Reflection microscopy and geochemistry at DSDP Leg 55 Holes

Magnetic properties of volcanic rocks are controlled mainly by the physical and chemical state of their constituent ferromagnetic minerals. The most important parameters determining magnetic properties are concentration, composition, grain size, and oxidation state. In sea floor basalts, the main ferromagnetic minerals are titanomagnetites which are either unoxidized or, more commonly, have undergone various degrees of posteruptive low-temperature oxidation to become cationdeficient titanomagnetites, or titanomaghemites. The effects of this low-temperature alteration are seen in the increase of Curie temperature and decrease of saturation magnetization and lattice parameter of ferromagnetic minerals (Readman and O'Reilly, 1972). It is now believed that titanomaghemitization of newly formed mid-ocean ridge crust proceeds with a time constant of about 1 m.y., accompanying drastic decrease of the intensity of the natural remanent magnetization (NRM) (Johnson and Atwater, 1977).

EPOCA Svalbard 2009 benthic experiment: Serripes study, 2009

Ocean acidification influences sediment/water nitrogen fluxes, possibly by impacting on the microbial process of ammonia oxidation. To investigate this further, undisturbed sediment cores collected from Ny Alesund harbour (Svalbard) were incubated with seawater adjusted to CO2 concentrations of 380, 540, 760, 1,120 and 3,000 µatm. DNA and RNA were extracted from the sediment surface after 14 days' exposure and the abundance of bacterial and archaeal ammonia oxidising (amoA) genes and transcripts quantified using quantitative polymerase chain reaction. While there was no change to the abundance of bacterial amoA genes, an increase to 760 µatm pCO2 reduced the abundance of bacterial amoA transcripts by 65 %, and this was accompanied by a shift in the composition of the active community. In contrast, archaeal amoA gene and transcript abundance both doubled at 3,000 µatm, with an increase in species richness also apparent. This suggests that ammonia oxidising bacteria and archaea in marine sediments have different pH optima, and the impact of elevated CO2 on N cycling may be dependent on the relative abundances of these two major microbial groups. Further evidence of a shift in the balance of key N cycling groups was also evident: the abundance of nirS-type denitrifier transcripts decreased alongside bacterial amoA transcripts, indicating that NO3 ? produced by bacterial nitrification fuelled denitrification. An increase in the abundance of Planctomycete-specific 16S rRNA, the vast majority of which grouped with known anammox bacteria, was also apparent at 3,000 µatm pCO2. This could indicate a possible shift from coupled nitrification-denitrification to anammox activity at elevated CO2.

The identification of a 9-cis retinol dehydrogenase in the mouse embryo reveals a pathway for synthesis of 9-cis retinoic acid

The ligand-controlled retinoic acid (RA) receptors and retinoid X receptors are important for several physiological processes, including normal embryonic development, but little is known about how their ligands, all-trans and 9-cis RA, are generated. Here we report the identification of a stereo-specific 9-cis retinol dehydrogenase, which is abundantly expressed in embryonic tissues known to be targets in the retinoid signaling pathway. The membrane-bound enzyme is a member of the short-chain alcohol dehydrogenase/reductase superfamily, able to oxidize 9-cis retinol into 9-cis retinaldehyde, an intermediate in 9-cis RA biosynthesis. Analysis by nonradioactive in situ hybridization in mouse embryos shows that expression of the enzyme is temporally and spatially well controlled during embryogenesis with prominent expression in parts of the developing central nervous system, sensory organs, somites and myotomes, and several tissues of endodermal origin. The identification of this enzyme reveals a pathway in RA biosynthesis, where 9-cis retinol is generated for subsequent oxidation to 9-cis RA.

