Pore water geochemistry of Håkon Mosby mud volcano sediments measured at station PS74/172-1_PUC-136 (Z3-S2, old flow surface)

Pore water and turnover rates were determined for surface sediment cores obtained in 2009 and 2010. The pore water was extracted with Rhizons (Rhizon CSS: length 5 cm, pore diameter 0.15 µm; Rhizosphere Research Products, Wageningen, Netherlands) in 1 cm-resolution and immediately fixed in 5% zinc acetate (ZnAc) solution for sulfate, and sulfide analyses. The samples were diluted, filtered and the concentrations measured with non-suppressed anion exchange chromatography (Waters IC-Pak anion exchange column, waters 430 conductivity detector). The total sulfide concentrations (H2S + HS- + S**2-) were determined using the diamine complexation method (doi:10.4319/lo.1969.14.3.0454). Samples for dissolved inorganic carbon (DIC) and alkalinity measurements were preserved by adding 2 µl saturated mercury chloride (HgCl2) solution and stored headspace-free in gas-tight glass vials. DIC and alkalinity were measured using the flow injection method (detector VWR scientific model 1054) (doi:10.4319/lo.1992.37.5.1113). Dissolved sulfide was eliminated prior to the DIC measurement by adding 0.5 M molybdate solution (doi:10.4319/lo.1995.40.5.1011). Nutrient subsamples (10 - 15 ml) were stored at - 20 °C prior to concentration measurements with a Skalar Continuous-Flow Analyzer (doi:10.1002/9783527613984).

Absorption and mobility of foliar-applied boron in soybean as affected by plant boron status and application as a polyol complex

In the present study (i) the impact of plant Boron (B) status on foliar B absorption and (ii) the effect of B complexation with polyols (sorbitol or mannitol) on B absorption and translocation was investigated. Soybean (Glycine max (L.) Meer.) plants grown in nutrient solution containing 0 μM, 10 μM, 30 μM or 100 μM 11B labelled boric acid (BA) were treated with 50 mM 10B labelled BA applied to the basal parts of two leaflets of one leaf, either pure or in combination with 500 mM sorbitol or mannitol. After one week, 10B concentrations in different plant parts were determined. In B deficient leaves (0 μM 11B), 10B absorption was significantly lower than in all other treatments (9.7% of the applied dose vs. 26%–32%). The application of BA in combination with polyols increased absorption by 18–25% as compared to pure BA. The absolute amount of applied 10B moving out of the application zone was lowest in plants with 0 μM 11B supply (1.1% of the applied dose) and highest in those grown in 100 μM 11B (2.8%). The presence of sorbitol significantly decreased the share of mobile 10B in relation to the amount absorbed. The results suggest that 11B deficiency reduces the permeability of the leaf surface for BA. The addition of polyols may increase 10B absorption, but did not improve 10B distribution within the plant, which was even hindered when applied a sorbitol complex.

Electrophoretic Deposition of Transparent ZnO Thin Films from Highly Stabilized Colloidal Suspensions

The parameters that control the stability of ZnO-nanoparticles suspensions and their deposition by electrophoretic deposition were studied, so as to organize the assembly and compaction of nanoparticles. The addition of cationic polyelectrolyte - Polyethylenimine (PEI) - with different molecular weights was investigated, in order to study their effectiveness and the influence of the molecular weight of the organic chain on suspensions dispersion. It was found that PEI with the highest molecular weight provided better dispersion conditions. Cathodic EPD was performed under previously optimized suspensions conditions and over electropolished stainless steel substrates. Experimental results showed that the EPD process in these conditions allows obtaining dense transparent ZnO thin films. Deposition times and intensities were optimized by analyzing the resulting thin films characteristics. Finally, the deposits were characterized by FE-SEM, AFM, and different spectroscopic techniques.

A theoretical study on the formation of iodine oxide aggregates and monohydrates

Biotic and abiotic emissions of molecular iodine and iodocarbons from the sea or the ice surface and the intertidal zone to the coastal/polar marine boundary layer lead to the formation of iodine oxides, which subsequently nucleate forming iodine oxide particles (IOPs). Although the link between coastal iodine emissions and ultrafine aerosol bursts is well established, the details of the nucleation mechanism have not yet been elucidated. In this paper, results of a theoretical study of a range of potentially relevant aggregation reactions of different iodine oxides, as well as complexation with water molecules, are reported. Thermochemical properties of these reactions are obtained from high level ab initio correlated calculations including spin–orbit corrections. The results show that the nucleation path most likely proceeds through dimerisation of I2O4. It is also shown that water can hinder gas-to-particle conversion to some extent, although complexation with key iodine oxides does not remove enough of these to stop IOP formation. A consistent picture of this process emerges from the theoretical study presented here and the findings of a new laboratory study reported in the accompanying paper (Gomez Martin et al., 2013).

