Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Genetic analysis of orotic acid predicted with Fourier transform infrared milk spectra
    Zaalberg, R.M. ; Buitenhuis, A.J. ; Sundekilde, U.K. ; Poulsen, N.A. ; Bovenhuis, H. - \ 2020
    Journal of Dairy Science 103 (2020)4. - ISSN 0022-0302 - p. 3334 - 3348.
    breed difference - cattle - orotic acid - spectroscopy

    Fourier transform infrared spectral analysis is a cheap and fast method to predict milk composition. A not very well studied milk component is orotic acid. Orotic acid is an intermediate in the biosynthesis pathway of pyrimidine nucleotides and is an indicator for the metabolic cattle disorder deficiency of uridine monophosphate synthase. The function of orotic acid in milk and its effect on calf health, health of humans consuming milk or milk products, manufacturing properties of milk, and its potential as an indicator trait are largely unknown. The aims of this study were to determine if milk orotic acid can be predicted from infrared milk spectra and to perform a large-scale phenotypic and genetic analysis of infrared-predicted milk orotic acid. An infrared prediction model for orotic acid was built using a training population of 292 Danish Holstein and 299 Danish Jersey cows, and a validation population of 381 Danish Holstein cows. Milk orotic acid concentration was determined with nuclear magnetic resonance spectroscopy. For genetic analysis of infrared orotic acid, 3 study populations were used: 3,210 Danish Holstein cows, 3,360 Danish Jersey cows, and 1,349 Dutch Holstein Friesian cows. Using partial least square regression, a prediction model for orotic acid was built with 18 latent variables. The error of the prediction for the infrared model varied from 1.0 to 3.2 mg/L, and the accuracy varied from 0.68 to 0.86. Heritability of infrared orotic acid predicted with the standardized prediction model was 0.18 for Danish Holstein, 0.09 for Danish Jersey, and 0.37 for Dutch Holstein Friesian. We conclude that milk orotic acid can be predicted with moderate to good accuracy based on infrared milk spectra and that infrared-predicted orotic acid is heritable. The availability of a cheap and fast method to predict milk orotic acid opens up possibilities to study the largely unknown functions of milk orotic acid.

    Studying fast dynamics in biological complexes : from photosynthesis in vivo to single DNA molecules in vitro
    Farooq, Shazia - \ 2017
    Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): Johannes Hohlbein. - Wageningen : Wageningen University - ISBN 9789463431002 - 149
    biology - dna - proteins - interactions - probability analysis - förster resonance energy transfer - fluorescence - spectroscopy - photosynthesis - biologie - dna - eiwitten - interacties - waarschijnlijkheidsanalyse - förster resonantie-energieoverdracht - fluorescentie - spectroscopie - fotosynthese

    During the last decades, fluorescence spectroscopy has emerged as a powerful tool in the fields of biophysics, biotechnology, biochemistry, cellular biology and the medical sciences. These techniques are highly sensitive, and allow us to study the structure and dynamics of (bio)molecular systems (Valeur 2001). A significant advantage of fluorescence techniques is that they can often be non-invasive and measurements can be performed in real time. In this thesis different advanced fluorescence methods will be used to study two important biological processes: (1) DNA dynamics and (2) plant photosynthesis. The first part aims at improving the smFRET technique for the analysis of DNA dynamics and other fast conformational changes. This improvement is made by combining and developing instrumentation and data evaluation tools. The second part is the continuous development of time-resolved fluorescence spectroscopy methods, as well their application in the field of photosynthesis to study ultrafast processes in thylakoid membranes and leaves. The two fluorescence techniques are technically and conceptually very different, but they are both designed for analysis of biomolecular systems. In this thesis, the techniques are applied to study energy transfer and dynamical changes in DNAs, thylakoid membranes and leaves.

    REFERENCE: VALEUR B 2001. Molecular Fluorescence: Principles and Applications. 1 ed: Wiley-VCH.

    Electrically excited liquid water : lessons from floating water bridge
    Wexler, A.D. - \ 2016
    Wageningen University. Promotor(en): Cees Buisman, co-promotor(en): J. Woisetschläger; E.C. Fuchs. - Wageningen : Wageningen University - ISBN 9789462577039 - 223
    water - liquids - electric field - thermodynamics - bridges - equilibrium - disequilibrium - electrodynamics - nuclear magnetic resonance - neutron scattering - infrared spectroscopy - spectroscopy - gas chromatography - electrical conductivity - interferometry - spectral analysis - physics - water - vloeistoffen (liquids) - elektrisch veld - thermodynamica - bruggen - evenwicht - verstoord evenwicht - elektrodynamica - kernmagnetische resonantie - neutronenverstrooiing - infraroodspectroscopie - spectroscopie - gaschromatografie - elektrische geleidbaarheid - interferometrie - spectraalanalyse - fysica

    Water is essential to a healthy and secure world. Developing new technologies which can take full advantage of the unique attributes of water is important for meeting the ever increasing global demand while reducing the production footprint. Water exhibits unexpected departures in more than 70 physical and chemical properties compared to other molecular species of similar chemical composition. The principal cause for this behavior is ascribed to the large number of hydrogen bonds which form between neighboring water molecules. Hydrogen bonds are moderately strong in water and exhibit both electrostatic as well as covalent character. When examining the liquid state these interactions play a significantly role in moderating the interchange between dynamics and structure. In disordered materials such as a liquid there are three length scales of importance: 1) at the microscopic molecular level interactions dominate, 2) the macroscopic level where classical forces act upon the statistically isotropic medium, and 3) the mesoscopic level where heterogeneous interactions dominate through evolving transient structures each with unique dynamical behaviors. The mesoscale is important to most environmental and biological processes and is even more poorly understood than the liquid state in general. The aim of this thesis is to explore the extended molecular behavior of liquid water excited by strong electric field gradients.

    The floating water bridge belongs to a larger class of phenomena called electrohydrodynamic (EHD) liquid bridges. These self-suspending liquid catenaries can occur in a number of polar liquids provided the conductivity is low. They exhibit elevated temperatures and bidirectional flow patterns, as well as sub-Hz diameter oscillations. The flow behavior and dynamics of these bridges is complex but can be addressed by continuum level EHD theory. The polarizing effect of the electric field gradient accelerates the fluid tangentially along the surface resulting in a Taylor pump which supplies the bridge with liquid. The free hanging section is stable against gravity within a band of operational parameters whereby the electric field strength is sufficient confine fluid elements within the bridge. A standardized protocol for operating stable EHD bridges in multiple configurations is developed and presented. This is the primary tool used throughout the thesis and provides a macroscopic object for the experimental examination of how forces which typically only occur over a few nanometers in nature affect the organization of polar liquids, notably water. In order to examine the role that the electric field gradient plays in the observed molecular changes found in EHD bridges a simple point-plane electrode system was also employed.

    There are available a number of tools which provide complimentary information on chemical and physical processes occurring in the liquid state. A brief introduction is given on the interaction between electromagnetic waves and matter with respect to field theory and methods from atomic physics. The basis for interaction over different length scales is established. Electrochemical characterization includes the quantification and identification of the charge carrying species present, the relative proton concentration, and the complex dielectric response. The vibrational and rotational motion of molecules is measured with a combination of infrared emission spectroscopy and imaging and permits the detection of both the thermal bath and non-equilibrium molecular excited states. The local structure of the liquid matter contained in the bridge can be elucidated through the methods discussed here. X-rays provide information on the electron density whereas neutrons reveal nuclear positions. Together with isotope substitution a complete picture of the motionally averaged local structure of the liquid in the bridge can be recovered. QENS is a special case of inelastic scattering which permits the measurement of diffusion, relaxation, and other slow energy or mass transfer modes in materials using a time-of-flight spectrometer. This data compliments the NMR methods used herein specifically to probe the environment of protons in the system; and to provide clues about the strength of both intra- intermolecular coupling in the system. Very small perturbations in the optical properties of a liquid can be detected using interferometry; these ultimately reflect changes in the polarizability of the liquid which can arise from changes in physical properties. Raman scattering is an inelastic method which can probe changes to the polarizability of a liquid that reflect shifts in the local molecular environment and can be used to determine both local and non-local vibrational coupling.

    Magnetic resonance imaging was used to track the flow field present in the bridge without the use of tracer particles; revealing that the bridge has a layered structure, with distinct flow regimes lying one on top of the other. Investigation of the electrochemistry in the water bridge found that protons account for 87% of the charge transport in the bridge. Impedance spectroscopy and pH measurement corroborate the finding that a proton gradient forms across the entire system. The results from elastic neutron and X-ray scattering reveal that the static structure is unchanged within the given accuracy of the employed measurements. However, the systematic analysis of the data using a reverse Monte Carlo computer simulation revealed significant dynamical changes that are reliable above the limited instrument precision. The imposed electric field of an EHD bridge distorts the local Coulombic interactions between molecules altering the dielectric relaxation pathway so that it becomes more favorable for the absorbed energy to become trapped locally for a longer period of time. The electric field in the bridge system is not uniform. Strong field gradients are present which stimulate changes in the molecular polarizability, generating gradients of physical properties, and restricting the allowed rotational-vibrational relaxation transitions. These trends are comparable to those from ultrafast relaxation measurements where the vibrational lifetime of the OH stretch of HDO was found to be significantly shorter in the bridge than in the neat liquid. This absorbed energy, however, remained trapped in a local intermediate state longer in the bridge before being released as a thermal perturbation. The nuclear relaxation dynamics in a glycerol bridge showed similar behavior where the transverse and longitudinal magnetization lifetimes diverged from the expectation values given the systems temperature.

    From the experimental observations several features of electrically excited water appear. At the gross continuum level the operation of a floating water bridge results in the production of a charge imbalance between anolyte and catholyte. This is in part due to the enhanced proton mobility in the bridge. Protons no longer are confined to the hydrogen bond mediated Grotthuss mechanism but can travel even faster through a delocalized state. This means that charge can be pumped faster than it can be neutralized resulting in the observed electrochemical differences. The energy level of protons in the conduction channel is the difference between the ground and excited state levels observed as a non-thermal emission feature in the mid-infrared. The proton channel will be active over relatively short distances and will experience interruptions due to fluctuations in molecular position driven by local force gradients. These channels are localized and discontinuous providing the physical basis for the onset of mesoscale dynamic heterogeneity in the excited liquid. The picture begins to emerge whereby local trapping states and long-range cooperative coupling modes dynamically exchange energy. The energy exchange is far from equilibrium and supports multiple transfer mechanisms. At the mesoscale the excited state exhibits traits of a chaotic dynamical system and provides a varied energetic landscape whereby rotational-vibrational transition dipoles, nuclear spin states, and thermodynamic potentials, such as the configurational entropy, non-adiabatically – that is there is a pumping of heat in response to the induced fluctuating gradient fields. The transfer of perturbations from local to collective modes and vice versa requires that the chemical, thermal, and electromagnetic potentials present in the molecular milieu be linked to the entropy production.

    This early foray into the non-equilibrium dynamics and mesoscale organization of electrically excited liquid water opens an opportunity to develop technologies which better mimic nature. Taking biological systems as the exemplary standard by which to compare it is necessary to develop soft matter based technical systems which take advantage of the link between electric, magnetic, and thermal fields to drive chemical and physical processes with higher efficiency. Water, as well as other polar liquids, can be locally controlled so as to induce spatial variation in the chemical potential whereby one can imagine a reactor where disparate physical or chemical process can occur in close proximity without the need for rigid segregating structures. Furthermore, this level of control is dynamical such that the organization of the partitioning in the liquid can be changed in time so that the total energy requirement of the intended process is optimized. With such an approach it is conceivable that the size, complexity, and energetic costs of performing many industrial and municipal processes can be reduced. Rather than treating liquids as bulk fluids the opportunity presents itself to use the internal structure and dynamics of liquids to build fluid technologies.

    On the use of the observation-wise k-fold operation in PCA cross-validation
    Saccenti, E. ; Camacho, J. - \ 2015
    Journal of Chemometrics 29 (2015)8. - ISSN 0886-9383 - p. 467 - 478.
    principal component analysis - missing data - models - number - spectroscopy - mspc - pls
    Cross-validation (CV) is a common approach for determining the optimal number of components in a principal component analysis model. To guarantee the independence between model testing and calibration, the observationwise k-fold operation is commonly implemented in each cross-validation step. This operation renders the CV algorithm computationally intensive, and it is the main limitation to apply CV on very large data sets. In this paper, we carry out an empirical and theoretical investigation of the use of this operation in the element-wise k-fold (ekf) algorithm, the state-of-the-art CV algorithm. We show that when very large data sets need to be cross-validated and the computational time is a matter of concern, the observation-wise k-fold operation can be skipped. The theoretical properties of the resulting modified algorithm, referred to as column-wise k-fold (ckf) algorithm, are derived. Also, its performance is evaluated with several artificial and real data sets. We suggest the ckf algorithm to be a valid alternative to the standard ekf to reduce the computational time needed to cross-validate a data set
    The supramolecular organization of a peptide-based nanocarrier at high molecular detail
    Rad-Malekshahi, M. ; Visscher, K.M. ; Rodrigues, J.P.G.L.M. ; Vries, R.J. de; Hennink, W.E. ; Baldus, M. ; Bonvin, A.M.J.J. ; Mastrobattista, E. - \ 2015
    Journal of the American Chemical Society 137 (2015)24. - ISSN 0002-7863 - p. 7775 - 7784.
    solid-state nmr - protein secondary structure - chemical-shift index - force-field - polypeptide vesicles - drug-delivery - beta-sheet - dynamics - nanovesicles - spectroscopy
    Nanovesicles self-assembled from amphiphilic peptides are promising candidates for applications in drug delivery. However, complete high-resolution data on the local and supramolecular organization of such materials has been elusive thus far, which is a substantial obstacle to their rational design. In the absence of precise information, nanovesicles built of amphiphilic “lipid-like” peptides are generally assumed to resemble liposomes that are organized from bilayers of peptides with a tail-to-tail ordering. Using the nanocarrier formed by the amphiphilic self-assembling peptide 2 (SA2 peptide) as an example, we derive the local and global organization of a multimega-Dalton peptide-based nanocarrier at high molecular detail and at close-to physiological conditions. By integrating a multitude of experimental techniques (solid-state NMR, AFM, SLS, DLS, FT-IR, CD) with large- and multiscale MD simulations, we show that SA2 nanocarriers are built of interdigitated antiparallel ß-sheets, which bear little resemblance to phospholipid liposomes. Our atomic level study allows analyzing the vesicle surface structure and dynamics as well as the intermolecular forces between peptides, providing a number of potential leads to improve and tune the biophysical properties of the nanocarrier. The herein presented approach may be of general utility to investigate peptide-based nanomaterials at high-resolution and at physiological conditions.
    Probing functional (re)organisation in photosynthesis by time-resolved fluorescence spectroscopy
    Ünlü, C. - \ 2015
    Wageningen University. Promotor(en): Herbert van Amerongen. - Wageningen : Wageningen University - ISBN 9789462572829 - 118
    algen - fotosynthese - light harvesting complexen - fotosysteem ii - fluorescentie - spectroscopie - chlamydomonas reinhardtii - algae - photosynthesis - light harvesting complexes - photosystem ii - fluorescence - spectroscopy - chlamydomonas reinhardtii


    The possible mechanisms for reorganisation of outer LHCs of PSII (LHCII) upon state transitions in Chlamydomonas reinhardtii have been discussed for several decades [38, 43-54]. For a long time people adhered to the opinion that upon the transition from state 1 to state 2, 80% of LHCII detaches from PSII and attaches completely to PSI in Chlamydomonas reinhardtii [38, 45]. This thesis provides new insights for the mechanism of state transitions in Chlamydomonas reinhardtii. In the remainder of this thesis, the role of minor light-harvesting complexes in excitation energy transfer to reaction centers of photosystem II are discussed as well as multiexciton dynamics of the alloyed ZnCdTe quantum dots are studied in detail.