No ·NO from NO synthase

The nitric-oxide synthase (NOS; EC 1.14.13.39) reaction is formulated as a partially tetrahydrobiopterin (H4Bip)-dependent 5-electron oxidation of a terminal guanidino nitrogen of l-arginine (Arg) associated with stoichiometric consumption of dioxygen (O2) and 1.5 mol of NADPH to form l-citrulline (Cit) and nitric oxide (·NO). Analysis of NOS activity has relied largely on indirect methods such as quantification of nitrite/nitrate or the coproduct Cit; we therefore sought to directly quantify ·NO formation from purified NOS. However, by two independent methods, NOS did not yield detectable ·NO unless superoxide dismutase (SOD; EC 1.15.1.1) was present. In the presence of H4Bip, internal ·NO standards were only partially recovered and the dismutation of superoxide (O2⨪), which otherwise scavenges ·NO to yield ONOO−, was a plausible mechanism of action of SOD. Under these conditions, a reaction between NADPH and ONOO− resulted in considerable overestimation of enzymatic NADPH consumption. SOD lowered the NADPH:Cit stoichiometry to 0.8–1.1, suggesting either that additional reducing equivalents besides NADPH are required to explain Arg oxidation to ·NO or that ·NO was not primarily formed. The latter was supported by an additional set of experiments in the absence of H4Bip. Here, recovery of internal ·NO standards was unaffected. Thus, a second activity of SOD, the conversion of nitroxyl (NO−) to ·NO, was a more likely mechanism of action of SOD. Detection of NOS-derived nitrous oxide (N2O) and hydroxylamine (NH2OH), which cannot arise from ·NO decomposition, was consistent with formation of an ·NO precursor molecule such as NO−. When, in the presence of SOD, glutathione was added, S-nitrosoglutathione was detected. Our results indicate that ·NO is not the primary reaction product of NOS-catalyzed Arg turnover and an alternative reaction mechanism and stoichiometry have to be taken into account.

Energy-driven subunit rotation at the interface between subunit a and the c oligomer in the FO sector of Escherichia coli ATP synthase

Subunit rotation within the F1 catalytic sector of the ATP synthase has been well documented, identifying the synthase as the smallest known rotary motor. In the membrane-embedded FO sector, it is thought that proton transport occurs at a rotor/stator interface between the oligomeric ring of c subunits (rotor) and the single-copy a subunit (stator). Here we report evidence for an energy-dependent rotation at this interface. FOF1 was expressed with a pair of substituted cysteines positioned to allow an intersubunit disulfide crosslink between subunit a and a c subunit [aN214C/cM65C; Jiang, W. & Fillingame, R. H. (1998) Proc. Natl. Acad. Sci. USA 95, 6607–6612]. Membranes were treated with N,N′-dicyclohexyl-[14C]carbodiimide to radiolabel the D61 residue on less than 20% of the c subunits. After oxidation to form an a–c crosslink, the c subunit properly aligned to crosslink to subunit a was found to contain very little 14C label relative to other members of the c ring. However, exposure to MgATP before oxidation significantly increased the radiolabel in the a–c crosslink, indicating that a different c subunit was now aligned with subunit a. This increase was not induced by exposure to MgADP/Pi. Furthermore, preincubation with MgADP and azide to inhibit F1 or with high concentrations of N,N′-dicyclohexylcarbodiimide to label most c subunits prevented the ATP effect. These results provide evidence for an energy-dependent rotation of the c ring relative to subunit a.

Oxidative DNA damage and senescence of human diploid fibroblast cells.

Human diploid fibroblast cells cease growth in culture after a finite number of population doublings. To address the cause of growth cessation in senescent IMR-90 human fibroblast cells, we determined the level of oxidative DNA damage by using 8-oxoguanine excised from DNA and 8-oxo-2'-deoxyguanosine in DNA as markers. Senescent cells excise from DNA four times more 8-oxoguanine per day than do early-passage young cells. The steady-state level of 8-oxo-2'-deoxyguanosine in DNA is approximately 35% higher in senescent cells than in young cells. Measurement of protein carbonyls shows that senescent cells did not appear to have elevated protein oxidation. To reduce the level of oxidative damage, we cultured cells under a more physiological O2 concentration (3%) and compared the replicative life span to the cells cultured at the O2 concentration of air (20%). We found that cells grown under 3% O2 achieved 50% more population doublings during their lifetime. Such an extension of life span resulted from the delayed onset of senescence and elevation of growth rate and saturation density of cells at all passages. The spin-trapping agent alpha-phenyl-t-butyl nitrone (PBN), which can act as an antioxidant, also effectively delayed senescence and rejuvenated near senescent cells. The effect is dose-dependent and is most pronounced for cells at the stage just before entry into senescence. Our data support the hypothesis that oxidative DNA damage contributes to replicative cessation in human diploid fibroblast cells.

