Incorporation of [14C]Methanol and [14C]Bicarbonate by Hyphomicrobium sp. 53-49 under Various Growth Conditions: Aerobic,Denitrifying and Autotrophic

A study was made of the incorporation of methanol and bicarbonate into the cell constituents of denitrifying or aerobic methanol grown and autotrophic H₂–O₂–CO₂ grown Hyphomicrobium sp. 53-49. Cells were incubated with [¹⁴C]methanol or [¹⁴C]bicarbonate, and the distribution of the radioactivity in the nonvolatile constituents of ethanol extracts of cells was examined. When denitrifying grown cells were incubated with [¹⁴C]methanol, the major part of the radioactivity was fixed to serine as the first stable compound. Aerobic methanol grown cells also fixed [¹⁴C]methanol mainly to serine. These results suggest that methanol grown cells assimilate methanol by the serine pathway. When denitrifying or aerobic methanol grown cells were incubated with [¹⁴C]bicarbonate, malate was mainly observed as a nonvolatile compound in the initial period of the incubation. Autotrophic grown cells also fixed the major part of [¹⁴C]bicarbonate to malate. In this case, phosphoglyceric acid was found in the phosphorylated compounds area.     

Endogenous Oxidative DNA Damage,Aging, and Cancer

Progress in identifying the important endogenous processes damaging DNA and developing methods to assay this damage in individuals is presented. This approach may aid studies on modulation of cancer and aging.

The endogenous background level of oxidant-induced DNA damage in vivo has been assayed by measuring 8-hydroxydeoxyguanosine (oh⁸dG), thymine glycol and thymidine glycol in urine and oh⁸dG in DNA. oh⁸dG is one of about 20 adducts found on oxidizing DNA, e.g., by radiation. The level of oxidative DNA damage as measured by oh⁸dG in normal rat liver is shown to be extensive, especially in mtDNA (1/130,000 bases in nuclear DNA and 1/8,000 bases in mitochondrial DNA). We also discuss three hitherto unrecognized antioxidants in man.     

NMR Study on The Tuning of North ⇆ South Equilibrium in Nucleos(t)ides by Metal Ion Interactions

Abstract

The NMR study on the interactions of dGpMe (1), MepdG (2) and dG (3) with Mg²⁺, Zn²⁺ and Hg²⁺ ions in D₂O solution has shown that binding of softer metal ions to N7 shifts N ? S pseudorotational equilibrium towards N-type conformations. At the same time the population of the anti conformers is slightly increased.     

Base pairing equilibria between polynucleotides and complementary monomers

Equilibrium dialysis measurements and optical melting curve data have been used to study the formation and stability of a number of complexes between polynucleotides and complementary monomers. The cooperativity parameter, (dθ/d ln c)_{θ = 0.5}, where θ is the fraction of U or C residues complexed, and c is the concentration of free monomer has been measured as 1.4 for the 2:1 poly U:d-adenosine-complex, and 2.0₅ for the 2:1 poly C:d-guanosiue complex at pH 7. The variation of T_m with c for several complexes has been used to calculate their partial molar enthalpies of formation at the midpoint of the transition: in 1.0 MNa ⁺ at pH 7, for the 2:1 complex of poly-U with 2-amino-adenine, this is ? 18.7 kcal/mole of 2-amino-adenine, for poly-U with adenosine it is ? 18.7 kcal/ mole; for poly-C with dG, it is ? 16.8 kcal/mole. These results do not agree very well with calorimetric integral heats of reaction reported in the literature.³³ Complexes with random copolymers were also studied. The random copolymer, poly-UC, can form a mixed complex with dG and either dA or 2-amino-adenosine; the binding of dG is enhanced by an adenine derivative and vice versa.Similarly, poly AC can form a mixed complex with dG and 3-methyl-xanthine. In each case, it appears that the ideal composition is a 2:1 hydrogen-bonded complex, but the actual stoichiometry is such that each base on the random polynucleotide binds less than one-half of a molecule of its complementary monomer. Poly UG can bind dG and dA, but in a less cooperative and specific way.     