    In chapter 2, we demonstrate with picosecond-fluorescence spectroscopy on C. reinhardtii cells that although LHCs indeed detach from Photosystem II in state-2 conditions only a fraction attaches to Photosystem I. The detached antenna complexes become protected against photodamage via shortening of the excited-state lifetime. It is discussed how the transition from state 1 to state 2 can protect C. reinhardtii in high-light conditions and how this differs from the situation in plants.

    In chapter 3, we study the picosecond fluorescence properties of Chlamydomonas reinhardtti over a broad range of wavelengths at 77K. It is observed that upon going from state 1 (relatively high 680nm/720nm fluorescence ratio) to state 2 (low ratio), a large part of the fluorescence of LHC/PSII becomes substantially quenched, probably because of LHC detachment from PSII, whereas the fluorescence of PSI hardly changes. These results are in agreement with the proposal in chapter 2 that the amount of LHC moving from PSII to PSI upon going from state 1 to state 2 is very limited.

    In chapter 4, we used picosecond-fluorescence spectroscopy to study excitation-energy transfer (EET) in thylakoids membranes isolated from A. thaliana wild-type plants and knockout lines depleted of either two (koCP26/24 and koCP29/24) or all minor Lhcs (NoM). In the absence of all minor Lhcs, the functional connection of LHCII to the PSII cores appears to be seriously impaired whereas the “disconnected” LHCII is substantially quenched. For both double knock-out mutants, excitation trapping in PSII is faster than in NoM thylakoids but slower than in WT thylakoids. In NoM thylakoids, the loss of all minor Lhcs is accompanied by an over-accumulation of LHCII, suggesting a compensating response to the reduced trapping efficiency in limiting light, which leads to a photosynthetic phenotype resembling that of low-light-acclimated plants. Finally, fluorescence kinetics and biochemical results show that the missing minor complexes are not replaced by other Lhcs, implying that they are unique among the antenna subunits and crucial for the functioning and macro-organization of PSII.

    In chapter 5, we have performed picosecond fluorescence measurements on ZnCdTe ternary quantum dots at room temperature by using a streak-camera setup in order to investigate in detail the fluorescence kinetics for ZnCdTe quantum dots with different size and structure by using different excitation laser intensities. Our data show that the changes in fluorescence kinetics are mostly related to the changes in structure and size. In heterogeneous structured ZnCdTe quantum dots, the fluorescence kinetics become faster as compared to homogeneous structured ZnCdTe quantum dots. Also, in both homogeneous and heterogeneous ZnCdTe quantum dots, a new peak is observed in the high-energy region of the emission spectrum when using high excitation intensities, which shows that the radiative processes that occur from higher energy states become more favoured as the excitation intensity increases.

    Covalent Attachment of 1-Alkenes to Oxidized Platinum Surfaces
    Alonso Carnicero, J.M. ; Fabre, B. ; Trilling, A.K. ; Scheres, L.M.W. ; Franssen, M.C.R. ; Zuilhof, H. - \ 2015
    Langmuir 31 (2015)9. - ISSN 0743-7463 - p. 2714 - 2721.
    self-assembled monolayers - organic monolayers - gold - alkanethiols - functionalization - spectroscopy - activation - alkenes - layers - films
    We report the formation of covalently bound alkyl layers onto oxidized Pt (PtOx) substrates by reaction with 1-alkenes as a novel way to bind organic molecules to metal surfaces. The organic layers were characterized by static contact angle, infrared reflection absorption spectroscopy (IRRAS), X-ray photoelectron spectroscopy (XPS), and atomic force microscopy (AFM). The grafted alkyl layers display a hydrolytic stability that is comparable to that of alkyl thiols on Au. PtOx-alkene attachment is compatible with terminal ester moieties enabling further anchoring of functional groups, such as redox-active ferrocene, and thus has great potential to extend monolayer chemistry on noble metals.
    Partitioning of humic acids between aqueous solution and hydrogel. 2. Impact of physicochemical conditions
    Zielinska, K. ; Town, R.M. ; Yasadi, K. ; Leeuwen, H.P. van - \ 2015
    Langmuir 31 (2015)1. - ISSN 0743-7463 - p. 283 - 291.
    ionic-strength - alginate gel - heavy-metals - fluorescence - substances - ph - aggregation - media - soil - spectroscopy
    The effects of the physicochemical features of aqueous medium on the mode of partitioning of humic acids (HAs) into a model biomimetic gel (alginate) and a synthetic polyacrylamide gel (PAAm) were explored. Experiments were performed under conditions of different pH and ionic strength as well as in the presence or absence of complexing divalent metal ions. The amount of HA penetrating the gel phase was determined by measuring its natural fluorescence by confocal laser scanning microscopy. In both gel types, the accumulation of HA was spatially heterogeneous, with a much higher concentration located within a thin film at the gel surface. The thickness of the surface film (ca. 15 µm) was similar for both types of gel and practically independent of pH, ionic strength, and the presence of complexing divalent metal ions. The extent of HA accumulation was found to be dependent on the composition of the medium and on the type of gel. Significantly more HA was accumulated in PAAm gel as compared to that in alginate gel. In general, more HA was accumulated at lower background salt concentration levels. The distribution of different types of HA species in the gel body was linked to their behavior in the medium and the differences in physicochemical conditions inside the two phases.
    Photopyroelectric assessment of the thermal effusivity of fresh hen egg and of rehydrated egg powders
    Szafner, G. ; Nemeth, C. ; Bicanic, D.D. ; Doka, O. - \ 2015
    Journal of Thermal Analysis and Calorimetry 120 (2015)1. - ISSN 1388-6150 - p. 363 - 368.
    conductivity - diffusivity - parameters - products - heat - spectroscopy - temperature - milk
    The availability of thermo-physical data of foods and their constituents is of general importance to food industry. The thermal effusivity e is one among the relevant thermodynamical quantities. The latter is normally calculated from the relationship e = (¿¿c)½, where c is specific heat, ¿ is the density, and ¿ is the thermal conductivity. The necessity for performing the time consuming independent measurements of these three quantities is the major reason that the existing database with effusivity of foods is not very wide. This paper describes the application of the inverse photopyroelectric (IPPE) technique that allows the determination of effusivity from a single measurement. This approach was used to directly measure thermal effusivity of fresh egg yolk, egg white, and white/yolk blends. In addition, thermal effusivity of rehydrated egg powders (white, yolk, and the whole egg powder) has been measured and compared to that of the fresh hen egg. In case of the egg white, effusivity of rehydrated egg powders was practically the same as that of the fresh egg. However, the difference in effusivity between fresh egg yolk and rehydrated egg yolk, and between the blend of fresh egg and the rehydrated whole egg power was significant. Finally, thermal effusivity of rehydrated egg yolk, egg white, and the whole egg powder was determined as a function of dilution factor.
    Fractionation of five technical lignins by selective extraction in green solvents and characterization of isolated fractions
    Boeriu, C.G. ; Fitigau, F. ; Gosselink, R.J.A. ; Frissen, A.E. ; Stoutjesdijk, J.H. ; Peter, F. - \ 2014
    Industrial Crops and Products 62 (2014). - ISSN 0926-6690 - p. 481 - 490.
    antioxidant activities - structural features - alcell(r) lignin - molecular-weight - kraft lignin - solubility - spectroscopy - prediction - ethanol - wood
    Lignins from softwood, hardwood, grass and wheat straw were fractionated by selective extraction at ambient temperature using green solvents like acetone/water solutions of 10, 30, 50, 70 and 90% (v/v) acetone and ethyl acetate. A comparison between the isolated fractions and unfractionated lignins was made in terms of extraction yield, lignin solubility factor, molecular weight distribution and functional group composition. Low molecular weight (LMW) lignin fractions with narrow dispersity are obtained by extraction with ethyl acetate and acetone–water solution containing 30% acetone, with yields depending on the type and the functional group content of lignins. A significant amount (56%) of the organosolv hardwood lignin with low molecular weight (Mw = 1868 g/mol) and low dispersity was isolated from ethyl acetate. Insoluble fractions with very high molecular weight (Mw between 10 and 17 kg/mol) are obtained in low yield from acetone–water solutions with 50, 70 and 90% acetone. LMW lignins are in general less condensed and have lower aliphatic hydroxyl content than parent lignins while the HMW fractions have a higher content of condensed hydroxyls. Principal component analysis on the chemical composition of lignins and isolated fractions determined from 31P NMR data showed the high heterogeneity of the technical lignins. Partial least squares models based on FT-IR spectral data were developed to predict the functional group content determined by quantitative 31P NMR analysis of technical lignins and lignin fractions. This approach can be used to develop simple, rapid and accurate analytical tools to monitor and control the selective fractionation of lignin.
    An Open Source Image Processing Method to Quantitatively Assess Tissue Growth after Non-Invasive Magnetic Resonance Imaging in Human Bone Marrow Stromal Cell Seeded 3D Polymeric Scaffolds
    Leferink, A.M. ; Fratila, R.M. ; Koenrades, M.A. ; Blitterswijk, C.A. van; Velders, A.H. ; Moroni, L. - \ 2014
    PLoS ONE 9 (2014)12. - ISSN 1932-6203
    intensity nonuniformity correction - iron-oxide nanoparticles - mesenchymal stem-cells - x-ray microtomography - engineered constructs - articular-cartilage - mri - microscopy - spectroscopy - perfusion
    Monitoring extracellular matrix (ECM) components is one of the key methods used to determine tissue quality in three-dimensional (3D) scaffolds for regenerative medicine and clinical purposes. This is even more important when multipotent human bone marrow stromal cells (hMSCs) are used, as it could offer a method to understand in real time the dynamics of stromal cell differentiation and eventually steer it into the desired lineage. Magnetic Resonance Imaging (MRI) is a promising tool to overcome the challenge of a limited transparency in opaque 3D scaffolds. Technical limitations of MRI involve non-uniform background intensity leading to fluctuating background signals and therewith complicating quantifications on the retrieved images. We present a post-imaging processing sequence that is able to correct for this non-uniform background intensity. To test the processing sequence we investigated the use of MRI for in vitro monitoring of tissue growth in three-dimensional poly(ethylene oxide terephthalate)-poly(butylene terephthalate) (PEOT/PBT) scaffolds. Results showed that MRI, without the need to use contrast agents, is a promising non-invasive tool to quantitatively monitor ECM production and cell distribution during in vitro culture in 3D porous tissue engineered constructs.
    Fast and nondestructive method for leaf level chlorophyll estimation using hyperspectral LiDAR
    Nevalainen, O. ; Hakala, T. ; Suomalainen, J.M. ; Mäkipää, R. ; Peltoniemi, M. ; Krooks, A. ; Kaasalainen, S. - \ 2014
    Agricultural and Forest Meteorology 198-199 (2014). - ISSN 0168-1923 - p. 250 - 258.
    supercontinuum laser source - vegetation indexes - reflectance spectra - precision agriculture - canopy reflectance - red edge - airborne - model - spectroscopy - validation
    We propose an empirical method for nondestructive estimation of chlorophyll in tree canopies. The first prototype of a full waveform hyperspectral LiDAR instrument has been developed by the Finnish Geodetic Institute (FGI). The instrument efficiently combines the benefits of passive and active remote sensing sensors. It is able to produce 3D point clouds with spectral information included for every point, which offers great potential in the field of environmental remote sensing. The investigation was conducted by using chlorophyll sensitive vegetation indices applied to hyperspectral LiDAR data and testing their performance in chlorophyll estimation. The amount of chlorophyll in vegetation is an important indicator of photosynthetic capacity and stress, and thus important for monitoring of forest condition and carbon sequestration on Earth. Performance of chlorophyll estimation was evaluated for 27 published vegetation indices applied to waveform LiDAR collected from ten Scots pine shoots. Reference data were collected by laboratory chlorophyll concentration analysis. The performance of the indices in chlorophyll estimation was determined by linear regression and leave-one-out cross-validation. The chlorophyll estimates derived from hyperspectral LiDAR linearly correlate with the laboratory analyzed chlorophyll concentrations, and they are able to represent a range of chlorophyll concentrations in Scots pine shoots (R2 = 0.88, RMSE = 0.10 mg/g). Furthermore, they are insensitive to measurement scale as nearly the same values of vegetation indices were measured in natural setting while scanning the whole canopy and from clipped shoots re-measured with hyperspectral LiDAR in laboratory. The results indicate that the hyperspectral LiDAR instrument has the potential to estimate vegetation biochemical parameters such as the chlorophyll concentration. The instrument holds much potential in various environmental applications and provides a significant improvement over single wavelength LiDAR or passive optical systems for environmental remote sensing.
    Monitoring plastic waste using FTIR-ATR spectroscopy
    Franeker, Jan Andries van - \ 2014
    water pollution - solid wastes - plastics - recycling - spectroscopy - marine areas - monitoring - waste treatment
    Strong antenna-enhanced fluorescence of a single light-harvesting complex shows photon anti-bunching
    Wientjes, E. ; Renger, J. ; Curto, A.G. ; Cogdell, R. ; Hulst, N.F. van - \ 2014
    Nature Communications 5 (2014). - ISSN 2041-1723 - 7 p.
    pigment-protein complexes - purple bacterial lh2 - exciton delocalization - molecule fluorescence - energy-transfer - optical antennas - nanoantennas - dynamics - spectroscopy - dna
    The nature of the highly efficient energy transfer in photosynthetic light-harvesting complexes is a subject of intense research. Unfortunately, the low fluorescence efficiency and limited photostability hampers the study of individual light-harvesting complexes at ambient conditions. Here we demonstrate an over 500-fold fluorescence enhancement of lightharvesting complex 2 (LH2) at the single-molecule level by coupling to a gold nanoantenna. The resonant antenna produces an excitation enhancement of circa 100 times and a fluorescence lifetime shortening to B20 ps. The radiative rate enhancement results in a 5.5-fold-improved fluorescence quantum efficiency. Exploiting the unique brightness, we have recorded the first photon antibunching of a single light-harvesting complex under ambient conditions, showing that the 27 bacteriochlorophylls coordinated by LH2 act as a nonclassical single-photon emitter. The presented bright antenna-enhanced LH2 emission is a highly promising system to study energy transfer and the role of quantum coherence at the level of single complexes.
    NMR Nanoparticle Diffusometry in Hydrogels: Enhancing Sensitivity and Selectivity
    Kort, D.W. de; Duynhoven, J.P.M. van; Hoeben, F.J.M. ; Janssen, H.M. ; As, H. van - \ 2014
    Analytical Chemistry 86 (2014). - ISSN 0003-2700 - p. 9229 - 9235.
    fluorescence recovery - laplace inversion - polymer-solutions - field gradient - diffusion - resolution - mobility - gels - spectroscopy - kinetics
    From the diffusional behavior of nanoparticles in heterogeneous hydrogels, quantitative information about submicron structural features of the polymer matrix can be derived. Pulsed-gradient spin-echo NMR is often the method of choice because it measures diffusion of the whole ensemble of nanoparticles. However, in 1H diffusion-ordered spectroscopy (DOSY), low-intensity nanoparticle signals have to be separated from a highly protonated background. To circumvent this, we prepared 19F labeled, PEGylated, water-soluble dendritic nanoparticles with a 19F loading of ~7 wt % to enable background free 19F DOSY experiments. 19F nanoparticle diffusometry was benchmarked against 1H diffusion-T2 correlation spectroscopy (DRCOSY), which has a stronger signal separation potential than the commonly used 1H DOSY experiment. We used bootstrap data resampling to estimate confidence intervals and stabilize 2D-Laplace inversion of DRCOSY data with high noise levels and artifacts, allowing quantitative diffusometry even at low magnetic field strengths (30 MHz). The employed methods offer significant advantages in terms of sensitivity and selectivity.
    Response of the photosynthetic system to altered protein composition and changes in environmental conditions
    Tóth, T. - \ 2014
    Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): G. Garab; L. Kovács. - Wageningen : Wageningen University - ISBN 9789462570504 - 178
    fotosynthese - in vivo experimenten - spectroscopie - plantenpigmenten - eiwitsamenstelling - cadmium - photosynthesis - in vivo experimentation - spectroscopy - plant pigments - protein composition - cadmium

    The photosynthetic thylakoid membrane has a hierarchically ordered structure containing pigment-protein complexes that capture solar radiation and convert it into chemical energy. Its highly dynamic structure is capable to continuously respond to the altered environmental conditions, e.g., light quality and quantity, temperature changes and nutrient availability. Having detailed knowledge about the photosynthetic apparatus and its regulating factors is of paramount importance for the potential use of photosynthesis as alternative energy source or for removing toxic pollutants.

