Depolymerisation and biodegradation of a synthetic tanning agent by activated sludges, the bacteria Arthrobacter globiformis and Comamonas testosteroni, and the fungus Cunninghamella polymorpha

Degradation of a synthetic tanning agent CNSF (a condensation product of 2-naphthatenesulfonic acid (2-NSA) and formaldehyde) by four activated sludges, two previously characterised bacterial strains, Arthrobacter sp. 2AC and Comamonas sp. 4BC, and the fungus Cunninghamella polymorpha, was studied in batch culture at 25 degrees C by determining the changes in the concentrations of CNSF and its component monomers and oligomers (n2-n11). The loss of individual oligomers was correlated with the length of the NSA-CH2 chain. Approximately 25% of the total CNSF was degraded (i.e. mineralised) by the microbes contained in the four activated sludges and by the two bacterial isolates but with different lag phases and at different overall rates. The decline in CNSF concentration was due almost entirely to the biodegradation of the monomers (34.3% of CNSF) and, in particular, 2-NSA (27% of CNSF). There was no change in the n2-n 11 components. The growth of C. polymorpha, on the other hand, arose from extracellular depolymerisation of CNSF oligomers and the biodegradation of the lower molecular mass products. Between 38% and 42% of total CNSF was degraded by C. polymorpha at 25 degrees C. The order of oligomer degradation was inversely related to degree of polymerisation. Eighty percent and 90% of the n4 and n5 and 100% oligomers n6-n11 were degraded after 120 h. At a higher temperature (37 degrees C) oligomers n4-n11 were degraded completely after 120 h. A combination of biodegradation (75%) and sorption to fungal biomass (25%) accounted for the measured loss of all oligomers from the solution phase. The CNSF degradation rates and the volume of fungal biomass produced (and therefore the extent of biosorption) were dependent on the presence of a second carbon source (both optimum at glucose 5 g/l). This is the first report that identifies and distinguishes between depolymerisation, sorption and biodegradation processes in the removal of CNSF and its component oligomers. The use of combinations of the depolymerising fungus C. polymorpha, and the monomer-degrading bacteria, Arthrobacter sp. 2AC and Comamonas sp. 4BC, have potential for wastewater treatment.

Chemical and structural disorder in eumelanins: A possible explanation for broadband absorbance

We report the results of an experimental and theoretical study of the electronic and structural properties of a key eumelanin precursor-5,6,-dihydroxyindole-2-carboxylic acid ( DHICA) - and its dimeric forms. We have used optical spectroscopy to follow the oxidative polymerization of DHICA to eumelanin and observe red shifting and broadening of the absorption spectrum as the reaction proceeds. First principles density functional theory calculations indicate that DHICA oligomers ( possible reaction products of oxidative polymerization) have the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital red-shifted gaps with respect to the monomer. Furthermore, different bonding configurations ( leading to oligomers with different structures) produce a range of gaps. These experimental and theoretical results lend support to the chemical disorder model where the broadband monotonic absorption characteristic of all melanins is a consequence of the superposition of a large number of nonhomogeneously broadened Gaussian transitions associated with each of the components of a melanin ensemble. These results suggest that the traditional model of eumelanin as an amorphous organic semiconductor is not required to explain its optical properties and should be thoroughly reexamined. These results have significant implications for our understanding of the physics, chemistry, and biological function of these important biological macromolecules. Indeed, one may speculate that the robust functionality of melanins in vitro is a direct consequence of its heterogeneity, i.e., chemical disorder is a "low cost" natural resource in these systems

Quantitative fluorescence spectra and quantum yield map of synthetic pheomelanin

Spectroscopic studies of pheomelanin and its constituents have been sparse. These data present what is by far the most complete description of the fluorescence characteristics of synthetic pheomelanin. Emission spectra between 260 and 600 nm were acquired,for excitation wavelengths between 250 and 500 nm at 1-nm intervals. A quantum yield map is also presented, correcting the fluorescence intensities for differences in species concentration and molar absorptivity. These fluorescence features exhibit interesting similarities and differences to eumelanin, and these data are interpreted with respect to possible chemical structures. Overall, these data suggest that pheomelanin oligomers may be more tightly coupled than those of eumelanin. Finally, the quantum yield is shown to be on the order of 10(-4) and exhibit a complex dependence on excitation energy, varying by a factor of 4 across the energies employed here. (c) 2006 Wiley Periodicals, Inc.