NMR Studies of a DNA Containing 8-Methoxydeoxyguanosine

Abstract

¹H NMR experiments have been undertaken to elucidate the structural effects of methoxy substitution at the C8 of a deoxyguanosine residue in a self-complementary dodecadeoxyribonucleotide, d(C-G-C-mo⁸G-A-A-T-T-C-G-C-G), duplex, which has an 8-methoxy-2′-deoxyguanosine (mo⁸dG) residue at the 4th position. NMR data indicate that the mo⁸dG residue takes an anti glycosidic conformation in a mo⁸dG(anti):dC(anti) base-pair structure in a B-form duplex. The thermal stability of the duplex is reduced, but the overall structure is much the same as that of the unmodified d(C-G-C-G-A-A-T-T-C-G-C-G) duplex.     

Lipids and DNA oxidation in Staphylococcus aureus as a consequence of oxidative stress generated by ciprofloxacin

Ciprofloxacin induced an increment of reactive oxygen species in sensitive strains of Staphylococcus aureus leading to oxidative stress detected by chemiluminescence while resistant strains did not suffer such stress. Oxidation of lipids was performed by employing thiobarbituric acid reaction to detect the formation of the amplified intermediate between reactive species oxygen and cytoplasmic macromolecules, namely malondialdehyde (MDA). The sensitive strain presented higher peroxidation of lipids than the resistant strain. The oxidative consequence for DNA was investigated by means of bacteria incubation with ciprofloxacin and posterior extraction of DNA, which was studied by high performance liquid chromatography (HPLC). Sensitive S. aureus ATCC 29213 showed an increase of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) respect controls without antibiotic; there was evident increase of the ratio between 8-oxodG and deoxyguanosine (dG) as a consequence of oxidation of dG to 8-oxodG considered the major DNA marker of oxidative stress. The resistant strain showed low oxidation of DNA and the analysis of 8-oxodG/dG ratio indicated lesser formation of 8-oxodG than S. aureus ATCC 29213.     

Competition between ligands of glycosyltransferases and horseradish peroxidase for binding sites on intracellular and plasma membranes of HeLa cells

Summary A micro-method for the semi-quantitation of surface-bound horseradish peroxidase (HRP) was developed and was applied to study the competition between ligands of glycosyltransferases and HRP for binding sites on the surface of HeLa cells. Dried coverslip cultures of HeLa cells, fixed in methanol, were placed on 0.3 ml of the incubation medium on parafilm and were incubated for 45 min at 37° C. The incubation medium contained HRP, lysozyme and Ca²⁺ in HEPES buffer, pH 7.2. After washing, the cells were incubated for 60 min at 37° C in HEPES buffer containing 20 mM Ca²⁺. After this treatment, the plasma membranes showed a strong cytochemical reaction for HRP. Most of the HRP was released into buffer solution during a 5 h incubation at 37° C in the absence of Ca²⁺, and was measured by spectrophotometry. The addition of 20 mM Ca²⁺ to the buffer solution prevented the release of most of the HRP from the plasma membranes thus showing that the binding of HRP required Ca²⁺. Ligands of glycosyltransferases were added to the incubation medium with HRP. The amount of HRP released from the cells decreased in relation to the competing potency and concentration of these ligands. The method was applied to estimate the concentration of some ligands of galactosyltransferase and sialyltransferase that caused a 50% decrease in the release of previously-bound HRP. CMP-neuraminic acid and gangliosides showed a higher competing potency to the surface binding of HRP than UDP-galactose and chitotriose. The spectrophotometric analysis was correlated (on duplicate samples) with cytochemical observations. When dried HeLa cells, fixed in methanol, were incubated with HRP, lysozyme and Ca²⁺, without being subsequently incubated with Ca²⁺-containing buffer solution, HRP was also bound to membranes of intracellular granules. Cytochemical observations showed that UDP-galactose and chitotriose competed with the binding of HRP to most of these intracellular membranes whereas CMP-neuraminic acid and gangliosides did not. The possible binding of HRP to galactosyltransferase or sialyltransferase on cellular membranes is discussed.     

A One Step Synthesis of O6-Methyl-2′-deoxyguanosine

Abstract

A single step chemical synthesis of N⁷-methyl-2′-deoxyguanosine (m⁷dG), N¹-methyl-2′-deoxyguanosine (m¹dG) and O⁶-methyl-2′-deoxyguanosine (m⁶dG) is described. The products were separated on the silical gel plates and characterized by nuclear magnetic resonance and mass spectrometry.     

