NMR methods for in situ biofilm metabolism studies

Novel procedures and instrumentation are described for nuclear magnetic resonance (NMR) spectroscopy and imaging studies of live, in situ microbial films. A perfused NMR/optical microscope sample chamber containing a planar biofilm support was integrated into a recirculation/dilution flow loop growth reactor system and used to grow in situ Shewanella oneidensis strain MR-1 biofilms. Localized NMR techniques were developed and used to non-invasively monitor time-resolved metabolite concentrations and to image the biomass volume and distribution. As a first illustration of the feasibility of the methodology an initial 13C-labeled lactate metabolic pathway study was performed, yielding results consistent with existing genomic data for MR-1. These results represent progress toward our ultimate goal of correlating time- and depth-resolved metabolism and mass transport with gene expression in live in situ biofilms using combined NMR/optical microscopy techniques.     

In situ studies of metabolism in benthic reef communities

Summary 1. Rates of net photosynthesis and respiration were determined in situ forTridacna and coral species and their contained zooxanthellae at depths from 9 to 18 m.2. Integrated daily total net photosynthesis to respiration ratios (P/R ratio) were calculated from these data to obtain the potential contribution of algal photosynthesis to the energy budget of the coral-algal symbiotic association.3. The integrated daily P/R ratios varied between 0.79 and .89. Maximum ratios of photosynthesis to respiration rates ranged from 1.15 forMussa arrgulosa to 2.91 forManicina areolata.4. Similar measurements were made on mixed benthic communities off southeastern Florida (USA) in a clean, unpolluted area and in an area influenced by the effluent of Biscayne Bay (USA). Very significant differences were found.

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In-situ-Studien über den Stoffwechsel benthonischer Lebensgemeinschaften des Korallenriffs

Kurzfassung Im Rahmen mehrerer amerikanischer Unterwasser-Forschungsprogramme wurden Stoffwechseluntersuchungen in verschiedenen Korallenriffen an Benthostieren durchgeführt, die in symbiotischer Partnerschaft mit Zooxanthellen leben. An Korallen- undTridacna-Arten wurden in situ die Beziehungen zwischen Nettophotosynthese und Sauerstoffverbrauch (P/R-Verhältnis) gemessen. Als Maximalwert wurde beiManicina areolata ein P/R-Verhältnis von 2,9 ermittelt. Die auf einen Zeitraum von 24 Stunden bezogenen Durchschnittswerte lagen zwischen 0,79 und 0,89. Es wurde festgestellt, daß die photosynthetische Aktivität der Korallen in verunreinigten Riffgebieten stark absinkt.

     

Experimental and theoretical studies of mechanical unfolding of different proteins

Mechanical properties of proteins are important for a wide range of biological processes including cell adhesion, muscle contraction, and protein translocation across biological membranes. It is necessary to reveal how proteins achieve their required mechanical stability under natural conditions in order to understand the biological processes and also to use the knowledge for constructing new biomaterials for medical and industrial purposes. In this connection, it is important to know how a protein will behave in response to various impacts. Theoretical and experimental works on mechanical unfolding of globular proteins will be considered in detail in this review.     

Experimental and theoretical studies of albendazole, oxibendazole, and tioxidazole

An investigation of the therapeutic effectiveness of albendazole (ABZ, methyl 5-[propylthio]benzimidazole-2-carbamate), oxibendazole (OBZ, methyl 5-[n-propoxy]benzimidazole-2-carbamate), and tioxidazole (TIOX, methyl 6-[n-propoxy]benzothiazole-2-carbamate) against Hymenolepis diminuta in experimentally infected rats is reported. All of the anthelmintics tested were effective therapeutically as a single oral dose against adult tapeworms, however, at different dose levels. The rank order of in vivo anthelmintic potency was ABZ greater than OBZ greater than TIOX. Molecular modeling revealed that drug efficacy depends on the orientation of the propyl group at position 5 on the heterocyclic ring system and on the magnitude of the molecular dipole moment.     