    The thesis provides new information about the role of various carotenoid molecules for the structure and energy transfer capacity of photosynthetic complexes in cyanobacteria. Our results demonstrate that besides the known structural importance of carotenoids they are also required for the oligomerisation of photosystems and for maintaining the structure of the light-harvesting antenna complexes, called phycobilisomes.

    Part of the thesis focuses on the Photosystem II (PSII) macro-organisation in the chloroplast thylakoid membrane of plants. The general importance of a small-molecular-weight protein, PsbW is demonstrated for the organisation of the PSII supercomplexes and the formation of the parallel rows of PSII and the accompanying psi-type circular dichroism signal. A new, circular dichroism (CD) spectroscopy-based fingerprinting method is described that can be used to study the PSII macrodomain organization. CD is a potentially powerful method to follow the dynamic changes of the pigment-protein complex organisation of chloroplast membranes in vivo.

    In this thesis the cadmium-induced toxic effects on photosynthetic processes are also investigated. The observed changes can be merged into a cascade mechanism model. Such detailed knowledge of toxic events is crucial for the effective use of cyanobacteria to remove the cadmium pollution from water.In conclusion, this thesis contributes to our knowledge about the structure and dynamics of the photosynthetic apparatus at various organisational levels.

    A systematic approach to obtain validated partial least square models for predicting lipoprotein subclasses from serum NMR spectra
    Mihaleva, V.V. ; Schalkwijk, D.B. van; Graaf, A.A. de; Duynhoven, J.P.M. van; Dorsten, F.A. van; Vervoort, J.J.M. ; Smilde, A.K. ; Westerhuis, J.A. ; Jacobs, D.M. - \ 2014
    Analytical Chemistry 86 (2014)1. - ISSN 0003-2700 - p. 543 - 550.
    nuclear-magnetic-resonance - low-density lipoprotein - plasma-lipoproteins - insulin-resistance - regression-models - spectroscopy - quantification - chromatography - abnormalities - chemometrics
    A systematic approach is described for building validated PLS models that predict cholesterol and triglyceride concentrations in lipoprotein subclasses in fasting serum from a normolipidemic, healthy population. The PLS models were built on diffusion-edited (1)H NMR spectra and calibrated on HPLC-derived lipoprotein subclasses. The PLS models were validated using an independent test set. In addition to total VLDL, LDL, and HDL lipoproteins, statistically significant PLS models were obtained for 13 subclasses, including 5 VLDLs (particle size 64-31.3 nm), 4 LDLs (particle size 28.6-20.7 nm) and 4 HDLs (particle size 13.5-9.8 nm). The best models were obtained for triglycerides in VLDL (0.82
    Automated quantum mechanical total line shape fitting model for quantitative NMR-based profiling of human serum metabolites
    Mihaleva, V. ; Korhonen, S.P. ; Duynhoven, J.P.M. van; Niemitz, M. ; Vervoort, J.J.M. ; Jacobs, D.M. - \ 2014
    Analytical and Bioanalytical Chemistry 406 (2014)13. - ISSN 1618-2642 - p. 3091 - 3102.
    h-1-nmr spectra - metabolomics - spectroscopy - quantification - deconvolution
    An automated quantum mechanical total line shape (QMTLS) fitting model was implemented for quantitative nuclear magnetic resonance (NMR)-based profiling of 42 metabolites in ultrafiltrated human serum samples. Each metabolite was described by a set of chemical shifts, J-couplings, and line widths. These parameters were optimized for each metabolite in each sample by iteratively minimizing the difference between the calculated and the experimental spectrum. In total, 92.0 to 98.1 % of the signal intensities in the experimental spectrum could be explained by the calculated spectrum. The model was validated by comparison to signal integration of metabolites with isolated signals and by means of standard additions. Metabolites present at average concentration higher than 50 µM were quantified with average absolute relative error less than 10 % when using different initial parameters for the fitting procedure. Furthermore, the biological applicability of the QMTLS model was demonstrated on 287 samples from an intervention study in 37 human volunteers undergoing an exercise challenge. Our automated QMTLS model was able to cope with the large dynamic range of metabolite concentrations in serum and proved to be suitable for high-throughput analysis.
    Multivariate PAT solutions for biopharmaceutical cultivation: current progress and limitations
    Mercier, S.M. ; Diepenbroek, B. ; Wijffels, R.H. ; Streefland, M. - \ 2014
    Trends in Biotechnology 32 (2014)6. - ISSN 0167-7799 - p. 329 - 336.
    process analytical technology - principal component analysis - monitoring batch processes - cell-culture - biotechnology - spectroscopy - quality - chromatography - fermentation - chemometrics
    Increasingly elaborate and voluminous datasets are generated by the (bio)pharmaceutical industry and are a major challenge for application of PAT and QbD principles. Multivariate data analysis (MVDA) is required to delineate relevant process information from large multi-factorial and multi-collinear datasets. Here the key role of MVDA for industrial (bio)process data is discussed, with a focus on progress and limitations of MVDA as a PAT solution for biopharmaceutical cultivation processes. MVDA based models were proven useful and should be routinely implemented for bioprocesses. It is concluded that although the highest level of PAT with process control within its design space in real-time during manufacturing is not reached yet, MVDA will be central to reach this ultimate objective for cell cultivations.
    Calcium phosphate granulation in anaerobic treatment of black water: a new approach to phosphorus recovery
    Tervahauta, T.H. ; Weijden, R.D. van der; Flemming, R.L. ; Hernández, L. ; Zeeman, G. ; Buisman, C.J.N. - \ 2014
    Water Research 48 (2014)1. - ISSN 0043-1354 - p. 632 - 642.
    afvalwaterbehandeling - afvalhergebruik - slibzuivering - calciumfosfaten - fosfor - terugwinning - spectroscopie - infraroodspectroscopie - anaërobe behandeling - biobased economy - waste water treatment - waste utilization - sludge treatment - calcium phosphates - phosphorus - recovery - spectroscopy - infrared spectroscopy - anaerobic treatment - biobased economy - waste-water - precipitation - hydroxyapatite - struvite
    Recovery of phosphorus from wastewater as calcium phosphate could diminish the need for mining of scarce phosphate rock resources. This study introduces a novel approach to phosphorus recovery by precipitation of calcium phosphate granules in anaerobic treatment of black water. The granules formed in the Upflow Anaerobic Sludge Blanket (UASB) reactor at lab- and demonstration-scale were analyzed for chemical composition and mineralogy by Inductively Coupled Plasma-Atomic Emission Spectroscopy (ICP-AES), Electron microprobe (EMP), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy and micro X-ray Diffraction (XRD). The granules had a diameter of 1–2 mm, organic content of 33 wt%, and phosphorus content of 11–13 wt%. Three calcium phosphate phases were identified in the granules: hydroxyapatite, calcium phosphate hydrate and carbonated hydroxyapatite. Without any addition of chemicals, 7 gP/person/year can be recovered with the calcium phosphate granules, representing 2% of the incoming phosphorus in the UASB reactor. As the heavy metal content was lower compared to other phosphorus recovery products, phosphate rock and phosphorus fertilizer, the calcium phosphate granules could be considered as a new phosphorus product.
    Distance Measurements on Orthogonally Spin-Labeled Membrane Spanning WALP23 Polypeptides
    Lueders, P. ; Jäger, H. ; Hemminga, M.A. ; Jeschke, G. ; Yulikov, M. - \ 2013
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 117 (2013)7. - ISSN 1520-6106 - p. 2061 - 2068.
    electron double-resonance - trichogin ga-iv - alpha-helical peptides - dipole-dipole interactions - islet amyloid polypeptide - field pulsed epr - hydrophobic mismatch - phospholipid membrane - gd3+ complexes - spectroscopy
    EPR-based Gd(III)-nitroxide distance measurements were performed on a series of membrane-incorporated orthogonally labeled WALP23 polypeptides. The obtained distance distributions were stable upon the change of detection frequency from 10 GHz (X-band) to 35 GHz (Q-band). The alpha-helical pitch of WALP23 polypeptide could be experimentally observed, despite the flexibility of the two spin labels. The spectroscopic properties of Gd(III) ions and nitroxide radicals allow detecting both types of paramagnetic species selectively in different EPR experiments. In particular, this spectroscopic selectivity allows for supplementing Gd(III)-nitroxide distance measurements with independent checks of polypeptide aggregation and with measurements of the local environment of the nitroxide spin labels. All mentioned additional checks do not require preparation of further samples, as it is the case in the experiments with pairs of identical nitroxide spin labels.
    Emission enhancement and lifetime modification of phosphorescence on silver nanoparticle aggregates
    Gill, R. ; Tian, L. ; Amerongen, H. van; Subramaniam, V. - \ 2013
    Physical Chemistry Chemical Physics 15 (2013). - ISSN 1463-9076 - p. 15734 - 15739.
    single-molecule fluorescence - oxygen generation - luminescence - spectroscopy - photochemistry - complexes - yields
    Silver nanoparticle aggregates have been shown to support very large enhancements of fluorescence intensity from organic dye molecules coupled with an extreme reduction in observed fluorescence lifetimes. Here we show that for the same type of aggregates, similar enhancement factors (similar to 75 x in intensity and similar to 3400 x in lifetime compared to the native radiative lifetime) are observed for a ruthenium-based phosphorescent dye (when taking into account the effect of charge and the excitation/emission wavelengths). Additionally, the inherently long native phosphorescence lifetimes practically enable more detailed analyses of the distribution of lifetimes (compared with the case with fluorescence decays). It was thus possible to unambiguously observe the deviation from mono-exponential decay which we attribute to emission from a distribution of fluorophores with different lifetimes, as we could expect from a random aggregation process. We believe that combining phosphorescent dyes with plasmonic structures, even down to the single dye level, will offer a convenient approach to better characterize plasmonic systems in detail.
    (Quasi-) 2D aggregation of polystyrene-b-dextran at the air-water interface
    Bosker, W.T.E. ; Cohen Stuart, M.A. ; Norde, W. - \ 2013
    Langmuir 29 (2013)8. - ISSN 0743-7463 - p. 2667 - 2675.
    diblock copolymer monolayers - surface micelle formation - block polyelectrolytes - air/water interface - molecular-dynamics - solid-state - behavior - brushes - polymers - spectroscopy
    Polystyrene-b-dextran (PS-b-Dextran) copolymers can be used to prepare dextran brushes at solid surfaces, applying Langmuir–Blodgett deposition. When recording the interfacial pressure versus area isotherms of a PS-b-Dextran monolayer, time-dependent hysteresis was observed upon compression and expansion. We argue that this is due to (quasi-) 2D aggregation of the copolymer at the air–water surface, with three contributions. First, at large area per molecule, a zero surface pressure is measured; we ascribe this to self-assembly of block copolymers into surface micelles. At intermediate area we identify a second regime (“desorption regime”) where aggregation into large patches occurs due to van der Waals attraction between PS blocks. At high surface pressure (“brush regime”) we observe hysteretic behavior attributed to H-bonding between dextran chains. When compared to hysteresis of other amphiphilic diblock copolymers (also containing PS, e.g., polystyrene-b-poly(ethylene oxide)) a general criterion can be formulated concerning the extent of hysteresis: when the hydrophobic (PS) block is of equal size as (or bigger than) the hydrophilic block, the hysteresis is maximal. The (quasi-) 2D aggregation of PS-b-Dextran has significant implications for the preparation of dextran brushes at solid surfaces using Langmuir–Blodgett deposition. For each grafting density the monolayer needs to relax, up to several hours, prior to transfer.
    Spectroscopy-supported digital soil mapping
    Mulder, V.L. - \ 2013
    Wageningen University. Promotor(en): Michael Schaepman; Sytze de Bruin. - [S.l. : S.n. - ISBN 9789461736901 - 188
    bodemkarteringen - bodem - cartografie - spectroscopie - remote sensing - bodemsamenstelling - soil surveys - soil - mapping - spectroscopy - remote sensing - soil composition

    Global environmental changes have resulted in changes in key ecosystem services that soils provide. It is necessary to have up to date soil information on regional and global scales to ensure that these services continue to be provided. As a result, Digital Soil Mapping (DSM) research priorities are among others, advancing methods for data collection and analyses tailored towards large-scale mapping of soil properties. Scientifically, this thesis contributed to the development of methodologies, which aim to optimally use remote and proximal sensing (RS and PS) for DSM to facilitate regional soil mapping. The main contributions of this work with respect to the latter are (I) the critical evaluation of recent research achievements and identification of knowledge gaps for large-scale DSM using RS and PS data, (II) the development of a sparse RS-based sampling approach to represent major soil variability at regional scale, (III) the evaluation and development of different state-of-the-art methods to retrieve soil mineral information from PS, (IV) the improvement of spatially explicit soil prediction models and (V) the integration of RS and PS methods with geostatistical and DSM methods.

    A review on existing literature about the use of RS and PS for soil and terrain mapping was presented in Chapter 2. Recent work indicated the large potential of using RS and PS methods for DSM. However, for large-scale mapping, current methods will need to be extended beyond the plot. Improvements may be expected in the fields of developing more quantitative methods, enhanced geostatistical analysis and improved transferability to other areas. From these findings, three major research interests were selected: (I) soil sampling strategies, (II) retrieval of soil information from PS and (III) spatially continuous mapping of soil properties at larger scales using RS.