Building functional surfaces for biosensors development

Polyelectrolyte multilayers (PEM) built by layer-by-layer technique have been extensively studied over the last years, resulting in a wide variety of current and potential applications. This technique can be used to construct thin films with different functionalities, or to functionalize surfaces with substantial different properties of those of the underlying substrates. The multilayering process is achieved by the alternate adsorption of oppositely charged polyelectrolytes. In this work we get advantage of the protein resistant property of the Poly (l-lysine)-graft-(polyethyleneglycol) to create protein patterns. Proteins can be immobilized on a surface by unspecific physical adsorption, covalent binding or through specific interactions. The first protein used in this work was laccase, a copper-containing redox enzyme that catalyse the oxidation of a broad range of polyphenols and aromatic substrates, coupled to the reduction of O2 to H2O without need of cofactors. Applications of laccases have been reported in food, pulp, paper, and textile industry, and also in biosensor development. Some uses require the immobilization of the enzyme on solid supports by adsorption, covalent attachment, entrapment, etc, on several substrates. Especially for biosensor development, highly active, stable and reproducible immobilization of laccase is required.

Design and characterization of α-melanotropin peptide analogs cyclized through rhenium and technetium metal coordination

α-Melanocyte stimulating hormone (α-MSH) analogs, cyclized through site-specific rhenium (Re) and technetium (Tc) metal coordination, were structurally characterized and analyzed for their abilities to bind α-MSH receptors present on melanoma cells and in tumor-bearing mice. Results from receptor-binding assays conducted with B16 F1 murine melanoma cells indicated that receptor-binding affinity was reduced to approximately 1% of its original levels after Re incorporation into the cyclic Cys4,10, d-Phe7–α-MSH4-13 analog. Structural analysis of the Re–peptide complex showed that the disulfide bond of the original peptide was replaced by thiolate–metal–thiolate cyclization. A comparison of the metal-bound and metal-free structures indicated that metal complexation dramatically altered the structure of the receptor-binding core sequence. Redesign of the metal binding site resulted in a second-generation Re–peptide complex (ReCCMSH) that displayed a receptor-binding affinity of 2.9 nM, 25-fold higher than the initial Re–α-MSH analog. Characterization of the second-generation Re–peptide complex indicated that the peptide was still cyclized through Re coordination, but the structure of the receptor-binding sequence was no longer constrained. The corresponding 99mTc- and 188ReCCMSH complexes were synthesized and shown to be stable in phosphate-buffered saline and to challenges from diethylenetriaminepentaacetic acid (DTPA) and free cysteine. In vivo, the 99mTcCCMSH complex exhibited significant tumor uptake and retention and was effective in imaging melanoma in a murine-tumor model system. Cyclization of α-MSH analogs via 99mTc and 188Re yields chemically stable and biologically active molecules with potential melanoma-imaging and therapeutic properties.

Virus-sized self-assembling lamellar complexes between plasmid DNA and cationic micelles promote gene transfer

Gene therapy is based on the vectorization of genes to target cells and their subsequent expression. Cationic amphiphile-mediated delivery of plasmid DNA is the nonviral gene transfer method most often used. We examined the supramolecular structure of lipopolyamine/plasmid DNA complexes under various condensing conditions. Plasmid DNA complexation with lipopolyamine micelles whose mean diameter was 5 nm revealed three domains, depending on the lipopolyamine/plasmid DNA ratio. These domains respectively corresponded to negatively, neutrally, and positively charged complexes. Transmission electron microscopy and x-ray scattering experiments on complexes originating from these three domains showed that although their morphology depends on the lipopolyamine/plasmid DNA ratio, their particle structure consists of ordered domains characterized by even spacing of 80 Å, irrespective of the lipid/DNA ratio. The most active lipopolyamine/DNA complexes for gene transfer were positively charged. They were characterized by fully condensed DNA inside spherical particles (diameter: 50 nm) sandwiched between lipid bilayers. These results show that supercoiled plasmid DNA is able to transform lipopolyamine micelles into a supramolecular organization characterized by ordered lamellar domains.