Effects of elevated CO2 and O3 on the rate and duration of grain growth and harvest index in spring wheat (Triticum aestivum L.)

Wheat (Triticum aestivum L.) cv. Minaret was grown in open-top chambers (OTCs) in 1995 and 1996 under three carbon dioxide (CO₂) and two ozone (O₃) levels. Plants were harvested regularly between anthesis and maturity to examine the rate of grain growth (dG/dt; mg d^–1) and the rate of increase in harvest index (dHI/dt;% d^–1). The duration of grain filling was not affected by elevated CO₂ or O₃, but was 12 days shorter in 1995, when the daily mean temperature was over 3 °C higher than in 1996. Season-long exposure to elevated CO₂ (680 μmol mol^–1) significantly increased the rate of grain growth in both years and mean grain weight at maturity (MGW) was up to 11% higher than in the chambered ambient air control (chAA; 383 μmol mol^–1). However, the increase in final yield obtained under elevated CO₂ relative to the chAA control in 1996 resulted primarily from a 27% increase in grain number per unit ground area. dG/dt was significantly reduced by elevated O₃ under ambient CO₂ conditions in 1995, but final grain yield was not affected because of a concurrent increase in grain number. Neither dG/dt nor dHI/dt were affected by the higher mean O₃ concentrations applied in 1996 (77 vs. 66 nmol mol^–1); the differing effects of O₃ on grain growth in 1995 and 1996 observed in both the ambient and elevated CO₂ treatments may reflect the contrasting temperature environments experienced. Grain yield was nevetheless reduced under elevated O₃ in 1996, primarily because of a substantial decrease in grain number. The data obtained show that, although exposure to elevated CO₂ and O₃ individually or in combination may affect both dG/dt and dHI/dt, the presence of elevated CO₂ does not protect against substantial O₃-induced yield losses resulting from its direct deleterious impact on reproductive processes. The implications of these results for food production under future climatic conditions are considered.     

DNA polymorphism: spectroscopic and electro-optic characterizations of Z-DNA and other types of left-handed helical structures induced by Ni2+

CD and uv spectroscopy reveal that the synthetic polynucleotides poly(dG–dC) · poly(dG–dC) and poly(dG–m⁵dC) · poly(dG–m⁵dC) undergo a transition induced by small amounts of Ni⁺⁺ cation from a right-handed B-form to left-handed Z-type conformations. We describe the application of steady-state and transient electric birefringence to the characterization of the transition observed at very low ionic strength (10 mM Tris HCl, pH 7.4). Dialysis experiments show that the changes in spectroscopic and electro-optic properties upon addition of Ni⁺⁺ are completely reversible. The differences in shape of the inverted CD spectra suggest the existence of a family of left-handed conformations, depending on the polymer used and on the amounts of cation added. The stoichiometry required for inducing the Z-conformation of poly(dG–m⁵dC) is 1 cation/4 nucleotide phosphates. The transition is accompanied by a decrease in birefringence, an increase in length, and the more important contribution of a permanent or slowly induced dipole moment to the orientation mechanism. High concentrations of Ni⁺⁺ promote the Z → Z* transition. Upon increasing the Ni⁺⁺ concentration, poly(dG–dC) undergoes a biphasic transition, first to one intermediate conformation that is neither B- nor Z-like and then to a left-handed form that is probably different from Z*. These conversions are accompanied by regular decreases both in birefringence and in chain length, but no transient appears in the field-reversal experiments.     