Complexação de guaiacol com ß-ciclodextrina para tratamento de alveolite seca: avaliação in vitro e in vivo

A alveolite seca (AS) é uma das complicações pós-operatórias mais comuns e sintomáticas na odontologia, porém, até o momento não há um protocolo de tratamento definido. O composto fenólico guaiacol (Gu) é um dos materiais utilizados para revestimento intra-alveolar devido às suas propriedades analgésicas, antioxidantes e antimicrobianas. Contudo, sua desvantagem é a dificuldade de manipulação decorrente da sua baixa estabilidade, alta volatilidade e sensibilidade à oxidação. Para melhorar suas propriedades e aumentar sua aplicabilidade clínica, um complexo de inclusão de Gu com ß-ciclodextrina (ßcd) foi desenvolvido. A formação do complexo supramolecular de Gu:ßcd foi caracterizada mediante a ressonância magnética nuclear (RMN), nos experimentos de 1H e 2D ROESY. A atividade antibacteriana do Gu e Gu:ßcd frente a Escherichia coli, Staphylococcus aureus, Streptococcus mitis, Streptococcus mutans, Streptococcus sanguis e Aggregatibacter actinomycetemcomitans foi analisada pelo método da microdiluição e sua citotoxicidade em osteoblastos de calvária de rato, foi estudado com o ensaio do MTT. O processo de reparo alveolar induzido pelo Gu:ßcd foi avaliado histologicamente após tratamento de alveolite seca em molares inferiores de ratos. A RMN mostrou correlações espaciais entre os hidrogênios internos (H3 e H5) da ßcd e os hidrogênios aromáticos, H(a) e H(b) do Gu, confirmando a formação do complexo. A complexação do Gu na ßcd potencializou seu efeito antibacteriano e reduziu sua citotoxicidade em osteoblastos. O estudo in vivo evidenciou a ocorrência de ossificação no ápice alveolar dos ratos tratados com Gu:ßcd, no 7o dia. No 14o dia, as trabéculas ósseas ocuparam também o terço médio do alvéolo e no 21o dia, todo o alvéolo se encontrava preenchido por osso neoformado. Estes resultados foram similares ao controle negativo e superiores ao controle positivo (Alvogyl®). Os benefícios obtidos pela inclusão do Gu na ßcd foram demonstrados pela melhora das propriedades biológicas do Gu in vitro e o adequado reparo alveolar in vivo.

Electrocatalytic activity of Ni-doped nanoporous carbons in the electrooxidation of propargyl alcohol

Herein, we explore the immobilization of nickel on various carbon supports and their application as electrocatalysts for the oxidation of propargyl alcohol in alkaline medium. In comparison with massive and nanoparticulated nickel electrode systems, Ni-doped nanoporous carbons provided similar propargyl alcohol conversions for very low metallic contents. Nanoparticulated Ni on various carbon supports gave rise to the highest electrocatalytic activity in terms of product selectivity, with a clear dependence on Ni content. The results point to the importance of controlling the dispersion of the Ni phase within the carbon matrix for a full exploitation of the electroactive area of the metal. Additionally, a change in the mechanism of the propargyl alcohol electrooxidation was noted, which seems to be related to the physicochemical properties of the carbon support as well. Thus, the stereoselectivity of the electrooxidative reaction can be controlled by the active nickel content immobilized on the anode, with a preferential oxidation to (Z)-3-(2-propynoxy)-2-propenoic acid with high Ni-loading, and to propiolic acid with low loading of active Ni sites. Moreover, the formation of (E)-3-(2-propynoxy)-2-propenoic acid was discriminatory irrespective of the experimental conditions and Ni loadings on the carbon matrixes.