Experimental and theoretical studies of the structure of tellurate-borate glasses network

The structural properties of the xTeO₂·(1-x)B₂O₃ glasses (x = 0.6; 0.7) were investigated by FT-IR spectroscopy. From the analysis of the FTIR spectra, it is reasonable to assume that by the increasing of boron ions content, the tetrahedral [BO₄] units are gradually replaced by the trigonal [BO₃] units. The increase in the number of non-bridging oxygen atoms would decrease the connectivity of the glass network and will yield the depolymerization of the borate chains. The molecular structure and vibrational frequencies of the proposed structural models have been studied by exploring the density functional theory (DFT) calculations. The FTIR spectra of the xTeO₂·(1-x)B₂O₃ vitreous systems were compared with the calculated spectrum. This procedure allowed us to assign most of the observed IR bands.     

Experimental and theoretical studies on the excess capacity of Photosystem II

It has been recently suggested that compensatory changes in Photosystem II (PS II) electron turnover rates can protect photosynthesis from photoinhibition [Behrenfeld et al. (1998) Photosynth Res 58: 259–268]. We have further explored this feature of PS II using a rate electrode for simultaneous measurements of the steady-state rate of oxygen evolution and the oxygen flash yield depending on the background irradiance in both control and photoinhibited algal cells of Chlorella Böhm. Theoretical simulations based on the two-electron gate model agree qualitatively with experimental data if we assume an increase of the electron turnover rate in the remaining functional PS II centers of the photoinhibited sample. Our results confirm the hypothesis that the compensatory effect enables cells to maintain the maximal rates of photosynthesis even in the presence of moderate photoinhibition (decrease of up to 50% in the number of functional centers) and that the effect originates from the inner capacity of electron transport through PS II. The origin of the compensatory effect is briefly discussed.     

Experimental and theoretical studies of the three-dimensional structure of human interleukin-4

The structure of human interleukin 4 (IL-4) was predicted utilizing a series of experimental and theoretical techniques. Circular Dichroism (CD) spectroscopy indicated that IL-4 belonged to the all alpha-helix class of protein structures. Secondary structure prediction, site-directed mutagenesis, and CD spectroscopy suggested a predominantly alpha-helical structure, consistent with a four-helix bundle structural motif. A human/mouse IL-4 chimera was constructed to qualitatively evaluate alternative secondary structure predictions. The four predicted helices were assembled into tertiary structures using established algorithms. The mapping of three disulfide bridges in IL-4 provided additional constraints on possible tertiary structures. Using accessible surface contact area as a criterion, the most suitable structures were right handed all antiparallel four-helix bundles with two overhand loop connections. Successful loop closure and incorporation of the three disulfide constraints were possible while maintaining the expected shape, solvent accessibility, and steric interactions between loops and helices. Lastly, energy minimization was used to regularize the chain.     

Distribution of heparinase covalently immobilized to agarose: Experimental and theoretical studies

An immobilized enzyme reactor has been developed to remove heparin, the anticoagulant that is required in all extracorporeal devices for patients undergoing open-heart surgery or kidney dialysis. The device uses the enzyme heparinase (EC 4.2.2.7), which is covalently linked to agarose with cyanogen bromide. A critical parameter in the development of a model for the degradation of heparin catalyzed by immobilized heparinase is the radial concentration profile of the enzyme within the agarose matrix. Experimental determinations of bound enzyme con centrations have been conducted previously for several enzyme systems using radioactive or fluorescent labels. For the development of the heparinase reactor it is necessary to use catalytically but not electrophoretically pure enzyme, and thus it is not possible to use the labeling techniques. To obtain information about the bound enzyme distribution, an experimental study of the intrinsic binding kinetics of heparinase to cyanogen bromide-activated agarose was conducted. The binding reaction was studied as a function of both the concentration of heparinase and the gel-reactive group. At conditions of functional group excess, the binding kinetics were pseudo first order in heparinase concentration with a rate constant equal to 0.12 C(c[triple chemical bond]n) (h(-1)), where C(c[triple chemical bond]n) is the gel-reactive group concentration. The reactive group concentration remained constant within the 2-4-h experiments. Competitive binding between heparinase and the protein contaminants was unimportant. A model was formulated for the immobilization procedure based on the diffusion of heparinase within the porous network and the binding kinetics as determined above. The model predicted the immobilization of heparinase to be kinetically controlled and the enzyme to distribute uniformly within the agarose matrix. These experimental techniques could be applied to predict the immobilized enzyme distribution for different enzyme systems that are not electrophoretically pure.     