Anti-proliferative effects of novel Glyco-lipid-arsenicals (III) on MCF-7 human breast cancer cells

Arsenic trioxide appears to be effective in the treatment of pro-myelocytic leukaemia. The substituted phenylarsen(III)oxides are highly polar, they have a high tendency to undergo oxidation to As (V) and to form oligomers, to prevent this we protected the As-(OH)2 group as cyclic dithiaarsanes. To increase the compound's biological stability and passive diffusion we conjugated the compound of interest with lipoamino acids (Laas). Alternatively, we further conjugated the dithiaarsane derivative with a carbohydrate to utilize active transport systems and to target compound. We investigated two novel glyco-lipid arsenicals (III) (compounds 9 and 11) for their ability to initiate MCF-7 breast cancer cell death and characterized the mechanism by which death was initiated. A significant decrease in MCF-7 cell proliferation was observed using 1 μM and 10 μM compound (11) and 10 μM of compound (9). Treatment with compound (11) triggered apoptosis of MFC-7 cells while compound (9) induced inhibition of cellular proliferation was not via rapid induction of apoptosis and more likely reflected necrosis and/ or alterations in the cell cycle. Differences in the anti-proliferative potency of the two compounds indicate that structural modifications influence effectiveness. © 2006 Bentham Science Publishers Ltd.

Novel monoclonal antibody recognition of oxidative DNA damage adduct, deoxycytidine-glyoxal

Glyoxal, a reactive aldehyde, is a decomposition product of lipid hydroperoxides, oxidative deoxyribose breakdown, or autoxidation of sugars, such as glucose. It readily forms DNA adducts, generating potential carcinogens such as glyoxalated deoxycytidine (gdC). A major drawback in assessing gdC formation in cellular DNA has been methodologic sensitivity. We have developed an mAb that specifically recognizes gdC. Balb/c mice were immunized with DNA, oxidatively modified by UVC/hydrogen peroxide in the presence of endogenous metal ions. Although UVC is not normally considered an oxidizing agent, a UVC/hydrogen peroxide combination may lead to glyoxalated bases arising from hydroxyl radical damage to deoxyribose. This damaging system was used to induce numerous oxidative lesions including glyoxal DNA modifications, from which resulted a number of clones. Clone F3/9/H2/G5 showed increased reactivity toward glyoxal-modified DNA greater than that of the immunizing antigen. ELISA unequivocally showed Ab recognition toward gdC, which was confirmed by gas chromatography-mass spectrometry of the derivatized adduct after formic acid hydrolysis to the modified base. Binding of Ab F3/9 with glyoxalated and untreated oligomers containing deoxycytidine, deoxyguanosine, thymidine, and deoxyadenosine assessed by ELISA produced significant recognition (p 0.0001) of glyoxal-modified deoxycytidine greater than that of untreated oligomer. Additionally, inhibition ELISA studies using the glyoxalated and native deoxycytidine oligomer showed increased recognition for gdC with more than a 5-fold difference in IC50 values. DNA modified with increasing levels of iron (II)/EDTA produced a dose-dependent increase in Ab F3/9 binding. This was reduced in the presence of catalase or aminoguanidine. We have validated the potential of gdC as a marker of oxidative DNA damage and showed negligible cross-reactivity with 8-oxo-2'-deoxyguanosine or malondialdehyde-modified DNA as well as its utility in immunocytochemistry. Formation of the gdC adduct may involve intermediate structures; however, our results strongly suggest Ab F3/9 has major specificity for the predominant product, 5-hydroxyacetyl-dC.

Chemical synthesis of oligonucleotides containing (M+4) guanine

HPLC MS/MS has shown great potential in the measurement of DNA oxidative damage. Its accuracy depends on the use of multiply isotopically labelled internal standards. In this report, multiply isotopically labelled (M + 4) guanine internal standards were prepared in the form of base, nucleoside, as well as DNA oligomer. To our knowledge, this is the first chemical synthesis of oligomers containing (M + 4) guanine, and we believe that they can be used to develop a procedure that can make further improvement to the existing analytical procedures. Copyright © Taylor & Francis, Inc.

