Conformational studies of peptides representing a segment of TM7 from Vo-H+-V-ATPase in SDS micelles
Duarte, A.M. ; Jong, E.R. de; Koehorst, R.B.M. ; Hemminga, M.A. - \ 2010
European Biophysics Journal 39 (2010)4. - ISSN 0175-7571 - p. 639 - 646.
major coat protein - proton translocation channel - 5th transmembrane segment - dodecyl-sulfate micelles - membrane-proteins - escherichia-coli - nmr - bacteriophage-m13 - mimicking - detergent
The conformation of a transmembrane peptide, sMTM7, encompassing the cytoplasmic hemi-channel domain of the seventh transmembrane section of subunit a from V-ATPase from Saccharomyces cerevisiae solubilized in SDS solutions was studied by circular dichroism (CD) spectroscopy and fluorescence spectroscopy of the single tryptophan residue of this peptide. The results show that the peptide adopts an alpha-helical conformation or aggregated beta-sheet depending on the peptide-to-SDS ratio used. The results are compared with published data about a longer version of the peptide (i.e., MTM7). It is concluded that the bulky, positively charged arginine residue located in the center of both peptides has a destabilizing effect on the helical conformation of the SDS-solubilized peptides, leading to beta-sheet formation and subsequent aggregation.
Magnetic resonance microscopy of iron transport in methanogenic granules
Bartacek, J. ; Vergeldt, F.J. ; Gerkema, E. ; Jenicek, P. ; Lens, P. ; As, H. van - \ 2009
Journal of Magnetic Resonance 200 (2009)2. - ISSN 1090-7807 - p. 303 - 312.
heavy-metal uptake - porous-media - nmr - biofilm - sludge - diffusion - complexes - alginate - immobilization - biosorbents
Interactions between anaerobic biofilms and heavy metals such as iron, cobalt or nickel are largely unknown. Magnetic resonance imaging (MRI) is a non-invasive method that allows in situ studies of metal transport within biofilm matrixes. The present study investigates quantitatively the penetration of iron (1.75 mM) bound to ethylenediaminetetraacetate (EDTA) into the methanogenic granules (spherical biofilm). A spatial resolution of 109 × 109 × 218 µm3 and a temporal resolution of 11 min are achieved with 3D Turbo Spin Echo (TSE) measurements. The longitudinal relaxivity, i.e. the slope the dependence of the relaxation rate (1/T1) on the concentration of paramagnetic metal ions, was used to measure temporal changes in iron concentration in the methanogenic granules. It took up to 300 min for the iron–EDTA complex ([FeEDTA]2-) to penetrate into the methanogenic granules (3–4 mm in diameter). The diffusion was equally fast in all directions with irregularities such as diffusion-facilitating channels and diffusion-resistant zones. Despite these irregularities, the overall process could be modeled using Fick’s equations for diffusion in a sphere, because immobilization of [FeEDTA]2- in the granular matrix (or the presence of a reactive barrier) was not observed. The effective diffusion coefficient (Dejf) of [FeEDTA]2- was found to be 2.8 × 10-11 m2 s-1, i.e. approximately 4% of Dejf of [FeEDTA]2- in water. The Fickian model did not correspond to the processes taking place in the core of the granule (3–5% of the total volume of the granule), where up to 25% over-saturation by iron (compare to the concentration in the bulk solution) occurred
The effect of rice kernel microstructure on cooking behaviour: A combined µ-CT and MRI study
Mohoric, A. ; Vergeldt, F.J. ; Gerkema, E. ; Dalen, G. van; Doel, L.R. van den; Vliet, L.J. van; As, H. van; Duynhoven, J.P.M. van - \ 2009
Food Chemistry 115 (2009)4. - ISSN 0308-8146 - p. 1491 - 1499.