Effects of microwave irradiation on triglyceride transesterification: Experimental and theoretical studies

An improved reaction rate of biodiesel fuel formation was observed under microwave irradiation. Such irradiation is effective for not only heating during the reaction but also preheating. The advantages observed in this study suggest that a continuous process, that is, the introduction of reactant preheated by microwave irradiation into reactor will be feasible. The reasons for the improved reaction rate are explained through the use of optimized structures, dipole moments, IR spectra and activation energies obtained using molecular orbital calculations. Planar triolein formed by microwave irradiation has higher reactivity, a lower dipole moment, a lower activation energy and stronger vibration around the carboxyl carbon, and is more reactive than triolein with a higher dipole moment.     

Experimental and theoretical studies of emodin interacting with a lipid bilayer of DMPC

Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM^?). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM^? are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM^?, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM^? affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM^?. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.     

Experimental and theoretical studies of vacuum-ultraviolet electronic circular dichroism of hydroxy acids in aqueous solution

The electronic circular dichroism (ECD) spectra of three L-hydroxy acids (L-lactic acid, (+)-(S)-2-hydroxy-3-methylbutyric acid, and (-)-(S)-2-hydroxyisocaproic acid) were measured down to 160 nm in aqueous solution using a vacuum-ultraviolet ECD spectrophotometer. To assign the two positive peaks around 210 and 175 nm and the one negative peak around 190 nm in the observed spectra, the ECD spectrum of L-lactic acid was calculated using time-dependent density functional theory (DFT) for the optimized structures by DFT and a continuum model. The observed ECD spectrum was successfully reproduced as the average spectrum for four optimized structures with seven water molecules that localized around the COO(-) and OH groups of L-lactic acid. The positive peak around 210 nm and the negative peak around 185 nm in the calculated spectrum were attributable to the nπ* transition of the carboxyl group, with the latter peak also being influenced by the ππ* transition of the carboxyl group; however, the positive peak around 165 nm involved unassignable higher energy transitions. The comparison of the calculated ECD spectra for L-lactic acid and L-alanine revealed that the network with loose hydrogen bonding around the COO(-) and OH groups is responsible for the flexible conformation of hydroxy acids and complicated side-chain dependence of ECD spectra relative to amino acids.     

Experimental and theoretical studies of the conformational perturbations induced by an abasic site

The three-dimensional structure of the natural undecamer duplex d(CGCACACACGC). d(GCGTGTGTGCG) has been determined by the combined use of NMR spectroscopy and restrained molecular dynamics (rMD) and also by molecular mechanics calculations using the JUMNA program without experimental distance constraints. Both procedures have also been used to model the abasic structure d(CGCACOCACGC).d(GCGTGTGTGCG), where 'O' indicates a modified abasic site: 3-hydroxy-2-(hydroxymethyl) tetrahydrofuran. For the natural duplex, 134 interproton distances have been obtained by complete relaxation matrix analysis of the NOESY cross-peaks intensities, using MARDIGRAS software. These distances along with 100 torsion angles for sugar ring and additional data derived from canonical A and B-DNA, have been used for structures refinement by restrained molecular dynamics. Comparison of the natural oligomer with the abasic structure obtained earlier by NMR/rMD (Y. Coppel, N. Berthet, C. Coulombeau, Ce. Coulombeau, J. Garcia and J. Lhomme, Biochemistry 36, 4817-4830, 1997) confirms that the creation of an abasic site, in this sequence context, leads to marked helix kinking. It is also shown that the JUMNA procedure is capable of reproducing the overall structural features of the natural and damaged DNA conformations without the use of experimental constraints.     

Experimental and theoretical studies of DNA separations by capillary electrophoresis in entangled polymer solutions.

Studies of electrophoretic separations of DNA restriction fragments by capillary electrophoresis in solutions of (hydroxyethyl) cellulose (HEC) were performed. Rheological studies were used to confirm that the entanglement threshold (phi*) for the HEC solutions used is approximately 0.004 g/mL, in good agreement with theoretical predictions. A mesh size an order of magnitude smaller than that found in agarose gels (on a per weight basis) was calculated using polymer-entanglement theory and was confirmed by electrophoretic measurements. Electrophoretic migration was shown to follow the Ogston regime under most conditions. An approach for obtaining smaller mesh sizes is presented.     