Anti-inflammatory effects of 8-hydroxy-2′-deoxyguanosine on lipopolysaccharide-induced inflammation via Rac suppression in Balb/c mice

Recently, we observed that 8-hydroxyguanosine triphosphate and 8-hydroxy-2′-deoxyguanosine (oh⁸dG) inactivate Rac and consequently down-regulate the Rac-linked NADPH oxidase, iNOS, and Cox2. Based on these observations, we tested whether oh⁸dG has anti-inflammatory activity in vivo in lipopolysaccharide (LPS)-treated mice. LPS (1 mg/kg, ip)-treated mice exhibit marked inflammatory responses, including increases in proinflammatory cytokines (TNF-α, IL-6, IL-18, and IL-12p70) in serum and infiltration of neutrophils, increased translocation of NF-κB p50 from the cytosol to the nucleus, and phosphorylation of c-Jun in lung tissues. Mice were pretreated with oh⁸dG (up to 60 mg/kg, ip) 4 h before LPS injection, and this pretreatment dose-dependently inhibited the inflammatory responses; the inhibitions observed with 60 mg/kg oh⁸dG were statistically significant. At the same time, oh⁸dG pretreatment inactivated Rac in lung tissues. Oh⁸dG pretreatment (50 mg/kg, ip) also significantly protected against LPS-induced septic death. Furthermore, oh⁸dG was more effective than acetyl salicylic acid in inhibiting these inflammatory responses. 8-Hydroxyguanosine also had some effect but was much weaker than oh⁸dG. The effects of normal nucleosides (dG, G, and A) were negligible or not significant. These results support an anti-inflammatory activity for oh⁸dG, which could be ascribed to its Rac-inactivating action.     

Methodological considerations and factors affecting 8-hydroxy-2′-deoxyguanosine analysis

Oxidative stress is related to a number of diseases due to the formation of reactive oxygen species (ROS). There are also several substances found in the occupational environment or as life style related situations that generates ROS. A stable biomarker for oxidative stress on DNA is 8-hydroxy-2′-deoxyguanosine (8-OH-dG).

A potential problem in the work-up and analysis of 8-OH-dG is oxidation of dG with false high levels as a result of analysis. This paper summarizes and discusses some of the critical moments in terms of auto-oxidation. The removal of transition metals, low temperatures, absence of isotopes (or 2′-deoxyguanosine) and incubation times are all important factors. Removal of oxygen is complicated while the problem is reduced if a nitroxide (TEMPO) is added during work-up. Certain reducing agents and enzymes could be critical if added during work-up.

The application of the ³²P-HPLC method to analyze 8-OH-dG is discussed. The ³²P-HPLC method is suitable for 8-OH-dG analysis and avoids several factors that oxidizes dG by removal of dG before addition of isotopes. Factors of crucial importance (columns, eluents, gradients and detection of ³²P) for the analysis of 8-OH-dG are commented upon and certain recommendations are made to make it possible to apply the ³²P-HPLC methodology for this type of analysis.     

Solution Stability and Degradation Pathway of Deoxyribonucleoside Phosphoramidites in Acetonitrile

The impuritiy profiles of acetonitrile solutions of the four standard O‐cyanoethyl‐N,N‐diisopropyl‐phosphoramidites of 5′‐O‐dimethoxytrityl (DMT) protected deoxyribonucleosides (dG^ib, dA^bz, dC^bz, T) were analyzed by HPLC‐MS. The solution stability of the phosphoramidites decreases in the order T, dC>dA>dG. After five weeks storage under inert gas atmosphere the amidite purity was reduced by 2% (T, dC), 6% (dA), and 39% (dG), respectively. The main degradation pathways involve hydrolysis, elimination of acrylonitrile and autocatalytic acrylonitrile‐induced formation of cyanoethyl phosphonoamidates. Consequently, the rate of degradation is reduced by reducing the water concentration in solution with molecular sieves and by lowering the amidite concentration. Acid‐catalyzed hydrolysis could also be reduced by addition of small amounts of base.     

Multiplication of Legionella pneumophila in HeLa Cells in the Presence of Cytoskeleton and Metabolic Inhibitors

A study has been carried out on the action of cytoskeleton and metabolic inhibitors on intracellular multiplication in HeLa cells of a virulent strain of Legionella pneumophila serogroup 6. The effects of the substances were separately tested on both penetration and intracellular multiplication of L. pneumophila. Only cytochalasin A and 2-deoxy-d -glucose (2dG) affected bacterial internalisation, whereas intracellular multiplication was inhibited by cytochalasins A, B, C, D and J (D being the most active) and by 2dG with a dose-response effect. The action of 2dG was counteracted by 50 mM glucose. Experiments carried out with cytochalasin D and a rhodamine-phalloidin conjugate showed the involvement of cytoskeletal elements in intracellular multiplication of Legionella; compounds acting on microtubules had no effect.     