magnetic-resonance - water migration - puffed rice - nmr - grain - gelatinization - starch - profile - flour - model
In order to establish the underlying structure-dependent principles of instant cooking rice, a detailed investigation was carried out on rice kernels that were processed in eight different manners. Milling, parboiling, wet-processing and extrusion were applied, with and without a subsequent puffing treatment. The mesostructure of the rice kernels was examined by DSC and XRD, and the microstructure by µ-CT. Hydration behaviour during cooking was studied by MRI in a real-time manner. Based on simple descriptive models, three different classes of cooking behaviour can be discerned. The water ingress profiles during cooking of these three classes matched well with simulations from a model that was based on water demand of the starch mass and the porous microstructure of the kernels. Thus a clear correlation between meso/microstructure of a rice kernel and the cooking behaviour has been established
Intra- and inter-metabolite correlation spectroscopy of tomato metabolomics data obtained by liquid chromatography-mass spectrometry and nuclear magnetic resonance
Moco, S.I.A. ; Forshed, J. ; Vos, C.H. de; Bino, R.J. ; Vervoort, J.J.M. - \ 2008
Metabolomics 4 (2008)3. - ISSN 1573-3882 - p. 202 - 215.
multivariate-analysis - h-1-nmr spectroscopy - fruit - nmr - identification - lc/ms - fusion
Nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LCMS) are frequently used as technological platforms for metabolomics applications. In this study, the metabolic profiles of ripe fruits from 50 different tomato cultivars, including beef, cherry and round types, were recorded by both 1H NMR and accurate mass LC-quadrupole time-of-flight (QTOF) MS. Different analytical selectivities were found for these both profiling techniques. In fact, NMR and LCMS provided complementary data, as the metabolites detected belong to essentially different metabolic pathways. Yet, upon unsupervised multivariate analysis, both NMR and LCMS datasets revealed a clear segregation of, on the one hand, the cherry tomatoes and, on the other hand, the beef and round tomatoes. Intra-method (NMR¿NMR, LCMS¿LCMS) and inter-method (NMR¿LCMS) correlation analyses were performed enabling the annotation of metabolites from highly correlating metabolite signals. Signals belonging to the same metabolite or to chemically related metabolites are among the highest correlations found. Inter-method correlation analysis produced highly informative and complementary information for the identification of metabolites, even in de case of low abundant NMR signals. The applied approach appears to be a promising strategy in extending the analytical capacities of these metabolomics techniques with regard to the discovery and identification of biomarkers and yet unknown metabolites.
Molecular dynamics study of the solvation of an alpha-helical transmembrane peptide by DMSO
Duarte, A.M. ; Mierlo, C.P.M. van; Hemminga, M.A. - \ 2008
The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 112 (2008)29. - ISSN 1520-6106 - p. 8664 - 8671.
proton translocation channel - aib-rich peptide - yeast v-atpase - secondary-structure - force-field - simulations - proteins - nmr - dimethylsulfoxide - conformation
10-ns molecular dynamics study of the solvation of a hydrophobic transmembrane helical peptide in dimethyl sulfoxide (DMSO) is presented. The objective is to analyze how this aprotic polar solvent is able to solvate three groups of amino acid residues (i.e., polar, apolar, and charged) that are located in a stable helical region of a transmembrane peptide. The 25-residue peptide (sMTM7) used mimics the cytoplasmic proton hemichannel domain of the seventh transmembrane segment (TM7) from subunit a of H+-V-ATPase from Saccharomyces cerevisiae. The three-dimensional structure of peptide sMTM7 in DMSO has been previously solved by NMR spectroscopy. The radial and spatial distributions of the DMSO molecules surrounding the peptide as well as the number of hydrogen bonds between DMSO and the side chains of the amino acid residues involved are extracted from the molecular dynamics simulations. Analysis of the molecular dynamics trajectories shows that the amino acid side chains are fully embedded in DMSO. Polar and positively charged amino acid side chains have dipole¿dipole interactions with the oxygen atom of DMSO and form hydrogen bonds. Apolar residues become solvated by DMSO through the formation of a hydrophobic pocket in which the methyl groups of DMSO are pointing toward the hydrophobic side chains of the residues involved. The dual solvation properties of DMSO cause it to be a good membrane-mimicking solvent for transmembrane peptides that do not unfold due to the presence of DMSO.