Experimental and theoretical studies of cadmium ions absorption by a new reduced recombinant defensin

Heavy metal pollutants such as Cd, Hg, Pb, As, and Se are considered as both a global problem and a growing threat to the humanity. Being strongly poisonous to the metal-sensitive enzymes and leading to the growth inhibition and death of organisms, these metals have a toxic impact on the plants and animals. Inducing the metal-binding cysteine-rich peptides such as metallothioneins, phytochelatins, and defensins, higher organisms like plants and animals usually react to the heavy metal stress. In this study, a recombinant defensin protein was expressed in bean and its ability in the cadmium absorption was determined. Experimental studies revealed that this protein was able to absorb cadmium ions in reduced form more than oxide one. Molecular dynamics simulations were carried out in order to evaluation of experimental studies, using a model of Cd²⁺ or Na⁺ and Cl^– ions enclosed in a fully hydrated simulation box with the recombinant defensin. The theoretical results also suggested that the reduced recombinant defensin was more powerful in the absorption of Cd²⁺ than its oxide form. The present study is the first report of Cd²⁺ absorption potential of this new reduced recombinant defensin. The results unraveled that this recombinant defensin can be adopted as a molecular switch in the cadmium pollution of the environment and also the important role of sulfur groups in the absorption of cadmium ions.     

Experimental and theoretical studies of the optical and electrical characteristics of a high-pressure pulsed discharge in argon

The optical and electrical characteristics of pulsed discharges in pure Ar at pressures of up to 7 atm, at which the discharge becomes unstable, are studied in a simple experimental device with automatic preionization. The gas temperature in the discharge is estimated from the width of the recorded emission spectrum. An analytical model of the vibrational relaxation of Ar ^*₂ (v) is used to better determine the constants of the vibrational-translational relaxation of Ar ^*₂ (v) molecules in their collisions with Ar atoms. The zerodimensional numerical model of a pulsed discharge in Ar is modified. The experimental and calculated results are compared in detail. Good agreement is achieved between the measured and calculated time dependences of the electrode voltage and the intensity of spontaneous emission in the pressure range of 1–6 atm, as well as between the measured and calculated values of the gas temperature at pressures of 3–6 atm. Preliminary results from numerical studies of the possibility of achieving generation are discussed.

     

Oscillatory kinetics of the peroxidase-oxidase reaction in an open system. Experimental and theoretical studies.

1. The oscillations in the peroxidase (donor: hydrogen-peroxide oxidoreductase, EC 1.11.1.7)-catalyzed reaction between NADH and O2 are undamped when the reaction is carried out in a system open to both substrates and when 2,4-dichlorophenol and methylene blue are present in the solution. 2. The waveform of the oscillations changes when the concentration of peroxidase is varied. 3. The waveforms obtained experimentally can be simulated by a branched chain reaction model in which the branching is quadratic. 4. A correlation between the present knowledge of the reaction and the model can be made by combining well established and hypothetical reaction steps into a few reaction schemes. A selection among schemes however, is not possible at the present time. 5. Compound III participates in the reaction as an active intermediate. This is possible because dichlorophenol stimulates the break down of compound III.     

Experimental and theoretical studies of rate constant evaluation for the solute-matrix interaction in affinity chromatography.

In an investigation of the problem of determining kinetic parameters for the interaction of a solute with immobilized ligand sites on an affinity matrix, a combination of experimental studies and numerical simulations of frontal chromatography of methyl orange on Sephadex G-25 has yielded a simpler method than existing procedures for characterizing solute-matrix kinetics. A significant change in approach has entailed the direct evaluation of the kinetic contribution to boundary spreading from the flow-rate dependence of boundary variance under conditions of concentration-independent chromatographic migration (linear kinetics). This kinetic contribution is then interpreted in terms of an experimentally more appropriate form of a quantitative relationship for diffusion-free chromatographic migration (H. W. Hethcote and C. DeLisi, 1982, J. Chromatogr. 240, 269-281). Finally, the results of numerical simulations of concentration-dependent chromatographic migration (Langmuir kinetics) have indicated that rate constants should also be determinable under these conditions by extrapolation of their apparent values obtained by the above procedure to infinite dilution.