Petrography, chemistry and magnetic properties of ODP Leg 115 basalts

A detailed study of the Fe-Ti oxides in four basalt samples-one from each of the four holes drilled into basement on Ocean Drilling Program Leg 115 (Sites 706, 707, 713, and 715) has been performed. Ilmenite is present only in samples from Sites 706 and 715. In the sample from Site 715, Ti-magnetite intergrowths are characteristic of subaerial (?) high-temperature oxy-exsolution; Ti-magnetite in the other three samples has experienced pervasive low-temperature oxidation to Ti-maghemite, as evidenced by the double-humped, irreversible, saturation magnetization vs. temperature (Js/T) curves. The bulk susceptibility of these samples, which are similar in terms of major element chemistry, varies by a factor of ~20 and correlates semiquantitatively with the modal abundance of Fe-Ti spinel, as determined by image analysis with an electron microprobe. The variation in Fe-Ti oxide abundance correlates with average grain size: fine-grained samples contain less Fe-Ti oxide. This prompts the speculation that the crystallization rate may also influence Fe-Ti oxide abundance.

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.

Biomarkers

Introduction – Why do we need ‘biomarkers? Biomarkers of protein oxidation Introduction Major issues/questions Protein carbonyl biomarkers Biochemistry Methods of measurement Storage, stability and limitations in use Protein thiol biomarkers Biochemistry Methods of measurement Storage, stability and limitations on use Aliphatic amino acid biomarkers Biochemistry Methods of measurement Storage, stability and limitations on use Oxidised Tryptophan Biomarkers Biochemistry Method of measurement Storage, stability and limitations on use Oxidised tyrosine biomarkers Biochemistry Methods of measurement Storage, stability and limitations on use Formation of neoepitopes on oxidised proteins Validation of assays for protein oxidation biomarkers Relationship of protein oxidation to disease Modulation of protein oxidation biomarkers by antioxidants Future perspectives Introduction to lipid peroxidation biomarkers Introduction: biochemistry of lipid peroxidation Malondialdehyde Methods of measurement Storage, stability and limitations on use Conjugated dienes Method of measurement Storage, stability and limitations of use LDL lag phase Method of measurement Storage, stability and limitations of use Hydrocarbon gases Biochemistry Method of measurement Storage, stability and limitations on use Lipofuscin Biochemistry Method of measurement Storage, stability and limitation on use Lipid peroxides Biochemistry Method of measurement Storage, stability and limitations on use Isoprostanes Biochemistry Method of measurement Storage, stability and limitations on use Possible new biomarkers of lipid oxidation Relationship of lipid peroxidation to disease Modulation of lipid peroxidation biomarkers by antioxidants Functional consequences of lipid peroxidation Contribution of dietary intake to lipid peroxidation products Biomarkers of DNA oxidation Introduction Confounding factors Units and terminology Nuclear and mitochondrial DNA damage Lymphocytes as surrogate tissues Measurement of DNA damage with the comet assay Practical details Storage, stability, and limitations of the assay Measurement of DNA base oxidation by HPLC Practical details Storage, stability and limitations of the method Measurement of DNA base oxidation by GC–MS Biochemistry of 8-oxoguanine, adenine and fapy derivatives Methods of measurement Storage, stability and limitations of the method Analysis of guanine oxidation products in urine Method of measurement Limitations and criticisms Immunochemical methods Methods of measurement Storage, stability, and limitations of the assay 32P post-labelling Method of measurement Limitations and criticisms Validation of assays for DNA oxidation Oxo-dGuo in lymphocyte DNA Urinary measurements DNA–aldehyde adducts Biochemistry Method of measurement Products of reactive nitrogen species Endpoints arising from oxidative DNA damage Mutations Chromosome aberrations Micronuclei Site-specific DNA damage Relationship of DNA oxidation to disease Modulation of DNA oxidation biomarkers by antioxidants Direct and indirect effects of oxidative stress: measures of total oxidant/antioxidant levels Visualisation of cellular oxidants Biochemistry: histochemical detection of ROS Method of measurement Limitations, storage and stability Measurement of hydrogen peroxide Biochemistry Methods of measurement Storage, stability and limitations on use Measurement of the ratio of antioxidant/oxidised antioxidant Biochemistry Method of measurement Storage, stability and limitations on use Total antioxidant capacity Biochemistry Terminology Methods of measurement Storage, stability and limitations on use Validation of assays for direct oxidant and antioxidant biomarkers Relationship of oxidant/antioxidant measurement to disease Modulation of oxidant/antioxidant biomarkers by dietary antioxidants Induction of genes in response to oxidative stress Background Measurement of antioxidant responsive genes and proteins Effects of antioxidant intake on the activity of antioxidant enzymes