Segment TM7 from the cytoplasmic hemi-channel from Vo-H+-V-ATPase includes a flexible region that has a potential role in proton translocation
Duarte, A.M. ; Jong, E.R. de; Wechselberger, R. ; Mierlo, C.P.M. van; Hemminga, M.A. - \ 2007
Biochimica et Biophysica Acta. Biomembranes 1768 (2007)9. - ISSN 0005-2736 - p. 2263 - 2270.
mediated cross-linking - transmembrane segment - chemical-shifts - subunit - nmr - peptide - binding - system - pumps
A 900-MHz NMR study is reported of peptide sMTM7 that mimics the cytoplasmic proton hemi-channel domain of the seventh transmembrane segment (TM7) from subunit a of H+-V-ATPase from Saccharomyces cerevisiae. The peptide encompasses the amino acid residues known to actively participate in proton translocation. In addition, peptide sMTM7 contains the amino acid residues that upon mutation cause V-ATPase to become resistant against the inhibitor bafilomycin. 2D TOCSY and NOESY 1H¿1H NMR spectra are obtained of sMTM7 dissolved in d6-DMSO and are used to calculate the three-dimensional structure of the peptide. The NMR-based structures and corresponding dynamical features of peptide sMTM7 show that sMTM7 is composed of two ¿-helical regions. These regions are separated by a flexible hinge of two residues. The hinge acts as a ball-and-joint socket and both helical segments move independently with respect to one another. This movement in TM7 is suggested to cause the opening and closing of the cytoplasmic proton hemi-channel and enables proton translocation.
0.7 and 3 T MRI and sap flow in intact trees: xylem and phloem in action
Homan, N. ; Windt, C.W. ; Vergeldt, F.J. ; Gerkema, E. ; As, H. van - \ 2007
Applied Magnetic Resonance 32 (2007)1-2. - ISSN 0937-9347 - p. 157 - 170.
nuclear-magnetic-resonance - distance water transport - noninvasive measurement - ricinus-communis - plants - nmr - long - microscopy
Dedicated magnetic resonance imaging (MRI) hardware is described that allows imaging of sap flow in intact trees with a maximal trunk diameter of 4 cm and height of several meters. This setup is used to investigate xylem and phloem flow in an intact tree quantitatively. Due to the fragile gradients in pressure present in both xylem and phloem, methods to study xylem and phloem transport must be minimally invasive. MRI flow imaging by means of this hardware certainly fulfils this condition. Flow is quantified in terms of (averaged) velocity, volume flow (flux) and flow conducting area, either in imaging mode or as a nonspatially resolved total. Results obtained for one tree, imaged at two different field strengths (0.7 and 3 T), are compared. An overall shortening of observed T2 values is manifest going from 0.7 to 3 T. Although some susceptibility artefacts may be present at 3 T, the results are still reliable and the gain in sensitivity results in shorter measurement time (or higher signal-to-noise ratio) with respect to the 0.7 T system. The results demonstrate that by use of dedicated hardware, xylem and phloem flow and its mutual interaction, can be studied in intact trees in relation to the water balance and in response to environmental (stress) conditions
Intact plant magnetic resonance imaging to study dynamics in long-distance sap flow and flow-conducting surface area
Scheenen, T.W.J. ; Vergeldt, F.J. ; Heemskerk, A.M. ; As, H. van - \ 2007
Plant Physiology 144 (2007)2. - ISSN 0032-0889 - p. 1157 - 1165.
embolism repair - water transport - vessel contents - xylem vessel - phloem - nmr - microscopy - tissues - stems - mri
Due to the fragile pressure gradients present in the xylem and phloem, methods to study sap flow must be minimally invasive. Magnetic resonance imaging (MRI) meets this condition. A dedicated MRI method to study sap flow has been applied to quantify long-distance xylem flow and hydraulics in an intact cucumber (Cucumis sativus) plant. The accuracy of this MRI method to quantify sap flow and effective flow-conducting area is demonstrated by measuring the flow characteristics of the water in a virtual slice through the stem and comparing the results with water uptake data and microscopy. The in-plane image resolution of 120 x 120 µm was high enough to distinguish large individual xylem vessels. Cooling the roots of the plant severely inhibited water uptake by the roots and increased the hydraulic resistance of the plant stem. This increase is at least partially due to the formation of embolisms in the xylem vessels. Refilling the larger vessels seems to be a lengthy process. Refilling started in the night after root cooling and continued while neighboring vessels at a distance of not more than 0.4 mm transported an equal amount of water as before root cooling. Relative differences in volume flow in different vascular bundles suggest differences in xylem tension for different vascular bundles. The amount of data and detail that are presented for this single plant demonstrates new possibilities for using MRI in studying the dynamics of long-distance transport in plants.