    Budgetary constraints, limited time and available soil legacy data restricted the soil data acquisition, presented in Chapter 3. A 15.000 km2 area located in Northern Morocco served as test case. Here, a sample was collected using constrained Latin Hypercube Sampling (cLHS) of RS and elevation data. The RS data served as proxy for soil variability, as alternative for the required soil legacy data supporting the sampling strategy. The sampling aim was to optimally sample the variability in the RS data while minimizing the acquisition efforts. This sample resulted in a dataset representing major soil variability. The cLHS sample failed to express spatial correlation; constraining the LHS by a distance criterion favoured large spatial variability over short distances. The absence of spatial correlation in the sampled soil variability precludes the use of additional geostatistical analyses to spatially predict soil properties. Predicting soil properties using the cLHS sample is thus restricted to a modelled statistical relation between the sample and exhaustive predictor variables. For this, the RS data provided the necessary spatial information because of the strong spatial correlation while the spectral information provided the variability of the environment (Chapter 3 and 6). Concluding, the RS-based cLHS approach is considered a time and cost efficient method for acquiring information on soil resources over extended areas.

    This sample was further used for developing methods to derive soil mineral information from PS, and to characterize regional soil mineralogy using RS. In Chapter 4, the influences of complex scattering within the mixture and overlapping absorption features were investigated. This was done by comparing the success of PRISM’s MICA in determining mineralogy of natural samples and modelled spectra. The modelled spectra were developed by a linearly forward model of reflectance spectra, using the fraction of known constituents within the sample. The modelled spectra accounted for the co-occurrence of absorption features but eluded the complex interaction between the components. It was found that more minerals could be determined with higher accuracy using modelled reflectance. The absorption features in the natural samples were less distinct or even absent, which hampered the classification routine. Nevertheless, grouping the individual minerals into mineral categories significantly improved the classification accuracy. These mineral categories are particularly useful for regional scale studies, as key soil property for parent material characterization and soil formation. Characterizing regional soil mineralogy by mineral categories was further described in Chapter 6. Retrieval of refined information from natural samples, such as mineral abundances, is more complex; estimating abundances requires a method that accounts for the interaction between minerals within the intimate mixture. This can be done by addressing the interaction with a non-linear model (Chapter 5).

    Chapter 5 showed that mineral abundances in complex mixtures could be estimated using absorption features in the 2.1–2.4 µm wavelength region. First, the absorption behaviour of mineral mixtures was parameterized by exponential Gaussian optimization (EGO). Next, mineral abundances were successfully predicted by regression tree analysis, using these parameters as inputs. Estimating mineral abundances using prepared mixes of calcite, kaolinite, montmorillonite and dioctahedral mica or field samples proved the validity of the proposed method. Estimating mineral abundances of field samples showed the necessity to deconvolve spectra by EGO. Due to the nature of the field samples, the simple representation of the complex scattering behaviour by a few Gaussian bands required the parameters asymmetry and saturation to accurately deconvolve the spectra. Also, asymmetry of the EGO profiles showed to be an important parameter for estimating the abundances of the field samples. The robustness of the method in handling the omission of minerals during the training phase was tested by replacing part of the quartz with chlorite. It was found that the accuracy of the predicted mineral content was hardly affected. Concluding, the proposed method allowed for estimating more than two minerals within a mixture. This approach advances existing PS methods and has the potential to quantify a wider set of soil properties. With this method the soil science community was provided an improved inference method to derive and quantify soil properties

    The final challenge of this thesis was to spatially explicit model regional soil mineralogy using the sparse sample from Chapter 3. Prediction models have especially difficulties relating predictor variables to sampled properties having high spatial correlation. Chapter 6 presented a methodology that improved prediction models by using scale-dependent spatial variability observed in RS data. Mineral predictions were made using the abundances from X-ray diffraction analysis and mineral categories determined by PRISM. The models indicated that using the original RS data resulted in lower model performance than those models using scaled RS data. Key to the improved predictions was representing the variability of the RS data at the same scale as the sampled soil variability. This was realized by considering the medium and long-range spatial variability in the RS data. Using Fixed Rank Kriging allowed smoothing the massive RS datasets to these ranges. The resulting images resembled more closely the regional spatial variability of soil and environmental properties. Further improvements resulted from using multi-scale soil-landscape relationships to predict mineralogy. The maps of predicted mineralogy showed agreement between the mineral categories and abundances. Using a geostatistical approach in combination with a small sample, substantially improves the feasibility to quantitatively map regional mineralogy. Moreover, the spectroscopic method appeared sufficiently detailed to map major mineral variability. Finally, this approach has the potential for modelling various natural resources and thereby enhances the perspective of a global system for inventorying and monitoring the earth’s soil resources.

    With this thesis it is demonstrated that RS and PS methods are an important but also an essential source for regional-scale DSM. Following the main findings from this thesis, it can be concluded that: Improvements in regional-scale DSM result from the integrated use of RS and PS with geostatistical methods. In every step of the soil mapping process, spectroscopy can play a key role and can deliver data in a time and cost efficient manner. Nevertheless, there are issues that need to be resolved in the near future. Research priorities involve the development of operational tools to quantify soil properties, sensor integration, spatiotemporal modelling and the use of geostatistical methods that allow working with massive RS datasets. This will allow us in the near future to deliver more accurate and comprehensive information about soils, soil resources and ecosystem services provided by soils at regional and, ultimately, global scale.

    Jacobaea through the eyes of spectroscopy : identifying plant interactions with the (a)biotic environment by chemical variation effects on spectral reflectance patterns
    Almeida De Carvalho, S. - \ 2013
    Wageningen University. Promotor(en): Wim van der Putten; Andrew Skidmore, co-promotor(en): M. Macel; M. Schlerf. - S.l. : s.n. - ISBN 9789461737502 - 180
    senecio jacobaea - senecio erucifolius - pyrrolizidinealkaloïden - voedingsstoffen - spectraalanalyse - spectroscopie - bodemmicrobiologie - metabolieten - chemische analyse - plantensuccessie - senecio jacobaea - senecio erucifolius - pyrrolizidine alkaloids - nutrients - spectral analysis - spectroscopy - soil microbiology - metabolites - chemical analysis - plant succession

    Plants interact with a wide array of aboveground and belowground herbivores, pathogens, mutualists, and their natural enemies. These interactions are important drivers of spatio-temporal changes in vegetation, however, they may be difficult to be revealed without extensive sampling.In this thesis I investigated the potential of visible and near-infrared spectral measurements to detect plant chemical changes that may reflect interactions between plants and biotic or abiotic soil factors. First, I examined the relative contribution of pyrrolizidine alkaloids (PAs; these are defence compounds of Senecio-type plants against generalist herbivores) to the spectral reflectance features in the visible and short-wave infrared region. My hypothesis was that PAs can be predicted from specific spectral features of aboveground plant tissues. Since PA profiles and their relation to spectral features could be species specific I compared three different species, Jacobaea vulgaris, J. erucifolia and S. inaequidens subjected to nutrient and water treatments to stimulate plant chemical variation. Pyrrolizidine alkaloids were predicted best by spectral reflectance features in the case of Jacobaea vulgaris. I related the better results obtained with J. vulgaris to the existence of the correlation between PAs and nitrogen and the presence of the epoxide chemical structure in J. vulgaris.

    I also examined if different soil microbial communities influenced plant shoot spectral reflectance. I grew the same three plant species as before in sterilized soil and living soil collected from fields with J. vulgaris. I expected that soil biota would change shoot defence content and hyperspectral reflectance in plant species-specific ways. Indeed, the exposure to different soils caused plant chemical profiles to change and both chemical and spectral patterns discriminated plants according to the soil biotic conditions.

    I studied how primary and secondary plant metabolites varied during the growing season and vegetation successional stages. I used a well-studied chronosequence of abandoned arable fields and analysed the chemistry of both leaves and flowers of Jacobaea vulgaris throughout the seasons in fields of different successional status. My general hypothesis was that seasonal allocation of nutrients and defence metabolites to reproductive organs fitted the optimal defence theory, but that pattern was dependent on the successional stage of the vegetation. I found an interaction between season and succession stage, as plants from longer abandoned fields generally had flowers and leaves with higher N-oxides, especially in late Summer. Independent of the succession stage there was a seasonal allocation of nutrients and defence metabolites to flowers. Analyses of spectral reflectance of the field plants showed thatdefence compounds could be estimated more reliably in flowers, while in leaves primary compounds could be predicted best. Succession classes were successfully discriminated by the spectral patterns of flowers. Both chemical and spectral findings suggested that flowers are more sensitive to field ageing processes than leaves.


    The estimation of pyrrolizidine alkaloids by spectral reflectance features was better in Jacobaea vulgaris than in Senecio inaequidens or Jacobaea erucifolia (chapter 2). Differences in soil communities affect plant leaves’ chemistry and spectral reflectance patterns (chapter 3). Jacobaea vulgarisplants from recent and longer-abandoned fields showed the largest differences in chemical concentration, composition of defence compounds, and spectral reflectance patterns. Flowers were more discriminatory than leaves (chapters 4 and 5). There is a potential to detect plant-biotic interactions by analyzing spectral reflectance patterns (this thesis).
    Multivariate data analysis as a PAT tool for early bioprocess development data
    Mercier, S.M. ; Diepenbroek, B. ; Dalm, M.C.F. ; Wijffels, R.H. ; Streefland, M. - \ 2013
    Journal of Biotechnology 167 (2013)13. - ISSN 0168-1656 - p. 262 - 270.
    monitoring batch processes - cell-culture - chemometrics - spectroscopy - prediction - quality - design
    Early development datasets are typically unstructured, incomplete and truncated, yet they are readily available and contain relevant process information which is not extracted using classical data analysis techniques. In this paper, we illustrate the power of multivariate data analysis (MVDA) as a Process Analytical Technology tool to analyze early development data of a PER.C6® cell cultivation process. MVDA increased our understanding of the process studied. Principal component analysis enabled a thorough exploration of the dataset, identifying causes for batch deviations and revealing sensitivity of the process to scale. These findings were previously undetected using traditional univariate analysis. The lack of structure and gaps in the early development datasets made it impossible to fit them to more advanced partial least square regression models. This paper clearly shows that MVDA should be routinely used to analyze early development data to reveal relevant information for later development and scale-up. The value of these early development runs can be greatly enhanced if the experiments are well-structured and accompanied with full process analytics. This up-front investment will result in shorter and more efficient process development paths, resulting in lower overall development costs for new biopharmaceutical products.
    Fast and Robust Method To Determine Phenoyl and Acetyl Esters of Polysaccharides by Quantitative 1H NMR
    Neumüller, K.G. ; Carvalho de Souza, A. ; Rijn, J. van; Appeldoorn, M.M. ; Streekstra, H. ; Schols, H.A. ; Gruppen, H. - \ 2013
    Journal of Agricultural and Food Chemistry 61 (2013)26. - ISSN 0021-8561 - p. 6282 - 6287.
    acids - nmr - spectroscopy - extracts
    The acetyl (AcE), feruloyl (FE), and p-coumaroyl (pCE) ester contents of different cereal and grass polysaccharides were determined by a quantitative 1H NMR-based method. The repeatability and the robustness of the method were demonstrated by analyzing different plant polysaccharide preparations. Good sensitivity and selectivity for AcE, FE, and pCE were observed. Moreover, an optimized and easy sample preparation allowed for simultaneous quantification of AcE, FE, and pCE. The method is suitable for high-throughput analysis, and it is a good alternative for currently used analytical procedures. A comparison of the method presented to a conventional HPLC-based method showed that the results obtained are in good agreement, whereas the combination of the optimized sample preparation and analysis by the 1H NMR-based methodology results in significantly reduced analysis time.
    Sacha Inchi (Plukenetia volubilis): a seed source of polyunsaturated fatty acids, tocopherols, phytoserols, phenolic compounds and antioxidant capacity
    Chirinos, R. ; Zuloeta, G. ; Pedreschi Plasencia, R.P. - \ 2013
    Food Chemistry 141 (2013)3. - ISSN 0308-8146 - p. 1732 - 1739.
    chemical-composition - oxidative stability - united-states - l. seeds - oil - foods - spectroscopy - cultivars - flaxseed - assay
    Fatty acids (FA), phytosterols, tocopherols, phenolic compounds, total carotenoids and hydrophilic and lipophilic ORAC antioxidant capacities were evaluated in 16 cultivars of Sacha inchi (SI) seeds with the aim to valorise them and offer more information on the functional properties of SI seeds. A high a linolenic (a-Ln) fatty acid content was found in all cultivars (¿3, 12.8–16.0 g/100 g seed), followed by linoleic (L) fatty acid (¿6, 12.4–14.1 g/100 g seed). The ratio ¿6/¿3 was within the 0.83–1.09 range. ¿- and d-tocopherols were the most important tocopherols, whereas the most representative phytosterols were ß-sitosterol and stigmasterol. Contents of total phenolics, total carotenoids and hydrophilic and lipophilic antioxidant capacities ranged from 64.6 to 80 mg of gallic acid equivalent/100 g seed; from 0.07 to 0.09 mg of ß-carotene equivalent/100 g of seed; from 4.3 to 7.3 and, from 1.0 to 2.8 µmol of Trolox equivalent/g of seed, respectively, among the evaluated SI cultivars. Results showed significant differences (p <0.05) among the evaluated SI cultivars in the contents of ¿3, ¿6, antioxidant capacities and other evaluated phytochemicals. SI seeds should be considered as an important dietary source of health promoting phytochemicals.
    Fouling mechanisms of dairy streams during membrane distillation
    Hausmann, A. ; Sanciolo, P. ; Vasiljevic, T. ; Weeks, M. ; Schroën, C.G.P.H. ; Gray, S. ; Duke, M. - \ 2013
    Journal of Membrane Science 441 (2013). - ISSN 0376-7388 - p. 102 - 111.
    calcium-phosphate - skimmed-milk - osmotic distillation - whey proteins - ultrafiltration - microfiltration - adsorption - stability - spectroscopy - precursors
    This study reports on fouling mechanisms of skim milk and whey during membrane distillation (MD) using polytetrafluoroethylene (PTFE) membranes. Structural and elemental changes along the fouling layer from the anchorpoint at the membrane to the topsurface of the fouling layer have been investigated using synchrotron IR micro-spectroscopy and electron microscopy with associated energy dispersive X-ray spectroscopy(EDS)Initial adhesion of single components on a membrane representing a PTFEsurface was observed in-situ utilizing reflectometry.Whey components were found to penetrate into the membrane matrix while skim milk fouling remained on top of the membrane. Whey proteins had weaker attractive interaction with the membrane and adhesion depended more on the presence of phosphorus near the membrane surface and throughout to establish the fouling layer. This work has given detailed insight into the fouling mechanisms of MD membranes in major dairy streams, essential for maintaining membrane distillation as operational for acceptable times, therewith allowing further development of this emerging technology.
    Magnetic Resonance in Food Science - Food for Thought
    Duynhoven, J.P.M. van; Belton, P.S. ; Webb, G.A. ; As, H. van - \ 2013
    London : RSC Books - ISBN 9781849736343 - 235
    voedselwetenschappen - voedingsmiddelen - kernspintomografie - diagnostische technieken - voedselverwerking - spectroscopie - afbeelden - voedselkwaliteit - voedselveiligheid - food sciences - foods - magnetic resonance imaging - diagnostic techniques - food processing - spectroscopy - imagery - food quality - food safety
    There are many challenges and problems in food science and magnetic resonance methods may be used to provide answers and deepen both fundamental and practical knowledge. This book presents innovations in magnetic resonance and in particular applications to understanding the functionality of foods, their processing and stability and their impact on health, perception and behaviour. Coverage includes structure and function, emphasizing respectively applications of spectroscopy/relaxometry and imaging/diffusometry; high resolution NMR spectroscopy as applied to quality and safety and foodomics; and dedicated information on perception and behaviour demonstrating the progress that has been made in applications of fMRI in this field.
    Validation of fatty acid predictions in milk using mid-infrared spectrometry across cattle breeds
    Maurice - Van Eijndhoven, M.H.T. ; Soyeurt, H. ; Dehareng, F. ; Calus, M.P.L. - \ 2013
    Animal 7 (2013)2. - ISSN 1751-7311 - p. 348 - 354.
    gas-liquid chromatography - bovine-milk - short-communication - genetic-parameters - spectroscopy - protein
    The aim of this study was to investigate the accuracy to predict detailed fatty acid (FA) composition of bovine milk by mid-infrared spectrometry, for a cattle population that partly differed in terms of country, breed and methodology used to measure actual FA composition compared with the calibration data set. Calibration equations for predicting FA composition using mid-infrared spectrometry were developed in the European project RobustMilk and based on 1236 milk samples from multiple cattle breeds from Ireland, Scotland and the Walloon Region of Belgium. The validation data set contained 190 milk samples from cows in the Netherlands across four breeds: Dutch Friesian, Meuse-Rhine-Yssel, Groningen White Headed (GWH) and Jersey (JER). The FA measurements were performed using gas–liquid partition chromatography (GC) as the gold standard. Some FAs and groups of FAs were not considered because of differences in definition, as the capillary column of the GC was not the same as used to develop the calibration equations. Differences in performance of the calibration equations between breeds were mainly found by evaluating the standard error of validation and the average prediction error. In general, for the GWH breed the smallest differences were found between predicted and reference GC values and least variation in prediction errors, whereas for JER the largest differences were found between predicted and reference GC values and most variation in prediction errors. For the individual FAs 4:0, 6:0, 8:0, 10:0, 12:0, 14:0 and 16:0 and the groups’ saturated FAs, short-chain FAs and medium-chain FAs, predictions assessed for all breeds together were highly accurate (validation R2 > 0.80) with limited bias. For the individual FAs cis-14:1, cis-16:1 and 18:0, the calibration equations were moderately accurate (R2 in the range of 0.60 to 0.80) and for the individual FA 17:0 predictions were less accurate (R2 <0.60) with considerable bias. FA concentrations in the validation data set of our study were generally higher than those in the calibration data. This difference in the range of FA concentrations, mainly due to breed differences in our study, can cause lower accuracy. In conclusion, the RobustMilk calibration equations can be used to predict most FAs in milk from the four breeds in the Netherlands with only a minor loss of accuracy.
    Remote sensing image processing
    Camps-Valls, Gustavo ; Tuia, Devis ; Gómez-Chova, Luis ; Jiménez, Sandra ; Malo, Jesús - \ 2012
    Morgan and Claypool Publishers (Synthesis Lectures on Image, Video, and Multimedia Processing ) - ISBN 9781608458196 - 194 p.
    biophysical parameter - classification - computer vision - Earth observation - feature selection and extraction - image statistics - machine learning - manifold learning - morphology - pattern recognition - regression - remote sensing - retrieval - segmentation - spectral signature - spectroscopy - statistical learning - unmixing - vision science