Different dynamics in nuclear entry of subunits of the repair/transcription factor TFIIH

We report here the different ways in which four subunits of the basal transcription/repair factor TFIIH (XPB, XPD, p62 and p44) and the damage recognition XPC repair protein can enter the nucleus. We examined their nuclear localization by transiently expressing the gene products tagged with the enhanced green fluorescent protein (EGFP) in transfected 3T3 cells. In agreement with the identification of more than one putative nuclear localization signal (NLS) in their protein sequences, XPB, XPC, p62 and p44 chimeras were rapidly sorted to the nucleus. In contrast, the XPD–EGFP chimeras appeared mainly localized in the cytoplasm, with a minor fraction of transfectants showing the EGFP-based fluorescence also in the nucleus. The ability of the XPD chimeras to enter the nucleus was confirmed by western blotting on fractionated cell extracts and by functional complementation of the repair defect in the UV5 rodent cells, mutated in the XPD homologous gene. By deletion mutagenesis, we were unable to identify any sequence specific for nuclear localization. In particular, deletion of the putative NLS failed to affect subcellular localization and, conversely, the C-terminal part of XPD containing the putative NLS showed no specific nuclear accumulation. These findings suggest that the nuclear entry of XPD depends on its complexation with other proteins in the cytoplasm, possibly other components of the TFIIH complex.

Functional dynamics in the active site of the ribonuclease binase

Binase, a member of a family of microbial guanyl-specific ribonucleases, catalyzes the endonucleotic cleavage of single-stranded RNA. It shares 82% amino acid identity with the well-studied protein barnase. We used NMR spectroscopy to study the millisecond dynamics of this small enzyme, using several methods including the measurement of residual dipolar couplings in solution. Our data show that the active site of binase is flanked by loops that are flexible at the 300-μs time scale. One of the catalytic residues, His-101, is located on such a flexible loop. In contrast, the other catalytic residue, Glu-72, is located on a β-sheet, and is static. The residues Phe-55, part of the guanine base recognition site, and Tyr-102, stabilizing the base, are the most dynamic. Our findings suggest that binase possesses an active site that has a well-defined bottom, but which has sides that are flexible to facilitate substrate access/egress, and to deliver one of the catalytic residues. The motion in these loops does not change on complexation with the inhibitor d(CGAG) and compares well with the maximum kcat (1,500 s−1) of these ribonucleases. This observation indicates that the NMR-measured loop motions reflect the opening necessary for product release, which is apparently rate limiting for the overall turnover.

A rigid trans-spanning dinitrile ligand.

A rigid dinitrile ligand was synthesized from two xanthene units condensed to a naphthalene-1,4,5,8-diimide spacer. The rigidity and C shape of the ligand gave exclusively trans complexes with Pd(II), Ag(I), and Au(I). Evidence for complexation, coordination geometry, and stoichiometry was provided by a combination of 1H NMR, 19F NMR, and IR spectroscopy. The AuBF4 and PdCl2 complexes were shown to have a 1:1 (metal-to-ligand) stoichiometry and the AgBF4 complex was shown to have a 1:2 stoichiometry in solution. The preorganization of the dinitrile ligand resulted in complexes much more stable than their monodentate counterparts.

Large electrostatic differences in the binding thermodynamics of a cationic peptide to oligomeric and polymeric DNA.

Results presented here demonstrate that the thermodynamics of oligocation binding to polymeric and oligomeric DNA are not equivalent because of long-range electrostatic effects. At physiological cation concentrations (0.1-0.3 M) the binding of an oligolysine octacation KWK6-NH2 (+8 charge) to single-stranded poly(dT) is much stronger per site and significantly more salt concentration dependent than the binding of the same ligand to an oligonucleotide, dT(pdT)10 (-10 charge). These large differences are consistent with Poisson-Boltzmann calculations for a model that characterizes the charge distributions with key preaveraged structural parameters. Therefore, both the experimental and the theoretical results presented here show that the polyelectrolyte character of a polymeric nucleic acid makes a large contribution to both the magnitude and the salt concentration dependence of its binding interactions with simple oligocationic ligands.

Calicheamicin-DNA complexes: warhead alignment and saccharide recognition of the minor groove.

The solution structures of calicheamicin gamma 1I, its cycloaromatized analog (calicheamicin epsilon), and its aryl tetrasaccharide complexed to a common DNA hairpin duplex have been determined by NMR and distance-refined molecular dynamics computations. Sequence specificity is associated with carbohydrate-DNA recognition that places the aryl tetrasaccharide component of all three ligands in similar orientations in the minor groove at the d(T-C-C-T).d(A-G-G-A) segment. The complementary fit of the ligands and the DNA minor groove binding site creates numerous van der Waals contacts as well as hydrogen bonding interactions. Notable are the iodine and sulfur atoms of calicheamicin that hydrogen bond with the exposed amino proton of the 5'- and 3'-guanines, respectively, of the d(A-G-G-A) segment. The sequence-specific carbohydrate binding orients the enediyne aglycone of calicheamicin gamma 1I such that its C3 and C6 proradical centers are adjacent to the cleavage sites. While the enediyne aglycone of calicheamicin gamma 1I is tilted relative to the helix axis and spans the minor groove, the cycloaromatized aglycone is aligned approximately parallel to the helix axis in the respective complexes. Specific localized conformational perturbations in the DNA have been identified from imino proton complexation shifts and changes in specific sugar pucker patterns on complex formation. The helical parameters for the carbohydrate binding site are comparable with corresponding values in B-DNA fibers while a widening of the groove is observed at the adjacent aglycone binding site.