Intramolecular cycloaddition/cycloreversion of (E)-3 beta,17 beta-diacetoxy-5,10-secoandrost-1(10)-en-5-one
Khripach, V.A. ; Zhabinskii, V.N. ; Kuchto, A.I. ; Zhiburtovich, Y.Y. ; Gromak, V.V. ; Groen, M.B. ; Louw, J. van der; Groot, Æ. de - \ 2006
Tetrahedron Letters 47 (2006)38. - ISSN 0040-4039 - p. 6715 - 6718.
medium-sized ring - secosteroids - reactivity - steroids - nmr - program
Treatment of 3 beta,17 beta-diacetoxy-5,10-secoandrost-1(10)-en-5-one with (BF3Et2O)-Et-. was shown to proceed with cleavage of the macrocycle and formation of a new compound containing a cyclopentenone ring. Based on DFT calculations, an intramolecular Lewis acid promoted [2+2]cycloaddition, followed by a cycloreversion of the intermediate oxetane, is proposed as a possible reaction mechanism.
Effects of cold-girdling on flows in the transport phloem in Ricinus communis: is mass flow ihibited?
Peuke, A.D. ; Windt, C.W. ; As, H. van - \ 2006
Plant, Cell & Environment 29 (2006)1. - ISSN 0140-7791 - p. 15 - 25.
nuclear-magnetic-resonance - water-flow - sieve tubes - noninvasive measurement - assimilate transport - phaseolus-vulgaris - solute transport - plants - translocation - nmr
The effects of cold girdling of the transport phloem at the hypocotyl of Ricinus communis on solute and water transport were investigated. Effects on the chemical composition of saps of phloem and xylem as well as of stem tissue were studied by conventional techniques and the water flow in the phloem was investigated by NMR imaging. Cold girdling reduced the concentration of sucrose but not that of inorganic solutes or amino acids in phloem saps. The possibility that cold treatment inhibited the retrieval of sucrose into the phloem, following leaching from the sieve tubes along a chemical gradient is discussed. Leaching of other solutes did not occur, as a result of missing promoting gradients in stem tissue. Following 3 d of cold girdling, sugar concentration increased and starch was synthesized and accumulated in stem tissue above the cold girdling region and along the cold-treated phloem pathway due to leaching of sugars from the phloem. Only in the very first period of cold girdling (<15-30 min) was mass flow inhibited, but recovered in the rest of cold treatment period to values similar to the control period before and the recovery period after the cold treatment. It is concluded that cold treatment affected phloem transport through two independent and reversible processes: (1) a permanent leaching of sucrose from the phloem stem without normal retrieval during cold treatment, and (2) a short-term inhibition of mass flow at the beginning of cold treatment, possibly involving P proteins. Possible further mechanisms for reversible inhibition of water flow are discussed
Building-Up a comprehensive database of flavonoids based on nuclear magnetic resonance data.
Moco, S.I.A. ; Tseng, L. ; Spraul, M. ; Chen, Z. ; Vervoort, J.J.M. - \ 2006
Chromatographia 64 (2006)9/10. - ISSN 0009-5893 - p. 503 - 508.
The improvements in separation and analysis of complex mixtures by LC-NMR during the last decade have shifted its emphasis from data acquisition to data analysis. For correct data analysis, not only high quality datasets are necessary, but adequate software and adequate databases for semi (or fully)-automated assignments of complex molecules are needed. Only by using NMR, when necessary in combination with MS, the identification of molecules, as present for example in natural products, can be achieved. Here we report on the ongoing efforts required for the construction of an NMR database of flavonoids, implemented for automated assignments of flavonoids. The procedure is demonstrated for a series of flavonoids
Investigating the Permanent Electric Dipole Moment of ß-Lactoglobulin Fibrils, Using Transient Electric Birefringence
Rogers, S.S. ; Venema, P. ; Ploeg, J.P.M. van der; Linden, E. van der; Sagis, L.M.C. ; Donald, A.M. - \ 2006
Biopolymers 82 (2006)3. - ISSN 0006-3525 - p. 241 - 252.