    Earth observation is the field of science concerned with the problem of monitoring and modeling the processes on the Earth surface and their interaction with the atmosphere.The Earth is continuously monitored with advanced optical and radar sensors.The images are analyzed and processed to deliver useful products to individual users, agencies and public administrations.To deal with these problems, remote sensing image processing is nowadays a mature research area, and the techniques developed in the field allow many real-life applications with great societal value.For instance, urban monitoring, fire detection or flood prediction can have a great impact on economical and environmental issues. To attain such objectives, the remote sensing community has turned into a multidisciplinary field of science that embraces physics, signal theory, computer science, electronics and communications. From a machine learning and signal/image processing point of view, all the applications are tackled under specific formalisms, such as classification and clustering, regression and function approximation, data coding, restoration and enhancement, source unmixing, data fusion or feature selection and extraction. This book covers some of the fields in a comprehensive way.

    Use of NMR metabolomic plasma profiling methodologies to identify illicit growth-promoting administrations
    Graham, S.F. ; Ruiz Aracama, A. ; Lommen, A. ; Cannizzo, F.T. ; Biolatti, B. ; Elliott, C.T. ; Mooney, M.H. - \ 2012
    Analytical and Bioanalytical Chemistry 403 (2012)2. - ISSN 1618-2642 - p. 573 - 582.
    veal calves - cattle - dexamethasone - spectroscopy - urine - h-1 - 17-beta-estradiol - metabolites - hormones - h-1-nmr
    Detection of growth-promoter use in animal production systems still proves to be an analytical challenge despite years of activity in the field. This study reports on the capability of NMR metabolomic profiling techniques to discriminate between plasma samples obtained from cattle treated with different groups of growth-promoting hormones (dexamethasone, prednisolone, oestradiol) based on recorded metabolite profiles. Two methods of NMR analysis were investigated-a Carr-Purcell-Meiboom-Gill (CPMG)-pulse sequence technique and a conventional H-1 NMR method using pre-extracted plasma. Using the CPMG method, 17 distinct metabolites could be identified from the spectra. H-1 NMR analysis of extracted plasma facilitated identification of 23 metabolites-six more than the alternative method and all within the aromatic region. Multivariate statistical analysis of acquired data from both forms of NMR analysis separated the plasma metabolite profiles into distinct sample cluster sets representative of the different animal study groups. Samples from both sets of corticosteroid-treated animals-dexamethasone and prednisolone-were found to be clustered relatively closely and had similar alterations to identified metabolite panels. Distinctive metabolite profiles, different from those observed within plasma from corticosteroid-treated animal plasma, were observed in oestradiol-treated animals and samples from these animals formed a cluster spatially isolated from control animal plasma samples. These findings suggest the potential use of NMR methodologies of plasma metabolite analysis as a high-throughput screening technique to aid detection of growth promoter use.
    Microscopic Origin of the Fast Blue-Green Luminescence from Chemically Synthesized Non-Oxidized Silicon Quantum Dots
    Dohnalová, K. ; Gregorkiewicz, T. ; Fucíková, A. ; Valenta, J. ; Umesh, C. ; Paulusse, J.M.J. ; Zuilhof, H. ; Humpolícková, J. ; Hof, M. van - \ 2012
    Small 8 (2012)20. - ISSN 1613-6810 - p. 3185 - 3191.
    light-emission - confinement regime - electronic states - si nanocrystals - porous silicon - photoluminescence - nanoparticles - alkyl - nanoclusters - spectroscopy
    The microscopic origin of the bright nanosecond blue-green photoluminescence (PL), frequently reported for synthesized organically terminated Si quantum dots (Si-QDs), has not been fully resolved, hampering potential applications of this interesting material. Here a comprehensive study of the PL from alkyl-terminated Si-QDs of 2-3 nm size, prepared by wet chemical synthesis is reported. Results obtained on the ensemble and those from the single nano-object level are compared, and they provide conclusive evidence that efficient and tunable emission arises due to radiative recombination of electron-hole pairs confined in the Si-QDs. This understanding paves the way towards applications of chemical synthesis for the development of Si-QDs with tunable sizes and bandgaps.
    Hexadecadienyl Monolayers on Hydrogen-Terminated Si(III): Faster Monolayer Formation and Improved Surface Coverage Using the Enyne Moiety
    Rijksen, B.M.G. ; Pujari, S.P. ; Scheres, L.M.W. ; Rijn, C.J.M. van; Baio, J.E. ; Weidner, T. ; Zuilhof, H. - \ 2012
    Langmuir 28 (2012)16. - ISSN 0743-7463 - p. 6577 - 6588.
    self-assembled monolayers - silicon surfaces - alkyl monolayers - organic monolayers - x-ray - molecular simulation - visible-light - si - spectroscopy - attachment
    To further improve the coverage of organic monolayers on hydrogen-terminated silicon (H–Si) surfaces with respect to the hitherto best agents (1-alkynes), it was hypothesized that enynes (H–C=C–HC-CH–R) would be even better reagents for dense monolayer formation. To investigate whether the increased delocalization of ß-carbon radicals by the enyne functionality indeed lowers the activation barrier, the kinetics of monolayer formation by hexadec-3-en-1-yne and 1-hexadecyne on H–Si(111) were followed by studying partially incomplete monolayers. Ellipsometry and static contact angle measurements indeed showed a faster increase of layer thickness and hydrophobicity for the hexadec-3-en-1-yne-derived monolayers. This more rapid monolayer formation was supported by IRRAS and XPS measurements that for the enyne show a faster increase of the CH2 stretching bands and the amount of carbon at the surface (C/Si ratio), respectively. Monolayer formation at room temperature yielded plateau values for hexadec-3-en-1-yne and 1-hexadecyne after 8 and 16 h, respectively. Additional experiments were performed for 16 h at 80° to ensure full completion of the layers, which allows comparison of the quality of both layers. Ellipsometry thicknesses (2.0 nm) and contact angles (111–112°) indicated a high quality of both layers. XPS, in combination with DFT calculations, revealed terminal attachment of hexadec-3-en-1-yne to the H–Si surface, leading to dienyl monolayers. Moreover, analysis of the Si2p region showed no surface oxidation. Quantitative XPS measurements, obtained via rotating Si samples, showed a higher surface coverage for C16 dienyl layers than for C16 alkenyl layers (63% vs 59%). The dense packing of the layers was confirmed by IRRAS and NEXAFS results. Molecular mechanics simulations were undertaken to understand the differences in reactivity and surface coverage. Alkenyl layers show more favorable packing energies for surface coverages up to 50–55%. At higher coverages, this packing energy rises quickly, and there the dienyl packing becomes more favorable. When the binding energies are included the difference becomes more pronounced, and dense packing of dienyl layers becomes more favorable by 2–3 kcal/mol. These combined data show that enynes provide the highest-quality organic monolayers reported on H–Si up to now.
    Charge transport across metal/molecular (alkyl) monolayer-Si junctions is dominated by the LUMO level
    Yaffe, O. ; Qi, Y. ; Scheres, L.M.W. ; Puniredd, S.R. ; Segev, L. ; Ely, T. ; Haick, H. ; Zuilhof, H. ; Vilan, A. ; Kronik, L. ; Kahn, A. ; Cahen, D. - \ 2012
    Physical Review. B : Condensed Matter and Materials Physics 85 (2012)4. - ISSN 1098-0121
    self-assembled monolayers - electronic transport - molecular electronics - organic-molecules - chain monolayers - spectroscopy - polyethylene - conductance - films - photoemission
    We compare the charge transport characteristics of heavy-doped p(++)- and n(++)-Si-alkyl chain/Hg junctions. Based on negative differential resistance in an analogous semiconductor-inorganic insulator/metal junction we suggest that for both p(++)- and n(++)-type junctions, the energy difference between the Fermi level and lowest unoccupied molecular orbital (LUMO), i.e., electron tunneling, controls charge transport. This conclusion is supported by results from photoelectron spectroscopy (ultraviolet photoemission spectroscopy, inverse photoelectron spectroscopy, and x-ray photoemission spectroscopy) for the molecule-Si band alignment at equilibrium, which clearly indicate that the energy difference between the Fermi level and the LUMO is much smaller than that between the Fermi level and the highest occupied molecular orbital (HOMO). Furthermore, the experimentally determined Fermi level - LUMO energy difference, agrees with the non-resonant tunneling barrier height, deduced from the exponential length attenuation of the current.
    An Investigation of Polyamides Based on Isoidide-2,5-dimethyleneamine as a Green Rigid Building Block with Enhanced Reactivity
    Wu, J. ; Jasinska-Walc, L. ; Dudenko, D. ; Rozanski, A. ; Hansen, M.R. ; Es, D.S. van; Koning, C.E. - \ 2012
    Macromolecules 45 (2012)23. - ISSN 0024-9297 - p. 9333 - 9346.
    solid-state-nmr - infrared temperature - renewable resources - brill transition - isosorbide - isohexide - polymers - mas - spectroscopy - crystals
    Novel, semicrystalline polyamides and copolyamides were synthesized from a new carbohydrate-based diamine, namely isoidide-2,5-dimethyleneamine (IIDMA). In combination with 1,6-hexamethylene diamine (1,6-HDA) as well as the biobased sebacic acid (SA) or brassylic acid (BrA), the desired copolyamides were obtained via melt polymerization of the nylon salts followed by a solid-state polycondensation (SSPC) process. Depending on the chemical compositions, the number average molecular weights (Mn) of the polyamides were in the range of 4000–49000 g/mol. With increasing IIDMA content in the synthesized copolyamides, their corresponding glass transition temperatures (Tg) increased from 50 °C to approximately 60–67 °C while the melting temperatures (Tm) decreased from 220 to 160 °C. The chemical structures of the polyamides were analyzed by NMR and FT-IR spectroscopy. Both differential scanning calorimetry (DSC) and wide-angle X-ray diffraction (WAXD) analyses revealed the semicrystalline character of these novel copolyamides. Variable-temperature (VT) 13C{1H} cross-polarization/magic-angle spinning (CP/MAS) NMR and FT-IR techniques were employed to study the crystal structures as well as the distribution of IIDMA moieties over the crystalline and amorphous phases of the copolyamides. The performed ab initio calculations reveal that the stability of the IIDMA moieties is due to a pronounced “boat” conformation of the bicyclic rings. The incorporation of methylene segments in between the isohexide group and the amide groups enables the hydrogen bonds formation and organization of the polymer chain fragments. Given the sufficiently high Tm values (200 °C) of the copolyamides containing less than 50% of IIDMA, these biobased semicrystalline copolyamides can be useful for engineering plastic applica
    Organic matter of subsoil horizons under broadleaved forest: Highly processed or labile and plant-derived?
    Vancampenhout, K. ; Vos, B. de; Wouters, K. ; Swennen, R. ; Buurman, P. - \ 2012
    Soil Biology and Biochemistry 50 (2012)july. - ISSN 0038-0717 - p. 40 - 46.
    pyrolysis-gc/ms - chemical-composition - carbon pool - soils - stabilization - spectroscopy - ecosystems - mechanisms - fractions - chemistry
    Between 30 and 63% of the soil organic matter (SOM) is stored below 30 cm, making subsoil-SOM an important source and sink in the global carbon cycle. Nevertheless, detailed information on the composition of subsoil-SOM remains scarce. This study aims to evaluate the chemical composition of SOM in topsoil and subsoil horizons in broadleaved forests on acid loamy soils. Six sites were chosen in Northern Belgium under beech, oak and hybrid poplar, on Gleysols, Umbrisols, Cambisols and Albeluvisols on loamy Quaternary deposits. Analytical pyrolysis–gas chromatography/mass spectrometry (pyrolysis–GC/MS) was performed on the dialyzed alkaline extract, which represents between 41 and 90% of the total organic carbon for the selected sites. All extracts show a significant shift in chemical composition between the topsoil and the subsoil. While topsoil-SOM mainly differs according to input and nutrient status, subsoil-SOM shows high relative amounts of alkanes and alkenes or polysaccharides for coarse and fine textured soils respectively. Lignins, lignin-derived phenols or aromatics were not major contributors to subsoil-SOM, regardless of soil type. Furthermore, results show that very labile plant-derived molecules are present in the subsoil, i.e. long-chain aliphatics and (cellulose-derived) anhydrosugars. The organic matter signature of the subsoil samples was evaluated for typical indications of fresh material, decay, podzolisation and anaerobic processes, and indicates root input and stabilization of certain labile plant-derived compounds against microbial decay to be important in the subsoil.
    Using a genetic algorithm as an optimal band selector in the mid and thermal infrared (2.5-14 µm) to discriminate vegetation species
    Ullah, S. ; Groen, T.A. ; Schlerf, M. ; Skidmore, A.K. ; Nieuwenhuis, W. ; Vaiphasa, C. - \ 2012
    Sensors 12 (2012)7. - ISSN 1424-8220 - p. 8755 - 8769.
    spectral discrimination - reflectance - spectroscopy - emissivity - imagery - leaves - identification - spectrometry - regression - plants
    Genetic variation between various plant species determines differences in their physio-chemical makeup and ultimately in their hyperspectral emissivity signatures. The hyperspectral emissivity signatures, on the one hand, account for the subtle physio-chemical changes in the vegetation, but on the other hand, highlight the problem of high dimensionality. The aim of this paper is to investigate the performance of genetic algorithms coupled with the spectral angle mapper (SAM) to identify a meaningful subset of wavebands sensitive enough to discriminate thirteen broadleaved vegetation species from the laboratory measured hyperspectral emissivities. The performance was evaluated using an overall classification accuracy and Jeffries Matusita distance. For the multiple plant species, the targeted bands based on genetic algorithms resulted in a high overall classification accuracy (90%). Concentrating on the pairwise comparison results, the selected wavebands based on genetic algorithms resulted in higher Jeffries Matusita (J-M) distances than randomly selected wavebands did. This study concludes that targeted wavebands from leaf emissivity spectra are able to discriminate vegetation species.
    Silver nanoparticle aggregates as highly efficient plasmonic antennas for fluorescence enhancement
    Gill, R. ; Tian, L. ; Somerville, W.R.C. ; Ru, E.C. Le; Amerongen, H. van; Subramaniam, V. - \ 2012
    The Journal of Physical Chemistry Part C: Nanomaterials and Interfaces 116 (2012)31. - ISSN 1932-7447 - p. 16687 - 16693.
    raman-scattering sers - field enhancement - optical antennas - hot-spots - surface - spectroscopy - molecule - nanoantennas - nanoshells - decay