The effect of PEO length on the self-assembly of poly(ethylene oxide)−tetrapeptide conjugates prepared by “click” chemistry

Two series of poly(ethylene oxide)-tetrapeptide conjugates have been prepared using a “Click” reaction between an alkyne-modified tetra(phenylalanine) or tetra(valine) and various azide-terminated poly(ethylene oxide) (PEO) oligomers. Three different PEO precursors were used to prepare these conjugates, with number-average molecular weights of 350, 1200, and 1800 Da. Assembly of mPEO-F4-OEt and mPEO-V4-OEt conjugates was achieved by dialysis of a THF solution of the conjugate against water or by direct aqueous rehydration of a thin film. The PEO length has a profound effect on the outcome of the self-assembly, with the F4 conjugates giving rise to nanotubes, fibers, and wormlike micelles, respectively, as the length of the PEO block is increased. For the V4 series, the propensity to form ß-sheets dominates, and hence, the self-assembled structures are reminiscent of those formed by peptides alone, even at the longer PEO lengths. Thus, this systematic study demonstrates that the self-assembly of PEO-peptides depends on both the nature of the peptides and the relative PEO block length.

Living cationic polymerization of isobutene

The polymerization of isobutene initiated by 1-chloro-1-phenylethane has been investigated, and molecular weight studies conducted using size exclusion chromatography. Polymerizations carried out in a 40/60 (v/v) mixture of dichloromethaneIcyclohexane, using titanium (IV) chloride as a catalyst in the presence of pyridine at -30 °C were found to be controlled and living. The number average molecular weights of the polymers increased linearly with monomer conversion, and the molecular weight distributions were between 1.15 and 1.20. Efficiencies of initiation were between 80 and 100%, and evidence was found to suggest that backbiting to the initiator had occurred, resulting in the formation of cyclic oligomers during the early stages of polymerization. The kinetics of polymerization can be explained in terms of active species in. equilibrium with dormant species. The effects of temperature. and dielectric constant on this equilibrium were studied and a model based upon the Fuoss equation was developed. Pyridine was found to behave as proton trap in the system, and when it was used in excess the rate of polymerization was retarded. By assuming that the catalyst and pyridine formed a one to one complex, it was possible to show that the reaction was second order with respect to the catalyst. The synthesis of low molecular weight polyisobutenes was studied. When the concentration of initiator was increased relative to that of the isobutene, such that the theoretical degree of polymerization was 20 or less, the rate of initiation was slow compared to propagation. The efficiency of initiation in these polymerizations was typically between 30 and 40 %. Optimal conditions of temperature. and.catalyst concentration were established, leading to a 60 % efficiency of initiation. A one-pot synthesis of phenol end-capped polyisobutene was attempted by adding phenol at the end of a living polymerization. Evidence to substantiate the existence of capped polymer chains in the resultant product was inconclusive. Block copolymerizations of oxetane and isobutene were conducted using 1-chloro-1phenylethane/TiCl4, but no copolymer or oxetane homopolymer could be isolated.

Atom transfer radical polymerisation - towards the synthesis of a fully-functional photorefractive polymer

Atom transfer radical polymerisation (ATRP) of styrene in xylene solution initiated with 1-phenylethyl bromide and mediated by CuBr/N-propyl-2- pyridinemethanimine catalyst complex was studied. The polymerisation was ill-controlled, yielding polymers with broad molecular weight distributions and values of number average molecular weight considerably higher than the theoretical values calculated from 100% initiator efficiency. The degree of control afforded over the polymerisation was enhanced by use of a more soluble catalyst complex, CuBr/N-octyl-2-pyridinemethanimine. Furthermore, the use of a more polar solvent, diglyme, generated a homogeneous catalyst complex that facilitated the production of polymers having narrow molecular weight distributions (1.10 < PDi < 1.20). The kinetics of the atom transfer radical polymerisation of methyl methacrylate at 90°C in diglyme solution initiated with ethyl-2-bromoisobutyrate and mediated by CuBr/N-octyl-2-pyridinemethanimine was studied and the orders of the reaction were established. The effect on the rate of polymerisation of the ratio of CuBr:N-octyl-2-pyridinemethanimine was also determined. The temperature dependencies of the rate of polymerisation of methyl methacrylate in diglyme solution and xylene solution were studied, and were found to be non-linear and dependent upon the polarity of the solvent. The use of highly polar aprotic solvents, such as N,N-dimethylformamide and dimethylsulphoxide, was found to be detrimental to the degree of control afforded over the polymerisation of methyl methacrylate. This was circumvented by use of a 5-fold excess, over that conventionally used, of catalyst complex. The atom transfer radical polymerisation of (4-nitrophenyl)-[3-[N-[2- (methacryloyloxy)ethyl]carbazolyl]]diazene in dimethyl sulphoxide solution was studied. Although homopolymerisation yielded only oligomers, copolymerisation of this monomer with methyl methacrylate was found to be readily achievable. Keywords: ATRP, Styrene; Methyl methacrylate; Polar solvents; Fully-functional photorefractive polymer. 2