amyloid fibrils - polyelectrolyte solutions - length distribution - protein - nmr - macromolecules - polarizability - spectroscopy - aggregation - constraints
Amyloid fibrils, which are polymeric assemblies of protein molecules, have been intensively studied on a structural level, yet due to complications such as the disorder within the molecules, several aspects of their structure remain mysterious. Similarly, the kinetics of assembly are not well understood. Here we investigate the electric dipole moment of ß-lactoglobulin fibrils, a model amyloid fibril system, by applying the technique of transient electric birefringence. This moment appears to be large, and comparable to the total moment of the constituent protein monomers if they were joined in a chain, head-to-tail, without changing conformation, suggesting an ordered joining of monomers in the fibril. Such an ordered assembly may have implications for the assembly mechanism of ß-lactoglobulin fibrils in particular, and amyloid fibrils in general
Plant metabolomics: from holistic hope, to hype, to hot topic
Hall, R.D. - \ 2006
New Phytologist 169 (2006)3. - ISSN 0028-646X - p. 453 - 468.
electrophoresis mass-spectrometry - systems biology - arabidopsis-thaliana - functional genomics - secondary metabolites - tomato - tool - nmr - transcriptomics - discrimination
In a short time, plant metabolomics has gone from being just an ambitious concept to being a rapidly growing, valuable technology applied in the stride to gain a more global picture of the molecular organization of multicellular organisms. The combination of improved analytical capabilities with newly designed, dedicated statistical, bioinformatics and data mining strategies, is beginning to broaden the horizons of our understanding of how plants are organized and how metabolism is both controlled but highly flexible. Metabolomics is predicted to play a significant, if not indispensable role in bridging the phenotype-genotype gap and thus in assisting us in our desire for full genome sequence annotation as part of the quest to link gene to function. Plants are a fabulously rich source of diverse functional biochemicals and metabolomics is also already proving valuable in an applied context. By creating unique opportunities for us to interrogate plant systems and characterize their biochemical composition, metabolomics will greatly assist in identifying and defining much of the still unexploited biodiversity available today
Identification of structural features of various (O-Acetylated) Xylo-Oligosaccharides from Xylan-Rich agricultural by-products: A review
Kabel, M.A. ; Schols, H.A. ; Voragen, A.G.J. - \ 2004
ACS symposium series 864 (2004). - ISSN 0097-6156 - p. 108 - 121.
anion-exchange chromatography - flight mass-spectrometry - wheat-flour arabinoxylan - aspergillus-awamori - h-1-nmr spectroscopy - side-chains - cell-walls - wood - nmr - glucuronoarabinoxylans
Hydrolysates obtained by hydrothermal treatment of four xylan rich by-products (wheat bran, brewery's spent grain, corn cobs and Eucalyptus wood) were characterised. Depending on the feedstock material studied, a wide variety of differently substituted xylo-oligosaccharides (XOS) and xylan-fragments were obtained. The structural features of the this way obtained arabinose, 4-O-methylglucuronic acid and O-acetyl substituted XOS are reviewed. High performance anion-exchange chromatography (HPAEC),reversed phase (RP)-high performance liquid chromatography (HPLC), mass spectrometry (MS), NMR spectroscopy, RP-HPLC-MS and RP-HPLC-NMR showed to be very useful for the separation and characterisation of the detailed structures of the substituted XOS
Conformation and orientation of a protein folding intermediate trapped by adsorption
Engel, M.F.M. ; Visser, A.J.W.G. ; Mierlo, C.P.M. van - \ 2004
Proceedings of the National Academy of Sciences of the United States of America 101 (2004)31. - ISSN 0027-8424 - p. 11316 - 11321.
bovine alpha-lactalbumin - hydrogen-exchange - stability - surface - binding - nmr
Although adsorption-induced conformational changes of proteins play an essential role during protein adsorption on interfaces, detailed information about these changes is lacking. To further the current understanding of protein adsorption, in this study, the orientation, conformation, and local stability of bovine a-lactalbumin (BLA) adsorbed on polystyrene nanospheres is characterized at the residue level by hydrogen/deuterium exchange and 2D NMR spectroscopy. Most of the adsorbed BLA molecules have conformational properties similar to BLA molecules in the acid-induced molten globule state (A state). A folding intermediate of BLA is thus induced and trapped by adsorption of the protein on the hydrophobic interface. Several residues, clustered on one side of the adsorbed folding intermediate of BLA, have altered amide proton exchange protection factors compared to those of the A state of BLA. This side preferentially interacts with the interface and includes residues in helix C, the calcium binding site, and part of the beta-domain. Local unfolding of this interacting part of the adsorbed protein seems to initiate the adsorption-induced unfolding of BLA. Adsorption-induced protein unfolding apparently resembles more the mechanical unfolding of a protein than the global unfolding of a protein as induced by denaturant, pH, or pressure. 2D macromolecular crowding prevented the minority of adsorbed BLA molecules, which arrived late at the interface, to unfold to the A state. Protein adsorption is a novel and challenging approach to probe features of the free energy landscapes accessible to unfolding proteins.