Molecular approaches to smart materials via interface recognition and conformationally switchable cavitands

In this thesis the molecular level design of functional materials and systems is reported. In the first part, tetraphosphonate cavitand (Tiiii) recognition properties towards amino acids are studied both in the solid state, through single crystal X-ray diffraction, and in solution, via NMR and ITC experiments. The complexation ability of these supramolecular receptors is then applied to the detection of biologically remarkable N-methylated amino acids and peptides using complex dynamic emulsions-based sensing platforms. In the second part, a general supramolecular approach for surface decoration with single-molecule magnets (SMMs) is presented. The self-assembly of SMMs is achieved through the formation of a multiple hydrogen bonds architecture (UPy-NaPy complexation). Finally we explore the possibility to impart auxetic behavior to polymeric material through the introduction of conformationally switchable monomers, namely tetraquinoxaline cavitands (QxCav). Their interconversion from a closed vase conformation to an extended kite form is studied first in solution, then in polymeric matrixes via pH and tensile stimuli by UV-Vis spectroscopy.

Dinâmica do fósforo no solo em função da adição de ácidos orgânicos de baixa massa molar

A baixa eficiência da adubação fosfatada em solos altamente intemperizados é devido, entre outros fatores, à adsorção do fósforo (P) à superfície das argilas silicatadas do tipo 1:1 e, principalmente, dos (hidr)óxidos de Fe e de Al. Manejos do solo que induzem a solubilização de formas de P indisponíveis para as plantas têm sido intensamente estudados nos últimos anos. Uma tentativa de aumentar a concentração de P disponível na solução do solo para sua absorção pelas plantas é a mobilização de P por ânions de ácidos orgânicos de baixa massa molar (AOBMM). Ânions derivados de AOBMM exsudados pelas raízes de plantas ou excretados por microrganismos são associados com algumas condições de rizosfera como deficiência de P e fitotoxidez de Al e interagem com o solo de forma a aumentar a biodisponibilidade de P. Dependendo dos atributos do solo, do grau de dissociação, das propriedades e do número de grupos carboxílicos dos ânions orgânicos, o P pode ser mobilizado do solo principalmente devido à dissolução complexométrica de minerais e à adsorção competitiva dos grupos funcionais carboxílicos e fosfato nos sítios de superfície coloidais. A capacidade dos ânions citrato, malato e oxalato em mobilizar P de amostras de um Neossolo Quartzarênico típico (RQ) e de um Latossolo Vermelho ácrico (LVwf) foi avaliada por meio de um estudo de lixiviação de ânions em colunas. Devido a não detecção de P nos efluentes das colunas com LVwf, foi realizado outro estudo em colunas, no qual somente citrato foi lixiviado, mas num volume maior, e as alterações das formas de P nas amostras desse solo induzidas pela lixiviação de citrato foram identificadas por espectroscopia de absorção de raios-X na borda K do fósforo (X-ray absorption near edge structure -XANES - spectroscopy). A capacidade dos ânions de AOBMM em solubilizar P foi mais dependente do teor de P disponível e de outros atributos do solo que do número de grupos funcionais carboxílicos dos ânions orgânicos. Somente o oxalato mobilizou P do RQ, enquanto todos os ânions de AOBMM foram capazes de mobilizar P do LVwf. Quando baixos volumes de solução contendo ânions de AOBMM foram lixiviados no solo, além do aumento do pH, a mobilização de P foi acompanhada pela mobilização de Al no RQ (pH água = 5), e pela mobilização de Ca no LVwf (pH água = 5.6), o que indica solubilização de P pela complexação de Al, Ca, ou Fe, de fosfatos insolúveis, ou pela inibição da precipitação de P com esses metais. Ao lixiviar um volume maior de citrato no LVwf, o P também não foi detectado nos efluentes das colunas, mas houve lixiviação intensa de Al e Fe, bem como mudanças nas proporções de formas de P no solo caracterizadas pelos espectros XANES. Embora tenhamos encontrado indícios da ação dos principais mecanismos de solubilização de P (dissolução complexométrica de minerais e troca de ligantes entre grupos funcionais carboxílicos e P adsorvido ao solo), os ânions de AOBMM mostraram pouco potencial de efetivamente aumentar a biodisponibilidade de P.