    The enhanced local fields around plasmonic structures can lead to enhancement of the excitation and modification of the emission quantum yield of fluorophores. So far, high enhancement of fluorescence intensity from dye molecules was demonstrated using bow-tie gap antenna made by e-beam lithography. However, the high manufacturing cost and the fact that currently there are no effective ways to place fluorophores only at the gap prevent the use of these structures for enhancing fluorescence-based biochemical assays. We report on the simultaneous modification of fluorescence intensity and lifetime of dye-labeled DNA in the presence of aggregated silver nanoparticles. The nanoparticle aggregates act as efficient plasmonic antennas, leading to more than 2 orders of magnitude enhancement of the average fluorescence. This is comparable to the best-reported fluorescence enhancement for a single molecule but here applies to the average signal detected from all fluorophores in the system. This highlights the remarkable efficiency of this system for surface-enhanced fluorescence. Moreover, we show that the fluorescence intensity enhancement varies with the plasmon resonance position and measure a significant reduction (300×) of the fluorescence lifetime. Both observations are shown to be in agreement with the electromagnetic model of surface-enhanced fluorescence.
    Process redesign for effective use of product quality information in meat chains
    Rijpkema, W.A. ; Rossi, R. ; Vorst, J.G.A.J. van der - \ 2012
    International Journal of Logistics research and applications 15 (2012)6. - ISSN 1367-5567 - p. 389 - 403.
    water-holding capacity - supply chain - decision-making - pork - flexibility - simulation - spectroscopy - perspective - technology - system
    To fulfil segmented consumer demand and add value, meat processors seek to exploit quality differences in meat products. Availability of product quality information is of key importance for this. We present a case study where an innovative sensor technology that provides estimates of an important meat quality feature is considered. Process design scenarios that differ with respect to sorting complexity, available product quality information, and use of temporary buffers are assessed using a discrete event simulation model. Results indicate that increasing sorting complexity by use of advanced product quality information results in a reduction of processing efficiency. Use of production buffers was found to increase processing flexibility and mitigate negative effects of high sorting complexity. This research illustrates how the use of advanced product quality information in logistics’ decision-making affects sorting performance, processing efficiency, and the optimal processing design, an area that has so far received little attention in literature.
    Soil biotic impact on plant species shoot chemistry and hyperspectral reflectance patterns
    Carvalho, S. de; Macel, M. ; Schlerf, M. ; Skidmore, A.K. ; Putten, W.H. van der - \ 2012
    New Phytologist 196 (2012)4. - ISSN 0028-646X - p. 1133 - 1144.
    borne pathogens - spectroscopy - community - leaf - accumulation - herbivores - prediction - invader - quality - forest
    Recent studies revealed that plant-soil biotic interactions may cause changes in above-ground plant chemistry. It would be a new step in below-ground-above-ground interaction research if such above-ground chemistry changes could be efficiently detected. Here we test how hyperspectral reflectance may be used to study such plant-soil biotic interactions in a nondestructive and rapid way. The native plant species Jacobaea vulgaris and Jacobaea erucifolius, and the exotic invader Senecio inaequidens were grown in different soil biotic conditions. Biomass, chemical content and shoot reflectance between 400 and 2500 nm wavelengths were determined. The data were analysed with multivariate statistics. Exposing the plants to soil biota enhanced the content of defence compounds. The highest increase (400%) was observed for the exotic invader S. inaequidens. Chemical and spectral data enabled plant species to be classified with an accuracy > 85%. Plants grown in different soil conditions were classified with 50-60% correctness. Our data suggest that soil microorganisms can affect plant chemistry and spectral reflectance. Further studies should test the potential to study plant-soil biotic interactions in the field. Such techniques could help to monitor, among other things, where invasive exotic plant species develop biotic resistance or the development of hotspots of crop soil diseases.
    Fluorescence of Alexa Fluor dye tracks protein folding
    Lindhoud, S. ; Westphal, A.H. ; Borst, J.W. ; Visser, A.J.W.G. ; Mierlo, C.P.M. van - \ 2012
    PLoS ONE 7 (2012)10. - ISSN 1932-6203 - 8 p.
    azotobacter-vinelandii apoflavodoxin - resonance energy-transfer - beta parallel protein - molten-globule state - flavodoxin-ii - molecules - pathway - chains - intermediate - spectroscopy
    Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET) are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488), which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.
    Structure and Molecular Dynamics in Renewable Polyamides from Dideoxy-Diamino Isohexide
    Jasinska-Walc, L. ; Koning, C.E. ; Es, D.S. van; Thiyagarajan, S. - \ 2012
    Macromolecules 45 (2012)14. - ISSN 0024-9297 - p. 5653 - 5666.
    folded lamellar crystals - solid-state nmr - infrared temperature - c-13 nmr - nylons 4 - spectroscopy - transition - morphology - resolution - amination
    The chemical structure, the conformation, and the flexibility of the polymer chain fragments present in the polyamides synthesized from 2,5-diamino-2,5-dideoxy-1,4;3,6- dianhydrosorbitol, 1,4-diaminobutane, and either sebacic or brassylic acid have been studied by liquid-state 2D NMR spectroscopy viz. correlation spectra (COSY) and heteronuclear multiple-bond correlation spectra (gHMBC), by 13C cross-polarization/magic-angle spinning (CP/MAS) NMR, by X-ray scattering, and by FT-IR spectroscopy. The presence of 2,5-diamino-2,5-dideoxy-1,4;3,6-dianhydrosorbitol in the crystal phase of the polyamides was probed by wide-angle X-ray diffraction (WAXD), FT-IR, and solid-state 13C NMR. The incorporation of dideoxy-diamino isohexide into the backbone of PA 4.10 or PA 4.13 induces formation of gauche type conformers and gives rise to pseudohexagonal packing of the polymer chains in these semicrystalline copolymers. The experimental determination of the polymer chain structure combined with ab initio calculations revealed the presence of three most abundant diaminoisosorbide (DAIS) conformers. The combination of the 13C chemical shifts of these three conformers could explain all experimental resonances in the region of 50-90 ppm. WAXD and DSC analysis show that the crystallinity, and hence the physical properties of the investigated compositions, can be tailored by the content of the bicyclic diamine in the backbone of the polyamides. ¦ INTRODUCTION The number and types of applications utilizing polyamides (PA) generate new trends in the selection of monomers used in their synthesis. Nowadays, biomass-derived chemicals offer an enormous potential to replace the depleting fossil feedstock and are considered as an environmentally friendly alternative. Despite the obvious benefits offered by renewable resources, bio-based polymers are often believed to be unsuitable for hightemperature industrial chemical processes and applications. However, our recent results1,2 have shown that, based on thorough understanding of the structure-property relationships of different polyamides, it is now possible to prepare fully bio-based polyamides having equally good properties as the ones from petrochemical origin. Widely reported renewable monomers in this field are sebacic acid, brassylic acid, 1,4- diaminobutane, or isohexides.3-13 As pointed out by Fenouillot,3 the use of starch-based 1,4;3,6-dianhydrohexitols (isosorbide, isomannide, and isoidide) or their diamino derivatives with D-manno or L-ido configuration affords entirely bio-based materials with a wide variety of applications.
    Disentangling picosecond events that complicate the quantative use of the calcium sensor YC3.60
    Laptenok, S. ; Stokkum, I.H.M. van; Borst, J.W. ; Oort, B.F. van; Visser, A.J.W.G. ; Amerongen, H. van - \ 2012
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 116 (2012)9. - ISSN 1520-6106 - p. 3013 - 3020.
    cyan fluorescent protein - resonance energy-transfer - time-resolved spectra - living cells - fret - photoconversion - ca2+ - yfp - spectroscopy - indicators
    Yellow Cameleon 3.60 (YC3.60) is a calcium sensor based on Förster resonance energy transfer (FRET). This sensor is composed of a calmodulin domain and a M13 peptide, which are located in between enhanced cyan-fluorescent protein (ECFP) and the Venus variant of enhanced yellow-fluorescent protein (EYFP). Depending on the calcium concentration, the efficiency of FRET from donor ECFP to acceptor EYFP is changing. In this study, we have recorded time-resolved fluorescence spectra of ECFP, EYFP, and YC3.60 in aqueous solution with picosecond time resolution, using different excitation wavelengths. Detailed insight in the FRET kinetics was obtained by using global and target analyses of time- and wavelength-resolved fluorescence of purified YC3.60 in calcium-free and calcium-bound conformations. The results clearly demonstrate that for both conformations, there are two distinct donor populations: a major one giving rise to FRET and a minor one not able to perform FRET. The transfer time for the calcium-bound conformation is 21 ps, whereas it is in the order of 1 ns for the calcium-free conformation. Ratio imaging of acceptor and donor fluorescence intensities of YC3.60 is usually applied to measure Ca(2+) concentrations in living cells. From the obtained results, it is clear that the intensity ratio is strongly influenced by the presence of donor molecules that do not take part in FRET, thereby significantly affecting the quantitative interpretation of the results.
    Online detection and quatification of ergot bodies in cereals using near infrared hyperspectral imaging
    Vermeulen, Ph. ; Fernandez - Pierna, J.A. ; Egmond, H.P. van; Dardenne, P. ; Baeten, V. - \ 2012
    Food Additives & Contaminants. Pt. A, Chemistry, Analysis, Control, Exposure & Risk Assessment 29 (2012)2. - ISSN 1944-0049 - p. 232 - 240.
    spectroscopy - alkaloids
    The occurrence of ergot bodies (sclerotia of Claviceps purpurea) in cereals presents a high toxicity risk for animals and humans due to the alkaloid content. To reduce this risk, the European Commission fixed an ergot concentration limit of 0.1% in all feedstuffs containing unground cereals, and a limit of 0.05% in ‘intervention’ cereals destined for humans. This study sought to develop a procedure based on near infrared hyperspectral imaging and multivariate image analysis to detect and quantify ergot contamination in cereals. Hyperspectral images were collected using an NIR hyperspectral line scan combined with a conveyor belt. All images consisted of lines of 320 pixels that were acquired at 209 wavelength channels (1100–2400¿nm). To test the procedure, several wheat samples with different levels of ergot contamination were prepared. The results showed a correlation higher than 0.99 between the predicted values obtained using chemometric tools such as partial least squares discriminant analysis or support vector machine and the reference values. For a wheat sample with a level of ergot contamination as low as 0.01 %, it was possible to identify groups of pixels detected as ergot to conclude that the sample was contaminated. In addition, no false positives were obtained with non-contaminated samples. The limit of detection was found to be 145¿mg/kg and the limit of quantification 341¿mg/kg. The reproducibility tests of the measurements performed over several weeks showed that the results were always within the limits allowed. Additional studies were done to optimise the parameters in terms of number of samples analysed per unit of time or conveyor belt speed. It was shown that ergot can be detected using a speed of 1–100¿mm/s and that a sample of 250¿g can be analysed in 1¿min
    Identifying plant species using mid-wave infrared (2.5-6µm) and thermal infrared (8-14µm) emissivity spectra
    Ullah, S. ; Schlerf, M. ; Skidmore, A.K. ; Hecker, C. - \ 2012
    Remote Sensing of Environment 118 (2012)4. - ISSN 0034-4257 - p. 95 - 102.
    salt-marsh vegetation - hyperspectral data - biomass estimation - reflectance - discrimination - indexes - imagery - leaves - classification - spectroscopy
    Plant species discrimination using remote sensing is generally limited by the similarity of their reflectance spectra in the visible, NIR and SWIR domains. Laboratory measured emissivity spectra in the mid infrared (MIR; 2.5µm-6µm) and the thermal infrared (TIR; 8µm-14µm) domain of different plant species, however, reveal significant differences. It is anticipated that with the advances in airborne and space borne hyperspectral thermal sensors, differentiation between plant species may improve. The laboratory emissivity spectra of thirteen common broad leaved species, comprising 3024 spectral bands in the MIR and TIR, were analyzed. For each wavelength the differences between the species were tested for significance using the one way analysis of variance (ANOVA) with the post-hoc Tukey HSD test. The emissivity spectra of the analyzed species were found to be statistically different at various wavebands. Subsequently, six spectral bands were selected (based on the histogram of separable pairs of species for each waveband) to quantify the separability between each species pair based on the Jefferies Matusita (JM) distance. Out of 78 combinations, 76 pairs had a significantly different JM distance. This means that careful selection of hyperspectral bands in the MIR and TIR (2.5µm-14µm) results in reliable species discrimination.
    Fluorescence and Atomic Force Microscopy Imaging of Wall Teichoic Acids in Lactobacillus plantarum
    Andre, G. ; Deghorain, M. ; Bron, P.A. ; Swam, I.I. van; Kleerebezem, M. ; Hols, P. ; Dufrene, Y.F. - \ 2011
    Acs Chemical Biology 6 (2011)4. - ISSN 1554-8929 - p. 366 - 376.
    gram-positive bacteria - staphylococcus-aureus - cell-wall - lipoteichoic acid - bacillus-subtilis - growth - localization - peptidoglycan - biosynthesis - spectroscopy
    Although teichoic acids are major constituents of bacterial cell walls, little is known about the relationships between their spatial localization and their functional roles. Here, we used single-molecule atomic force microscopy (AFM) combined with fluorescence microscopy to image the distribution of wall teichoic acids (WTAs) in. Lactobacillus plantarum, in relation with their physiological roles. Phenotype analysis of the wild-type strain and of mutant strains deficient for the synthesis of WTAs (Delta tagO) or cell wall polysaccharides (Delta cps1-4) revealed that WTAs are required for proper cell elongation and cell division. Nanoscale imaging by AFM showed that strains expressing WTAs have a highly polarized surface morphology, the poles being much smoother than the side walls. AFM and fluorescence imaging with specific lectin probes demonstrated that the polarized surface structure correlates with a heterogeneous distribution of WTAs, the latter being absent from the surface of the poles. These observations indicate that the polarized distribution of WTAs in L. plantarum plays a key role in controlling cell morphogenesis (surface roughness, cell shape, elongation, and division).