Magnetic resonance imaging of single rice kernels during cooking
Mohoric, A. ; Vergeldt, F.J. ; Gerkema, E. ; Jager, P.A. de; Duynhoven, J.P.M. van; Dalen, G. van; As, H. van - \ 2004
Journal of Magnetic Resonance 171 (2004)1. - ISSN 1090-7807 - p. 157 - 162.
water migration - nmr - grain - gelatinization - starch - model
The RARE imaging method was used to monitor the cooking of single rice kernels in real time and with high spatial resolution in three dimensions. The imaging sequence is optimized for rapid acquisition of signals with short relaxation times using centered out RARE. Short scan time and high spatial resolution are critical factors in the investigation of the cooking behavior of rice kernels since time and spatial averaging may lead to erroneous results. The results are confirming the general pattern of moisture ingress that has been suspected from previous (more limited) studies. Water uptake as determined by analysis of the MRI time series recorded during cooking compares well with gravimetric studies. This allows using these real-time MRI data for developing and validating models that describe the effect of kernel microstructure on its cooking behavior. (C) 2004 Elsevier Inc. All rights reserved.
Design of molecular beacons for AmpliDet RNA assay. Characterization of binding stability and probe specificity
Szemes, M. ; Schoen, C.D. - \ 2003
Analytical Biochemistry 315 (2003)2. - ISSN 0003-2697 - p. 189 - 201.
sequence-based amplification - nearest-neighbor thermodynamics - potato-virus-y - duplex stability - dna - mismatches - nmr - oligonucleotides - analogs
AmpliDet RNA is a real-time diagnostic method, the specificity of which is defined mainly by the molecular beacon (MB). MBs can be characterized according to the stability of their stem-and-loop structures and that of the probe–target duplex via the free energies accompanying their formation. By the application of thermodynamic models, we propose a prediction method for these ¿G0 parameters, which was compared to experimental analysis. The average absolute discrepancies for ¿G041 and for the melting temperatures of MB secondary structures were 0.30±0.26 kcal/mol and 2.15±1.5 °C, respectively. ¿G041 of probe–target interaction was predicted with a discrepancy of 1.2±1.0 kcal/mol. To characterize specificity, we formulated a model system with several MBs of highly similar sequence, but different lengths, and template RNAs carrying different types of mutations. We demonstrated the ability to detect a point mutation, or to tolerate one, irrespective of mismatch type. Of the nucleotide analogues tested, universal pyrimidine was found to increase MB tolerance substantially toward polymorphism. In the present study MBs were characterized under AmpliDet RNA conditions, with respect to probe stability, binding strength, and specificity, which led us to propose a design method, useful for probe design for AmpliDet RNA and adaptable to microarrays.
Diffusional properties of methanogenic granular sludge: 1H-NMR Characterisation
Lens, P.N.L. ; Gastesi, R. ; Vergeldt, F. ; Aelst, A.C. van; Pisabarro, G. ; As, H. van - \ 2003
Applied and Environmental Microbiology 69 (2003)11. - ISSN 0099-2240 - p. 6644 - 6649.
nuclear-magnetic-resonance - fatty-acid degradation - mass-transfer - transport processes - molecular-diffusion - porous-media - spin-echo - biofilms - nmr - coefficients
The diffusive properties of anaerobic methanogenic and sulfidogenic aggregates present in wastewater treatment bioreactors were studied using diffusion analysis by relaxation time-separated pulsed-field gradient nuclear magnetic resonance (NMR) spectroscopy and NMR imaging. NMR spectroscopy measurements were performed at 22degreesC with 10 ml of granular sludge at a magnetic field strength of 0.5 T (20 MHz resonance frequency for protons). Self-diffusion coefficients of H2O in the investigated series of mesophilic aggregates were found to be 51 to 78% lower than the self-diffusion coefficient of free water. Interestingly, self-diffusion coefficients of H2O were independent of the aggregate size for the size fractions investigated. Diffusional transport occurred faster in aggregates growing under nutrient-rich conditions (e.g., the bottom of a reactor) or at high (55degreesC) temperatures than in aggregates cultivated in nutrient-poor conditions or at low (10degreesC) temperatures. Exposure of aggregates to 2.5% glutaraldehyde or heat (70 or 90degreesC for 30 min) modified the diffusional transport up to 20%. In contrast, deactivation of aggregates by HgCl2 did not affect the H2O self-diffusion coefficient in aggregates. Analysis of NMR images of a single aggregate shows that methanogenic aggregates possess a spin-spin relaxation time and self-diffusion coefficient distribution, which are due to both physical (porosity) and chemical (metal sulfide precipitates) factors.
