-nitrogen GAE's operate simultaneously in the 1,3-thiazolidines, the former being dominant. (This is analogous to the normal and exo-anomeric effects in pyranoses, and also leads to an interesting application of Baldwin's rules.) The nitrogen-to-sulphur GAE is generally enhanced in the mercury(II) complexes (presumably via coordination at the sulphur); a 'competition' between the GAE and the amide resonance of the N-acyl moiety is apparent. There is evidence for a 'push-pull' charge transfer between the thiazolidine moieties in the mercury(II) complexes, and for a 'back-donation' of charge from the bromine atoms to the thiazolidine moieties in the HgBr2 complex. (The sulphur atom appears to be sp(2) hybridised in the mercury(II) complexes, possibly for stereoelectronic reasons.) These results are apparently relevant to the mode of action of the penicillins. (c) 2006 Elsevier B.V. All rights reserved.

Energy harvesting using ionic electro-active polymer thin films with Ag-based electrodes

In this paper we employ the phenomenon of bending deformation induced transport of cations via the polymer chains in the thickness direction of an electro-active polymer (EAP)-metal composite thin film for mechanical energy harvesting. While EAPs have been applied in the past in actuators and artificial muscles, promising applications of such materials in hydrodynamic and vibratory energy harvesting are reported in this paper. For this, functionalization of EAPs with metal electrodes is the key factor in improving the energy harvesting efficiency. Unlike Pt-based electrodes, Ag-based electrodes have been deposited on an EAP membrane made of Nafion. The developed ionic metal polymer composite (IPMC) membrane is subjected to a dynamic bending load, hydrodynamically, and evaluated for the voltage generated against an external electrical load. An increase of a few orders of magnitude has been observed in the harvested energy density and power density in air, deionized water and in electrolyte solutions with varying concentrations of sodium chloride (NaCl) as compared to Pt-based IPMC performances reported in the published literature. This will have potential applications in hydrodynamic and residual environmental energy harvesting to power sensors and actuators based on micro-andn nano-electro-mechanical systems (MEMS and NEMS) for biomedical,maerospace and oceanic applications.