The cationic ring-opening polymerization of cyclic ethers

The kinetics and mechanisms of ring opening polymerization and copolymerizntion of different cyclic ethers were studied using mainly a cationic system of iinitiation. BF30Et2/ethanediol. The cyclic ethers reacted differently showing that ring strain and basicity are the main driving forces in cationic ring opening polymerizaion. In most cases it was found that the degree of polymerization is controlled kinetically via terminations with the counterion and the monomers, and that the contribution of each type of reaction to the overall termination differs markedly. The Gel permeation chromatography studies showed that the molecular weight distribution of the samples of polyoxetanes were bimodal. This was in accordance with previous work establishing that the cyclic tetramer is found in much higher proportions than any of the other cyclic oligomers. However the molecular weight distribution of the copolymers made from oxetane and THF or from oxetane and oxepane were shown to be unimodal. These observations could be explained by a change in the structure of the growing end involved in the cationic polymerization. In addition crown ethers like dibenzo-crown-6 and compounds such as veratrole are believed to stabilise the propagating end and promote the formation of living polymers from oxetane.

The synthesis, characterisation and electrical conductivity of poly(styrene-co-acetylene)

A novel metathesis catalyst for the polymerisation of acetylene has been developed. The polyacetylene produced by this new catalyst has been characterised by infra-red and NMR spectroscopy. The conductivity of the pristine material has been studied as a function of temperature, pressure and frequency. The effect on the conductivity of doping the material has also been investigated. The new metathesis catalyst has been incorporated into an anionic-to-metathesis transformation reaction. This novel reaction has been used to prepare samples of poly(styrene-co-acetylene). The copolymer has been characterised using U.V./Visible, NMR, infra-red spectroscopy and the surface morphology looked at using scanning electron microscopy. GPC was also used to give some idea of the molecular weights of the materials prepared. The conductivity of the copolymer has been studied as a function of temperature, pressure and frequency. The effect of doping on the conductivity the material has also been investigated. The conductivity results obtained from both materials have been used to try and gain an insight into the mechanism of the conduction processes occurring within the materials. An attempt has also been made to synthesise polyacetylene oligomers (polyenes) by modifying the Ziegler/Natta type catalysts commonly used to synthesise polyacetylene. The polyenes were characterised using U.V./Visible and infra-red spectroscopy together with GPC and GCMS.

Functionalised polymers

Synthetic routes to polymers possessing functional groups were studied. Direct functionalisation of poly(vinyltoluene) by lithiation and carboxylation resulted in the expected carboxylic acid but reaction was complicated by the production of a mixture of products. Reaction occurred both at the polymer backbone and at the pendant methyl group. Reaction with ethyl formate was also difficult to control and a secondary alcohol was formed even when an excess of the carbonyl compounds was employed. Grignard formation of poly(bromostyrene) was successful but once formed, the derivative rearranged resulting in chain scission and degradation of the polymer. Therefore subsequent reactions of the Grignard reagent with carbonyl groups were unsuccessful in producing functionalised polymers. Reactions of vinyltoluene monomer were more successful. Although complications arose when lithiation and carboxylation of the monomer were carried out using lithium diisopropylamide because the carboxylic acid product reacted with the excess lithium diisopropylamide present, metallation by potassium t-butoxide followed by reaction with 2-(3-chloropropyl)-2-methyl-1,3-dioxalane resulted in the formation of 2-methyl-2(4-(vinylphenyl)-butyl-1,3,-dioxalane. The butyllithium initiated anionic polymerisation of this protected monomer resulted in a polymer which had a very narrow molecular weight distribution (Mw/Mn= 1.05) and subsequent hydrolysis of the polymer resulted in poly(6(vinylphenyl)-hexan-2-one) which was derivatised with 2,4 dinitrophenyl-hydrazine. Functionalisation by modification of the siloxane derivative 3-(methylpropenoxycarbonyl)ltrimethoxysilane was unsuccessful. The acid catalysed exchange reactions of this monomer with alcohols such as eugenol, octan-1-ol, pentan-1-ol, and hexan-1-ol were inefficient, resulting in a mixture of products and unreacted starting materials.