    Predicting bovine milk protein composition based on Fourier transform infrared spectra
    Rutten, M.J.M. ; Bovenhuis, H. ; Heck, J.M.L. ; Arendonk, J.A.M. van - \ 2011
    Journal of Dairy Science 94 (2011)11. - ISSN 0022-0302 - p. 5683 - 5690.
    dutch holstein-friesians - genetic-parameters - beta-lactoglobulin - coagulation properties - production traits - fat composition - dairy-cows - casein - genotypes - spectroscopy
    Phenotypic information on individual protein composition of cows is important for many aspects of dairy processing with cheese production as the center of gravity. However, measuring individual protein composition is expensive and time consuming. In this study, we investigated whether protein composition can be predicted based on inexpensive and routinely measured milk Fourier transform infrared (FTIR) spectra. Based on 900 calibration and 900 validation samples that had both capillary zone electrophoresis (CZE)-determined protein composition and FTIR spectra available, low to moderate validation R2 were reached (from 0.18 for aS1-casein to 0.56 for ß-lactoglobulin). The potential usefulness of this model on the phenotypic level was investigated by means of achieved selection differentials for 25% of the best animals. For a-lactalbumin (R2 = 0.20), the selection differential amounted to 0.18 g/100 g and for casein index (R2 = 0.50) to 1.24 g/100 g. We concluded that predictions of protein composition were not accurate enough to enable selection of individual animals. However, for specific purposes when, for example, groups of animals that meet a certain threshold are to be selected, the presented model could be useful in practice on the phenotypic level. The potential usefulness of this model on the genetic level was investigated by means of genetic correlations between CZE-determined and FTIR-predicted protein composition traits. The genetic correlations ranged from 0.62 (ß-casein) to 0.97 (whey). Thus, predictions of protein composition, when used as input to estimate breeding values, provide an excellent means for genetic improvement of protein composition. In addition, estimated repeatabilities based on 3 repeated observations of predicted protein composition showed that a considerable amount of prediction error can be removed using repeated observations.
    Time-resolved fluorescence and fluorescence anisotropy of fluorescein-labeled poly(N-isopropylacrylamide) incorporated in polymersomes
    Lee, J.S. ; Koehorst, R.B.M. ; Amerongen, H. van; Feijen, J. - \ 2011
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 115 (2011)45. - ISSN 1520-6106 - p. 13162 - 13167.
    energy migration - molecular-weight - phase-transition - temperature-dependence - gel - vesicles - spectroscopy - stability - hydrogels - systems
    The phase behavior of fluorescein isothiocyanate (FITC) labeled poly(N-isopropylacrylamide) (PNIPAAm) incorporated in polymersomes (Ps) was studied by monitoring the fluorescence lifetime (FL) and the time-resolved fluorescence anisotropy (TRFA) as a function of temperature at pH 7.4. Ps containing FITC-labeled PNIPAAm with a diameter less than 200 nm were prepared by injecting a THF solution of poly(ethylene glycol)-b-poly(d,l-lactide) (mPEG-PDLLA) and FITC tagged PNIPAAm (FITC-N) into phosphate buffered saline (PBS, pH 7.4). Solutions of free FITC (2 µM) and FITC-N (2 µM) in PBS were used as controls. The polarized fluorescence decay curves of FITC were fitted with one rotational correlation time (¿1) and the corresponding amplitude (ß1), while those for FITC-N were fitted with two rotational correlation times (¿1,2) and their corresponding amplitudes (ß1,2). Short rotational correlation times, ¿1, correspond with the rotation of the FITC molecule itself, whereas ¿2 corresponds to FITC-segmental rotation. FITC-N encapsulated in Ps (FITC-N/Ps) showed a decrease of the rotational motion upon increasing the temperature. The long rotational correlation time (¿2) of FITC-N increased 3 fold, going from 15 to 40 °C, reflecting a reduced rotational mobility. The residual anisotropy (ß8) of FITC-N/Ps at pH 7.4 showed a gradual increase, going from 15 to 25 °C followed by a gradual decrease at higher temperatures. These results are explained by a transition from coil to globule, a gradual increase of intermolecular aggregation, and possibly phase separation and hydrogel formation
    The effect of the fat content on the thermal effusivity of foods: an inverse photopyroelectric study
    Szafner, G. ; Bicanic, D.D. ; Doka, O. - \ 2011
    International journal of Food Properties 14 (2011)3. - ISSN 1094-2912 - p. 666 - 674.
    rheological characterization - light mayonnaises - milk - spectroscopy - acids - dsc
    Photopyroelectric (PPE) methods belong to the class of photothermal techniques and provide the means for determining some thermal properties of foods in a relatively fast and simple way. In particular, the inverse variant of the photopyroelectric method, abbreviated IPPE, was used here to determine thermal effusivity (also called heat penetration coefficient) of the sour cream and mayonnaise as a function of their fat content. In the sour cream the latter varied from 12 to 31 g/100 g as compared to 27 to 80 g/100 g range in mayonnaise; for both samples the effusivity decreased linearly with the increasing fat content. Each additional gram of fat in 100 g sour cream or mayonnaise resulted in 11.13 and 12.11 Ws1/2m-2K-1 drop in effusivity. Good agreement between the experimentally obtained data and the calculated effusivity was observed if both, the composition and the thermal properties of individual constituents of sour cream were known.
    Structural features and properties of soluble products derived from Eucalyptus globulus hemicelluloses
    Gullon, P. ; González-Muñoz, M.J. ; Gool, M.P. van; Schols, H.A. ; Hirsch, J. ; Ebringerová, A. ; Parajo, J.C. - \ 2011
    Food Chemistry 127 (2011)4. - ISSN 0308-8146 - p. 1798 - 1807.
    xylo-oligosaccharides - in-vitro - autohydrolysis liquors - intestinal microbiota - wood - xylooligosaccharides - fermentability - fermentation - spectroscopy - manufacture
    Eucalyptus globulus wood samples were subjected to double hydrothermal processing to remove extractives in the first stage, and to cause the selective solubilisation of 4-O-methylglucuronoxylan in the second stage. The hemicellulose-derived products present in the liquors from the second hydrothermal stage (substituted xylooligosaccharides, denoted XOS) were refined by treatments with membranes and ion exchange. The purified XOS product was assayed for composition and characterised by HPLC-RI, HPAEC-PAD, HPSEC, MALDI-TOF-MS and NMR techniques. The results suggested the presence of neutral and acidic XOS with a degree of acetylation of about 0.6. The fermentability of the refined XOS product by faecal inocula was assessed by measuring both substrate consumption and formation of short-chain fatty acids.
    A general approach for detecting folding intermediates from staedy-state and time-resolved fluorescence of single-tryptophan-containing proteins
    Laptenok, S. ; Visser, N.V. ; Ruchira, A. ; Westphal, A.H. ; Hoek, A. van; Mierlo, C.P.M. van; Stokkum, I.H.M. van; Amerongen, H. van; Visser, A.J.W.G. - \ 2011
    Biochemistry 50 (2011)17. - ISSN 0006-2960 - p. 3441 - 3450.
    azotobacter-vinelandii - apoflavodoxin - pathway - spectroscopy - peptide
    During denaturant-induced equilibrium (un)folding of wild-type apoflavodoxin from Azotobacter vinelandii, a molten globule-like folding intermediate is formed. This wild-type protein contains three tryptophans. In this study, we use a general approach to analyze time-resolved fluorescence and steady-state fluorescence data that are obtained upon denaturant-induced unfolding of a single-tryptophan-containing variant of apoflavodoxin [i.e., W74/F128/F167 (WFF) apoflavodoxin]. The experimental data are assembled in matrices, and subsequent singular-value decomposition of these matrices (i.e., based on either steady-state or time-resolved fluorescence data) shows the presence of three significant, and independent, components. Consequently, to further analyze the denaturation trajectories, we use a three-state protein folding model in which a folding intermediate and native and unfolded protein molecules take part. Using a global analysis procedure, we determine the relative concentrations of the species involved and show that the stability of WFF apoflavodoxin against global unfolding is 4.1 kcal/mol. Analysis of time-resolved anisotropy data of WFF apoflavodoxin unfolding reveals the remarkable observation that W74 is equally well fixed within both the native protein and the molten globule-like folding intermediate. Slight differences between the direct environments of W74 in the folding intermediate and native protein cause different rotameric populations of the indole in both folding species as fluorescence lifetime analysis reveals. Importantly, thermodynamic analyses of the spectral denaturation trajectories of the double-tryptophan-containing protein variants WWF apoflavodoxin and WFW apoflavodoxin show that these variants are significantly more stable (5.9 kcal/mol and 6.8 kcal/mol, respectively) than WFF apoflavodoxin (4.1 kcal/mol) Hence, tryptophan residues contribute considerably to the 10.5 kcal/mol thermodynamic stability of native wild-type apoflavodoxin
    The patterns of population differentiation in a Brassica rapa core collection
    Pino del Carpio, D. ; Basnet, R.K. ; Vos, R.C.H. de; Maliepaard, C.A. ; Visser, R.G.F. ; Bonnema, A.B. - \ 2011
    Theoretical and Applied Genetics 122 (2011)6. - ISSN 0040-5752 - p. 1105 - 1118.
    genetic diversity - morphological traits - l. - association - aflp - microsatellites - spectroscopy - metabolomics - frequencies - landraces
    With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data available has increased dramatically. Although many genetic diversity studies combine morphological and genetic data, metabolite profiling has yet to be integrated into these studies. For our study we selected 168 accessions representing the different morphotypes and geographic origins of Brassica rapa. Metabolite profiling was performed on all plants of this collection in the youngest expanded leaves, 5 weeks after transplanting and the same material was used for molecular marker profiling. During the same season a year later, 26 morphological characteristics were measured on plants that had been vernalized in the seedling stage. The number of groups and composition following a hierarchical clustering with molecular markers was highly correlated to the groups based on morphological traits (r = 0.420) and metabolic profiles (r = 0.476). To reveal the admixture levels in B. rapa, comparison with the results of the programme STRUCTURE was needed to obtain information on population substructure. To analyze 5546 metabolite (LC–MS) signals the groups identified with STRUCTURE were used for random forests classification. When comparing the random forests and STRUCTURE membership probabilities 86% of the accessions were allocated into the same subgroup. Our findings indicate that if extensive phenotypic data (metabolites) are available, classification based on this type of data is very comparable to genetic classification. These multivariate types of data and methodological approaches are valuable for the selection of accessions to study the genetics of selected traits and for genetic improvement programs, and additionally provide information on the evolution of the different morphotypes in B. rapa
    Annual balances of CH4 and N2O from a managed fen meadow using eddy covariance flux measurements
    Kroon, P.S. ; Schrier-Uijl, A.P. ; Hensen, A. ; Veenendaal, E.M. ; Jonker, H.J.J. - \ 2010
    European Journal of Soil Science 61 (2010)5. - ISSN 1351-0754 - p. 773 - 784.
    nitrous-oxide emissions - methane emission - peat soils - micrometeorological techniques - grassland systems - carbon - exchange - climate - spectroscopy - netherlands
    Annual terrestrial balances of methane (CH4) and nitrous oxide (N2O) are presented for a managed fen meadow in the Netherlands for 2006, 2007 and 2008, using eddy covariance (EC) flux measurements. Annual emissions derived from different methods are compared. The most accurate annual CH4 flux is achieved by gap filling EC fluxes with an empirical multivariate regression model, with soil temperature and mean wind velocity as driving variables. This model explains about 60% of the variability in observed daily CH4 fluxes. Annual N2O emissions can be separated into background emissions and event emissions due to fertilization. The background emission is estimated using a multivariate regression model also based on EC flux data, with soil temperature and mean wind velocity as driving variables. The event emissions are estimated using emission factors. The minimum direct emission factor is derived for six fertilization events by subtracting the background emission, and the IPCC default emission factor of 1% is used for the other events. In addition, the maximum direct emission factors are determined for the six events without subtracting the background emission. The average direct emission factor ranges from 1.2 to 2.8%, which is larger than the IPCC default value. Finally, the total terrestrial greenhouse gas balance is estimated at 16 Mg ha-1 year-1 in CO2-equivalents with contributions of 30, 25 and 45% by CO2, CH4 and N2O, respectively.
    ATP Changes the Fluorescence Lifetime of Cyan Fluorescent protein via an Interaction with His148
    Borst, J.W. ; Willemse, M. ; Slijkhuis, R. ; Krogt, G. ; Laptenok, S. ; Jalink, K. ; Wieringa, B. ; Fransen, J.A.M. - \ 2010
    PLoS ONE 5 (2010)11. - ISSN 1932-6203 - 7 p.
    energy-transfer - variant - fret - cell - spectroscopy - chromophore - binding - decays
    Recently, we described that ATP induces changes in YFP/CFP fluorescence intensities of Fluorescence Resonance Energy Transfer (FRET) sensors based on CFP-YFP. To get insight into this phenomenon, we employed fluorescence lifetime spectroscopy to analyze the influence of ATP on these fluorescent proteins in more detail. Using different donor and acceptor pairs we found that ATP only affected the CFP-YFP based versions. Subsequent analysis of purified monomers of the used proteins showed that ATP has a direct effect on the fluorescence lifetime properties of CFP. Since the fluorescence lifetime analysis of CFP is rather complicated by the existence of different lifetimes, we tested a variant of CFP, i.e. Cerulean, as a monomer and in our FRET constructs. Surprisingly, this CFP variant shows no ATP concentration dependent changes in the fluorescence lifetime. The most important difference between CFP and Cerulean is a histidine residue at position 148. Indeed, changing this histidine in CFP into an aspartic acid results in identical fluorescence properties as observed for the Cerulean fluorescent based FRET sensor. We therefore conclude that the changes in fluorescence lifetime of CFP are affected specifically by possible electrostatic interactions of the negative charge of ATP with the positively charged histidine at position 148. Clearly, further physicochemical characterization is needed to explain the sensitivity of CFP fluorescence properties to changes in environmental (i.e. ATP concentrations) conditions.
    Carotenoid fluorescence in Dunaliella salina
    Kleinegris, D.M.M. ; Es, M.A. van; Janssen, M.G.J. ; Brandenburg, W.A. ; Wijffels, R.H. - \ 2010