Location of O-acetyl substituents in xylo-oligosaccharides obtained from hydrothermally treated Eucalyptus wood
Kabel, M.A. ; Waard, P. de; Schols, H.A. ; Voragen, A.G.J. - \ 2003
Carbohydrate Research : an international journal 338 (2003)1. - ISSN 0008-6215 - p. 69 - 77.
anion-exchange chromatography - mimosa-scabrella bracatinga - acidic d-xylan - mass-spectrometry - liquid-chromatography - h-1-nmr spectroscopy - nmr - arabinoxylan - separation - wheat
A combination of techniques was used to localise the O-acetyl substituents in xylo-oligosaccharides, which are present in hydrolysates of hydrothermally treated Eucalyptus wood. Reversed-phase (RP)-high performance liquid chromatography (HPLC) coupled on-line to both a mass spectrometer and an evaporating light scattering (ELS) detector provided data about the order of elution of the various O-acetylated oligomers. The retention of the oligomers on the column depended on the number and position of the O-acetyl substituents within the xylo-oligosaccharides. One dimensional (1D)- and two dimensional (2D)-1H NMR spectroscopy was used to study the structural features of several xylotetramers separated by RP-HPLC, each having one O-acetyl substituent. O-Acetyl migration was proven to have occurred in these xylo-oligosaccharides. Mainly O-acetyl migration within the same xylosyl residue was observed. RP-HPLC–NMR was performed in order to study the structural features of the acetylated oligomers ‘on-line’ avoiding O-acetyl migration. Finally, the precise location of the 2-O- or 3-O-acetyl substituent in 6 xylotetramers and 4 xylotrimers separated by RP-HPLC was determined.
Liming effects on the chemical composition of the organic surface layer of a mature Norway spruce stand (Picea abies [L.] Karst.)
Rosenberg, W. ; Nierop, K.G.J. ; Knicker, H. ; Jager, P.A. de; Kreutzer, K. ; Weiá, T. - \ 2003
Soil Biology and Biochemistry 35 (2003). - ISSN 0038-0717 - p. 155 - 165.
tetramethylammonium hydroxide tmah - acid forest soils - microbial biomass - vegetation succession - matter - nitrogen - pyrolysis - origin - carbon - nmr
The application of lime in a mature Norway spruce (Picea abies [L.] Karst.) forest in southern Germany induced major changes in the activity of soil organisms and root growth. Since this may influence the chemical compostion of the soil organic matter (SOM) of the organic surface layer, its composition and changes due to the treatment were examined in this study. Fine roots of Norway spruce have a relatively low content of extractable lipids, a low alkyl C content (C-13 CPMAS NMR) and a high ratio of non-cellulosic to cellulosic carbohydrates (NC/CC, carbohydrate determination by MBTH and gas chromatography analyses) as compared to needles. Furthermore, they show high ratios of suberin/cutin compounds (thermally assisted hydrolysis and methylation, (THM)) and high ratios of eicosanic acid/phytadiene I in their lipid extracts (pyrolysis-GC/MS). Liming (4 t ha(-1) dolomite) of a Norway spruce organic surface layer decreased the proportion of alkyl C, the alkyl C/O-alkyl C ratio, and the content of extractable lipids. The NC/CC ratio and the abundance of suberin relative to cutin components increased. The contribution of the chlorophyll component phytadiene I decreased in relation to eicosanic acid. These changes are attributed to increased fine root formation in the organic layer after liming. Furthermore, the presence of less degraded lignin (THM, peak ratio of 3,4-dimethoxybenzoic acid, methyl ester/3,4-dimethoxy-benzaldehyde) on the limed plot is explained by the increased input of relatively fresh fine root material. On the other hand, the decrease in the carbon-to-nitrogen ratio may be attributed to the higher microbial activity after liming. (C) 2003 Elsevier Science Ltd. All rights reserved.