Chemical synthesis of DNA and RNA containing thio-substituted bases and their post-synthetic modifications

Modified oligonucleotides containing sulphur group have been useful tools for studies of carcinogenesis, protein or nucleic acid structures and functions, protein-nucleic acid interactions, and for antisense modulation of gene expression. One successful example has been the synthesis and study of oligodeoxynucleotides containing 6-thio-2'-deoxyguanine. 6-Thio-2-deoxyguanosine was first discovered as metabolic compound of 6- mercaptopurine (6-MP). Later, it was applied as drug to cure leukaemia. During the research of its toxicity, a method was developed to use the sulphur group as a versatile position for post-synthetic modification. The advantage of application of post-synthetic modification lies in its convenience. Synthesis of oligomers with normal sequences has become routine work in most laboratories. However, design and synthesis of a proper phosphoramidite monomer for a new modified nucleoside are always difficult tasks even for a skilful chemist. Thus an alternative method (post-synthetic method) has been invented to overcome the difficulties. This was achieved by incorporation of versatile nucleotides into oligomers which contain a leaving group, that is sufficiently stable to withstand the conditions of synthesis but can be substituted by nucleophiles after synthesis, to produce, a series of oligomers each containing a different modified base. In the current project, a phosphoramidite monomer with 6-thioguanine has been successfully synthesised and incorporated into RNA. A deprotection procedure, which is specific for RNA was designed for oligomers containing 6-thioguanosine. The results were validated by various methods (UV, HPLC, enzymatic digestion). Pioneer work in utilization of the versatile sulphur group for post-synthetic modification was also tested. Post-synthetic modification was also carried out on DNA with 6- deoxythioguanosine. Electrophilic reagents with various functional groups (alphatic, aromatic, fluorescent) and bi-functional groups have been attached with the oligomers.

Inorganic surface treatments for concrete protection

Carbonated cement paste surfaces were characterised prior to application of surface treatments. Their chemical and physical properties varied with distance from the surface and method of carbonation. From the surface inwards the pH of expressed pore solutions and porosity were observed to increase. Hardness increased after natural carbonation, but decreased after accelerated carbonation. Generally, accelerated carbonation caused more extreme changes. Investigations were carried out on four concrete surface hardening treatments; two sodium silicates and two silicofluorides. These treatments penetrated and hardened the surface of naturally dried uncarbonated cement paste to a depth fo 250m. Silicofluorides reacted with uncarbonated and carbonated cement pastes to form calcium fluoride. The question of how sodium silicates harden the surface remains unanswered. Surface hardeners do not significantly affect the rate of carbonation, and are unsuitable for re-alkalising carbonated cement paste. Water repellent treatments studied include a silane, a siloxane and a silicone. The silane exhibited the maximum penetration, up to 24mm under favourable conditions, but penetration in all cases was limited by moisture in the substrate. Water repellent treatments slow down water vapour diffusion but, with time, internal moisture levels should reflect external relative humidities. Water repellents may be used to reduce carbonation-induced corrosion where ingress of moisture from intermittent wetting may be slowed. However, treatment with water repellents can temporarily push the carbonation front deeper into the concrete.

A copper-hydrogen peroxide redox system induces dityrosine cross-links and chemokine oligomerisation

The activity of the chemoattractant cytokines, the chemokines, in vivo is enhanced by oligomerisation and aggregation on glycosaminoglycan (GAG), particularly heparan sulphate, side chains of proteoglycans. The chemokine RANTES (CCL5) is a T-lymphocyte and monocyte chemoattractant, which has a minimum tetrameric structure for in vivo activity and a propensity to form higher order oligomers. RANTES is unusual among the chemokines in having five tyrosine residues, an amino acid susceptible to oxidative cross-linking. Using fluorescence emission spectroscopy, Western blot analysis and LCMS-MS, we show that a copper/H2O2 redox system induces the formation of covalent dityrosine cross-links and RANTES oligomerisation with the formation of tetramers, as well as higher order oligomers. Amongst the transition metals tested, namely copper, nickel, mercury, iron and zinc, copper appeared unique in this respect. At high (400 µM) concentrations of H2O2, RANTES monomers, dimers and oligomers are destroyed, but heparan sulphate protects the chemokine from oxidative damage, promoting dityrosine cross-links and multimer formation under oxidative conditions. Low levels of dityrosine cross-links were detected in copper/H2O2-treated IL-8 (CXCL8), which has one tyrosine residue, and none were detected in ENA-78 (CXCL5), which has none. Redox-treated RANTES was fully functional in Boyden chamber assays of T-cell migration and receptor usage on activated T-cells following RANTES oligomerisation was not altered. Our results point to a protective, anti-oxidant, role for heparan sulphate and a previously unrecognised role for copper in chemokine oligomerisation that may offer an explanation for the known anti-inflammatory effect of copper-chelators such as penicillamine and tobramycin.