Growth of Hansenula polymorpha in a methanol-limited chemostat

Hansenula polymorpha has been grown in a methanol-limited continuous culture at a variety of dilution rates. Cell suspensions of the yeast grown at a dilution rate of 0.16 h^-1 showed a maximal capacity to oxidize excess methanol (QO ₂ ^max ) which was 1.6 times higher than the rate required to sustain the growth rate (Q _O2). When the dilution rate was decreased to 0.03 h^-1, QO ₂ ^max of the cells increased to a value of more than 20 times that of Q _O2. The enzymatic basis for this tremendous overcapacity for the oxidation of excess methanol at low growth rates was found to be the methanol oxidase content of the cells. The level of this enzyme increased from 7% to approximately 20% of the soluble protein when the growth rate was decreased from 0.16 to 0.03 h^-1. These results were explained on the basis of the poor affinity of methanol oxidase for its substrates. Methanol oxidase purified from Hansenula polymorpha showed an apparent K _mfor methanol of 1.3 mM in air saturated reaction mixtures and the apparent K _mof the enzyme for oxygen was 0.4 mM at a methanol concentration of 100 mM.The involvement of an oxygen dependent methanol oxidase in the dissimilation of methanol in Hansenula polymorpha was also reflected in the growth yield of the organism. The maximal yield of the yeast was found to be low (0.38 g cells/g methanol). This was not due to a very high maintenance energy requirement which was estimated to be 17 mg methanol/g cells x h.     

Regulatory flexibility of methylotrophic yeasts in chemostat cultures: Simultaneous assimilation of glucose and methanol at a fixed dilution rate

The influence of the composition of methanol/glucose-mixtures as only sources of carbon and energy on growth and regulation of the synthesis of enzymes involved in methanol-dissimilation was studied under chemostat conditions at a fixed dilution rate with the methylotrophic yeasts Hansenula polymorpha and Kloeckera sp. 2201. Both carbon sources were found to be utilized completely independently of the composition of the C₁/C₆ mixture. Using mixtures of ¹⁴C-labelled methanol and glucose the growth yield for glucose was found to be constant for all C₁/C₆-mixtures tested and both yeasts. The growth yield for methanol, however, was reduced by up to 25% when the proportion of methanol in the inflowing medium was lower than 20% (w/w with respect to glucose) for H. polymorpha and 50% (w/w with respect to glucose) for Kloeckera sp. 2201 respectively. During growth with C₁/C₆-mixtures containing higher C₁-proportions of methanol regular growth yields for methanol were recorded which corresponded to the growth yields found with methanol as the only carbon source.The regulation of the synthesis of the enzymes of the dissimilatory pathway for methanol was found to be under multiple control. Although glucose was present in the medium methanol had a positive effect on the synthesis of these enzymes. Thus, in addition to derepression induction by methanol was also observed. This inductive effect was found to increase with increasing proportions of methanol in the mixture. Depending on the enzyme, 10–40% methanol in the mixture resulted in a maximal induction with enzyme specific activities equal to those found in cells grown with methanol as the only carbon source. No further enhancements in enzyme specific activities were observed during growth on mixtures containing more than 40% methanol.Abbreviations and terms C₁ Methanol - C₆ glucose - C₁/C₆ mixture compositions are given in % (w/w) - C₀ concentration of ¹⁴C in the inflowing medium (DPM ml^-1) - C(t) concentration of ¹⁴C incorporated in cells as a function of time t (DPM ml^-1) - d dilution rate (h^-1) - DPM disintegrations per minute - q _s q _C1 and q _C6 are specific rates of consumption of substrate, methanol and glucose respectively [g (g cell dry weight)^-1 h^-1] - q _O2 and q _CO2 are the specific rates of oxygen consumption and carbon dioxide release [mmol (g cell dry weight)^-1 h^-1] - RQ respiration quotient (q _CO2 q _O2 ^-1) - s _C1 and s _C6 are the residual concentrations of methanol and glucose in the culture liquid (g l^-1) - s _O/C1 and s _O/C6 are the concentrations of methanol and glucose in the inflowing medium (g l^-1) - Sp.A. enzyme specific activity - x cell dry weight concentration (g l^-1) - Y _X/C1 and Y _X/C6 are growth yields on methanol and glucose respectively (g cell dry weight (g substrate)^-1 - Y _C/C1 growth yield with methanol with respect to carbon (g carbon assimilated (g carbon supplied)^-1 - _m maximum specific growth rate (h^-1)     