Novel high water content hydrogels

Hydrogels may be described as cross-linked hydrophilic polymers that swell but do not dissolve in water. The production of high water content hydrogels was the subject of investigation. Based upon copolymer compositions that had already achieved commercial success as biomaterials, new monomers were added or substituted in and the effects observed. The addition of N-isopropyl acrylamide to an acrylamide-based composition that had previously been designed to become a contact lens, produced materials that showed smart effects in that the water content showed dependence on the temperature of the hydrating solution. Such thermo-responsive materials have potential uses in drug delivery, ultrafiltration and cell culture surfaces. Proteoglycans in nature have an important role to play in structural support where a highly hydrophilic structure maintains lubricious surfaces. Certain functional groups that impart this hydrophilicity are present in certain sulphonate monomers, Bis(3-sulphopropyl ester) itaconate, dipotassium salt (SPI), 3-Sulphopropyl ester acrylate, potassium salt (SPA) and Sodium 2-(acrylamido)-2-methyl propane sulphonate (NaAMPS). These monomers were incorporated into a HEMA-based copolymer that had been designed initially as a contact lens and the resulting effects examined. Highly hydrophilic materials resulted that showed reduced protein deposition over the neutral core material. It is postulated that a sulphonate group would have a larger number of hydration shells around it than for example methacrylic acid, leading to more dynamic exchange and so reducing the adsorption of biological solutes. A cationic monomer was added to bring back the net anionic nature of the sulphonate hydrogels and the effects studied. Ionic interactions were found to cause a reduction in the water content of the resulting materials as the mobility of the network decreased, leading to stiffer but less extensible materials. The presence of a net dominant charge, whether negative or positive, appeared to act to reduce protein deposition, but increasing equivalence in the amount of both charges served to present a more 'neutral' surface and deposition subsequently increased. The grafting of hydrophilic hydrogel layers onto silicone elastomer was attempted and the results evaluated using dynamic contact angle measurements. Following plasma oxidation to reduce the surface energy barrier to aqueous grafting chemistry, it was found that the wettability of the modified elastomers could be significantly enhanced by such treatment. The SPA-grafted material in particular hinted at an osmotic drive for rehydration that may be exploited in biomaterials.

Effect of a tumour-derived lipid-mobilising factor on glucose and lipid metabolism in vivo

Treatment of ex-breeder male NMRI mice with lipid mobilising factor isolated from the urine of cachectic cancer patients, caused a significant increase in glucose oxidation to CO2, compared with control mice receiving phosphate buffered saline. Glucose utilisation by various tissues was determined by the 2-deoxyglucose tracer technique and shown to be elevated in brain, heart, brown adipose tissue and gastrocnemius muscle. The tissue glucose metabolic rate was increased almost three-fold in brain, accounting for the ability of lipid mobilising factor to decrease blood glucose levels. Lipid mobilising factor also increased overall lipid oxidation, as determined by the production of 14CO2 from [14C carboxy] triolein, being 67% greater than phosphate buffered saline controls over a 24 h period. There was a significant increase in [14C] lipid accumulation in plasma, liver and white and brown adipose tissue after administration of lipid mobilising factor. These results suggest that changes in carbohydrate metabolism and loss of adipose tissue, together with an increased whole body fatty acid oxidation in cachectic cancer patients, may arise from tumour production of lipid mobilising factor. © 2002 Cancer Research UK.

Optimising catalytic properties of supported sulfonic acid catalysts

Siliceous mesoporous molecular sieves (SBA-15) have been functionalised with propylsulfonic acid groups by both co-condensing 3-mercaptopropyltrimethoxysilane with the solid at the synthesis (sol-gel) stage and by grafting the same compound to pre-prepared SBA-15, followed, in both cases, by oxidation to sulfonic acid. The acidic and catalytic properties of the supported sulfonic acids prepared in the two ways have been compared, using ammonia adsorption calorimetry and the benzylation reaction between benzyl alcohol and toluene. Using a combination of X-ray photoelectron spectroscopy and other analytical techniques, the level of functionalisation and the extent of subsequent oxidation of tethered thiol to sulfonic acid, both in the bulk and close to the surface of SBA-15 particles, have been assessed. The research shows that the co-condensing route leads to higher levels of functionalisation than the grafting route. The extent of oxidation of added thiol to acid groups is similar using the two routes, about 70% near the surface and only 50% in the bulk. Comparison is made with polymer supported sulfonic acid catalysts, Amberlysts 15 and 35, and Nafion. Nafion shows the highest acid strength and the highest specific catalytic activity of all materials studied. Amongst the other materials, average acid strengths are broadly similar but there appears to be a relationship between the concentration of acid sites on the catalysts and their specific activity in the benzylation reaction. A model is proposed to explain this, in which clustering of sulfonic acid groups, even to a small extent, leads to disproportionately enhanced catalytic activity. © 2009 Elsevier B.V. All rights reserved.

Filogenia molecular das enzimas isocitrato liase e malato sintase e sua evolução em Viridiplanta

The plant metabolism consists of a complex network of physical and chemical events resulting in photosynthesis, respiration, synthesis and degradation of organic compounds. This is only possible due to the different kinds of responses to many environmental variations that a plant could be subject through evolution, leading also to conquering new surroundings. The glyoxylate cycle is a metabolic pathway found in glyoxysomes plant, which has unique role in the seedling establishment. Considered as a variation of the citric acid cycle, it uses an acetyl coenzyme A molecule, derived from lipids beta-oxidation to synthesize compounds which are used in carbohydrate synthesis. The Malate synthase (MLS) and Isocitrate lyase (ICL) enzyme of this cycle are unique and essential in regulating the biosynthesis of carbohydrates. Because of the absence of decarboxylation steps as rate-limiting steps, detailed studies of molecular phylogeny and evolution of these proteins enables the elucidation of the effects of this route presence in the evolutionary processes involved in their distribution across the genome from different plant species. Therefore, the aim of this study was to establish a relationship between the molecular evolution of the characteristics of enzymes from the glyoxylate cycle (isocitrate lyase and malate synthase) and their molecular phylogeny, among green plants (Viridiplantae). For this, amino acid and nucleotide sequences were used, from online repositories as UniProt and Genbank. Sequences were aligned and then subjected to an analysis of the best-fit substitution models. The phylogeny was rebuilt by distance methods (neighbor-joining) and discrete methods (maximum likelihood, maximum parsimony and Bayesian analysis). The identification of structural patterns in the evolution of the enzymes was made through homology modeling and structure prediction from protein sequences. Based on comparative analyzes of in silico models and from the results of phylogenetic inferences, both enzymes show significant structure conservation and their topologies in agreement with two processes of selection and specialization of the genes. Thus, confirming the relevance of new studies to elucidate the plant metabolism from an evolutionary perspective