Salicylic acid can regulate phloem unloading in the root tip

In three-day-old maize (Zea mays L.) seedlings, we removed the endosperm, coleoptile with leaflets, and adventitious roots. Primary roots were exposed to 0–10⁻³ M salicylic acid (SA) for 1–5 h; scutellum, to 10⁻² M 2-desoxy-D-glucose (2dG). 2dG-sucrose synthesized from 2dG was transported from scutella to the roots along the phloem. Its accumulation in 5-mm-long root tips was the measure of phloem unloading. At the concentrations higher than 10⁻⁴ M, SA suppressed unloading. Simultaneously, the uptake of ¹⁴C-5,5-dimethyloxazolidinedione (DMO) by root segments was inhibited, indicating cytoplasm acidification. 10⁻³ M SA also inhibited root respiration and growth. The lower SA concentrations (10⁻⁵ and 10⁻⁶ M) activated unloading under conditions of weak sucrose phloem transport to the root. They did not affect DMO uptake, respiration, and growth. 10⁻⁴ M SA stimulated unloading during 1- or 2-h exposure but did not affect it at longer treatments. A dependence of SA action on its concentration and exposure duration implies its involvement in the control of phloem unloading in the root tip.     

Reduction of nitrate byPseudomonas putrefaciens entrapped in composite agar layer/microporous membrane structures

Summary Composite structures consisting of aPseudomonas putrefaciens immobilized-cell agar layer bounded by a microporous membrane filter were used for water denitrification. With methanol as the C-source, one litre of high nitrate water (3 mM) was completely freed from NO ₃ ^– and NO ₂ ^– ions in 11 days at a rate of 90 mol N–NO ₃ ^– /day/g of agar gel, while no production of ammonium ions could be detected. When acetic acid was substituted for methanol, the denitrifying activity was lower. No noticeable contamination of the treated water due to cell leakage from the biocatalytic structures occurred during the incubation periods.     

Kinetics of phosphate-mediated oxidation of ferrous iron and formation of 8-oxo-2′-deoxyguanosine in solutions of free 2′-deoxyguanosine and calf thymus DNA

Formation of 7,8-dihydro-8-oxo-2′-deoxyguanosine (8-oxo-dG) in solutions of free 2′-deoxyguanosine (dG) and calf thymus DNA (DNA) was compared for the diffusion-dependent and localised production of oxygen radicals from phosphate-mediated oxidation of ferrous iron (Fe²⁺) to ferric iron (Fe³⁺). The oxidation of Fe²⁺ to Fe³⁺ was followed at 304 nm at pH 7.2 under aerobic conditions. Given that the concentration of Fe²⁺ ≥phosphate concentration, the rate of Fe²⁺ oxidation was significantly higher in DNA-phosphate as compared for the same concentration of inorganic phosphate. Phosphate catalysed oxidation of ferrous ions in solutions of dG or DNA led through the production of reactive oxygen species to the formation of 8-oxo-dG. The yield of 8-oxo-dG in solutions of dG or DNA correlated positively with the inorganic-/DNA-phosphate concentrations as well as with the concentrations of ferrous ions added. The yield of 8-oxo-dG per unit oxidised Fe²⁺ were similar for dG and DNA; thus, it differed markedly from radiation-induced 8-oxo-dG, where the yield in DNA was several fold higher.For DNA in solution, the localisation of the phosphate ferrous iron complex relative to the target is an important factor for the yield of 8-oxo-dG. This was supported from the observation that the yield of 8-oxo-dG in solutions of dG was significantly increased over that in DNA only when Fe²⁺ was oxidised in a high excess of inorganic phosphate (50 mM) and from the lower protection of DNA damage by the radical scavenger (hydroxymethyl)aminomethane (Tris)–HCl.