    Journal of Applied Phycology 22 (2010)5. - ISSN 0921-8971 - p. 645 - 649.
    beta-carotene - spectroscopy - pigments
    Dunaliella salina is a halotolerant green alga that is well known for its carotenoid producing capacity. The produced carotenoids are mainly stored in lipid globules. For various research purposes, such as production and extraction kinetics, we would like to determine and/or localise the carotenoid globules in vivo. In this study, we show that the carotenoid-rich globules emit clear green fluorescence, which can be used in, for example, fluorescence microscopy (e.g. CLSM) to obtain pictures of the cells and their carotenoid content.
    Electrical double-layer capacitance in room temperature ionic liquids: Ion size and specific adsorption effects
    Lauw, Y. ; Horne, M.D. ; Rodopoulos, T. ; Nelson, A. ; Leermakers, F.A.M. - \ 2010
    The Journal of Physical Chemistry Part B: Condensed Matter, Materials, Surfaces, Interfaces & Biophysical 114 (2010). - ISSN 1520-6106 - p. 11149 - 11154.
    interacting chain molecules - enhanced raman-scattering - sum-frequency generation - partial charge-transfer - differential capacitance - statistical-theory - surface-structure - electrode - interface - spectroscopy
    The electrical double-layer structure and capacitance in room temperature ionic liquids at electrified interfaces were systematically studied with use of the self-consistent mean-field theory. The capacitance curve departs from symmetry with respect to the point of zero charge when unequal ion-size is implemented or when specific adsorption of ions is introduced. For the case of unequal ion-size, the shape of the capacitance curve is strongly determined by the size of the counterion and only weakly influenced by the co-ion size. When present, specifically adsorbed ions would change the capacitance within a limited range of applied potential from the point of zero charge, which itself varies with the strength of specific adsorption.
    Monitoring photosynthesis in individual cells of Synechocytis sp. PCC 6803 on a picosecond timescale
    Krumova, S.K.B. ; Laptenok, S. ; Borst, J.W. ; Ughy, B. ; Gombos, Z. ; Aijani, G. ; Amerongen, H. van - \ 2010
    Biophysical Journal 99 (2010)6. - ISSN 0006-3495 - p. 2006 - 2015.
    fluorescence emission-spectra - excitation-energy transfer - intact photosystem-ii - thylakoid membrane - synechococcus 6301 - phycobilisome - kinetics - time - spectroscopy - chlorophyll
    Picosecond fluorescence kinetics of wild-type (WT) and mutant cells of Synechocystis sp. PCC 6803, were studied at the ensemble level with a streak-camera and at the cell level using fluorescence-lifetime-imaging microscopy (FLIM). The FLIM measurements are in good agreement with the ensemble measurements, but they (can) unveil variations between and within cells. The BE mutant cells, devoid of photosystem II (PSII) and of the light-harvesting phycobilisomes, allowed the study of photosystem I (PSI) in vivo for the first time, and the observed 6-ps equilibration process and 25-ps trapping process are the same as found previously for isolated PSI. No major differences are detected between different cells. The PAL mutant cells, devoid of phycobilisomes, show four lifetimes: 20 ps (PSI and PSII), 80 ps, 440 ps, and 2.8 ns (all due to PSII), but not all cells are identical and variations in the kinetics are traced back to differences in the PSI/PSII ratio. Finally, FLIM measurements on WT cells reveal that in some cells or parts of cells, phycobilisomes are disconnected from PSI/PSII. It is argued that the FLIM setup used can become instrumental in unraveling photosynthetic regulation mechanisms in the future
    High molecular weight glucan of the culinary medicinal mushroom Agaricus bisporus is an a-glucan that forms complexes with low molecular weight galactan
    Smiderle, F. ; Sassaki, G.L. ; Arkel, J. van; Lacomini, M. ; Wichers, H.J. ; Griensven, L.J.L.D. van - \ 2010
    Molecules 15 (2010)8. - ISSN 1420-3049 - p. 5818 - 5830.
    beta-glucans - flammulina-velutipes - edible mushroom - in-vitro - polysaccharide - pleurotus - extracts - glycogen - purification - spectroscopy
    An a-glucan was isolated from the culinary medicinal mushroom A. bisporus by hot water extraction, ethanol precipitation and DEAE-cellulose chromatography. The resulting material showed a single HMW peak excluded from a Sephadex G50 column that could completely be degraded by a-amylase treatment. After heating in 1% SDS a small additional peak of low MW eluted from the G50 column. The monosaccharide composition of the main peak was evaluated by HPLC, and was found to consist of a majority of glucose (97.6%), and a minor proportion of galactose (2.4%). Methylation analysis and degradation by a-amylase indicated the presence of an a-glucan with a main chain consisting of (1®4)-linked units, substituted at O-6 by a-D-glucopyranose single-units in the relation 1:8. Mono- (13C-, 1H-NMR) and bidimensional [1H (obs.),13C-HSQC] spectroscopy analysis confirmed the a-configuration of the Glcp residues by low frequency resonances of C-1 at d 100.6, 100.2, and 98.8 ppm and H-1 high field ones at d 5.06, 5.11, and 4.74 ppm. The DEPT-13C-NMR allowed assigning the non-substituted and O-substituted –CH2 signals at d 60.3/60.8 and 66.2 ppm, respectively. Other assignments were attributed to C-2, C-3, C-4, C-5 and C-6 of the non-reducing ends at d 71.8; 72.8; 70.0; 71.3 and 60.3/60.8 ppm, respectively. The minor proportion of galactose that was demonstrated was probably derived from a complex between the a-glucan and a low molecular weight galactan
    Nanowires Formed by the Co-Assembly of a Negatively Charged Low-Molecular Weight Gelator and a Zwitterionic Polythiophene
    Li, F. ; Ganesan, P. ; Jong, M.R. de; Aslund, A. ; Konradsson, P. ; Marcelis, A.T.M. ; Sudhölter, E.J.R. ; Cohen Stuart, M.A. ; Leermakers, F.A.M. - \ 2010
    ChemPhysChem 11 (2010). - ISSN 1439-4235 - p. 1956 - 1960.
    conjugated polyelectrolytes - spectroscopy - derivatives - organogels - alignment
    Conjugated organic nanowires have been prepared by co-assembling a carboxylate containing low-molecular weight gelator (LMWG) and an amino acid substituted polythiophene derivative (PTT). Upon introducing the zwitterionic polyelectrolyte PTT to a basic molecular solution of the organogelator, the negative charges on the LMWG are compensated by the positive charges of the PTT. As a result, nanowires form through co-assembly. These nanowires are visualized by both transmission electron microscopy (TEM) and atomic force microscopy (AFM). Depending on the concentration and ratio of the components these nanowires can be micrometers long. These measurements further suggest that the aggregates adopt a helical conformation. The morphology of these nanowires are studied with fluorescent confocal laser scanning microscopy (CLSM). The interactions between LMWG and PTT are characterized by steady-state and time-resolved fluorescence spectroscopy studies. The steady-state spectra indicate that the backbone of the PTT adopts a more planar and more aggregated conformation when interacting with LMWG. The time-resolved fluorescence decay studies confirm this interpretation.
    Estimating rapidly and precisely the concentration of beta carotene in mango homogenates by measuring the amplitude of optothermal signals, values of chromaticity indices and the intensities of Raman peaks
    Bicanic, D.D. ; Dimitrovski, D. ; Luterotti, S. ; Tiwisk, C. van; Buijnsters, J.G. ; Doka, O. - \ 2010
    Food Chemistry 121 (2010)3. - ISSN 0308-8146 - p. 832 - 838.
    liquid-chromatography - lycopene - window - quantification - spectroscopy - vegetables - separation - fruits - hplc
    Rapid, quantitative information about the micronutrients (including beta carotene) in mango fruit is often desired. High performance liquid chromatography (HPLC) and spectrophotometry (SP), the two widely used methods in practice to quantify carotenoids, both require a time consuming and expensive extraction of a pigment prior to the analysis itself. This paper compares the performances of the three candidate methods for the assessment of beta carotene in twenty one different mango homogenates to that of the HPLC as an established standard technique. The extraction is imperative in neither of the methods: the laser based optothermal window (OW), the resonance Raman spectroscopy and the tristimulus colorimetry. For the quantitative analysis however the availability of the calibration curve is a necessity. All candidate methods and in particular OW technique (compact instrument, low cost and the ease of operation) hold promise for a rapid screening/quantitative assessment of beta carotene in mango fruit
    Authentication of feeding fats: Classification of animal fats, fish oils and recycled cooking oils
    Ruth, S.M. van; Rozijn, M. ; Koot, A.H. ; Perez-Garcia, R. ; Kamp, H.J. van der; Codony, R. - \ 2010
    Animal Feed Science and Technology 155 (2010)1. - ISSN 0377-8401 - p. 65 - 73.
    reaction-mass-spectrometry - partial least-squares - trace gas-analysis - electronic nose - vegetable-oils - discrimination - spectroscopy - acids
    Classification of fats and oils involves the recognition of one/several markers typical of the product. The ideal marker(s) should be specific to the fat or oil. Not many chemical markers fulfill these criteria. Authenticity assessment is a difficult task, which in most cases requires the measurement of several markers and must take into account natural and technology-induced variation. The present study focuses on the identity prediction of three by-products of the fat industry (animal fats, fish oils, recycled cooking oils), which may be used for animal feeding. Their identities were predicted by their triacylglycerol fingerprints, their fatty acid fingerprints and their profiles of volatile organic compounds. Partial least square discriminant analysis allowed samples to be assigned successfully into their identity classes. Most successful were triacylglycerol and fatty acid fingerprints (both 96% correct classification). Proton transfer reaction mass spectra of the volatile compounds predicted the identity of the fats in 92% of the samples correctly.
    Molecular dynamics simulations reveal that AEDANS is an inert fluorescent probe for the study of membrane proteins
    Vos, W.L. ; Schor, M. ; Baumgaertner, A. ; Tieleman, D.P. ; Hemminga, M.A. - \ 2010
    European Biophysics Journal 39 (2010)2. - ISSN 0175-7571 - p. 229 - 239.
    major coat protein - transmembrane alpha-helix - energy-transfer - fret - orientation - conformation - spectroscopy - model - association - bilayers
    Computer simulations were carried out of a number of AEDANS-labeled single cysteine mutants of a small reference membrane protein, M13 major coat protein, covering 60% of its primary sequence. M13 major coat protein is a single membrane-spanning, a-helical membrane protein with a relatively large water-exposed region in the N-terminus. In 10-ns molecular dynamics simulations, we analyze the behavior of the AEDANS label and the native tryptophan, which were used as acceptor and donor in previous FRET experiments. The results indicate that AEDANS is a relatively inert environmental probe that can move unhindered through the lipid membrane when attached to a membrane protein
    Remote sensing of sun-induced fluorescence to improve modeling of diurnal courses of gross primary production (GPP)
    Damm, A. ; Elbers, J.A. ; Erler, A. ; Giolis, B. ; Hamdi, K. ; Hutjes, R.W.A. ; Kosvancova, M. ; Meroni, M. ; Migliettas, F. ; Moersch, A. ; Moreno, J. ; Schickling, A. ; Sonnenschein, R. ; Udelhoven, T. ; Linden, S. van der; Hostert, P. ; Rascher, U. - \ 2010
    Global Change Biology 16 (2010)1. - ISSN 1354-1013 - p. 171 - 186.
    koolstofcyclus - primaire productie - remote sensing - fluorescentie - spectroscopie - planten - fotosynthese - modelleren - carbon cycle - primary production - remote sensing - fluorescence - spectroscopy - plants - photosynthesis - modeling - light-use efficiency - induced chlorophyll fluorescence - photochemical reflectance index - net primary production - eddy covariance - photosynthetic efficiency - leaf senescence - photosystem-ii - carbon-dioxide - boreal forest
    Terrestrial gross primary production (GPP) is an important parameter to explore and quantify carbon fixation by plant ecosystems at various scales. Remote sensing (RS) offers a unique possibility to investigate GPP in a spatially explicit fashion; however, budgeting of terrestrial carbon cycles based on this approach still remains uncertain. To improve calculations, spatio-temporal variability of GPP must be investigated in more detail on local and regional scales. The overarching goal of this study is to enhance our knowledge on how environmentally induced changes of photosynthetic light-use efficiency (LUE) are linked with optical RS parameters. Diurnal courses of sun-induced fluorescence yield (FSyield) and the photochemical reflectance index of corn were derived from high-resolution spectrometric measurements and their potential as proxies for LUE was investigated. GPP was modeled using Monteith's LUE-concept and optical-based GPP and LUE values were compared with synoptically acquired eddy covariance data. It is shown that the diurnal response of complex physiological regulation of photosynthesis can be tracked reliably with the sun-induced fluorescence. Considering structural and physiological effects, this research shows for the first time that including sun-induced fluorescence into modeling approaches improves their results in predicting diurnal courses of GPP. Our results support the hypothesis that air- or spaceborne quantification of sun-induced fluorescence yield may become a powerful tool to better understand spatio-temporal variations of fluorescence yield, photosynthetic efficiency and plant stress on a global scale
    Global analysis of multiple gas chromatography-mass spectrometry (GC/MS) data sets: A method for resolution of co-eluting components with comparison to MCR-ALS
    Stokkum, I.H.M. van; Mullen, K.M. ; Mihaleva, V.V. - \ 2009
    Chemometrics and Intelligent Laboratory Systems 95 (2009)2. - ISSN 0169-7439 - p. 150 - 163.
    multivariate curve resolution - nonlinear least-squares - compound identification - liquid-chromatography - feasible solutions - spectral library - band boundaries - maximum - samples - spectroscopy
    Global analysis has been applied to resolve components in multiple gas chromatography-mass spectrometry (GC/MS) data sets. Global analysis methodology is based upon a parametrized model of the observed data, including random (and possibly also systematic) errors. Each elution profile is described as a function of a small number of parameters. We successfully based the description of elution profiles on an exponentially modified Gaussian. The mass spectra were described non-parametrically. Model usefulness is judged by the quality of the fit and whether the estimated parameters that describe the elution profiles and mass spectra of components are physically interpretable. Advantages of the method are most evident with multiple data sets and overlapping elution profiles. Differences between data sets are described by alignment parameters and by relative amplitude parameters. The estimated mass spectrum is identical between experiments. Global analysis and multivariate curve resolution alternating least squares (MCR-ALS) are the only methods currently developed for component resolution for the case of completely co-eluting compounds in mass spectrometry data. In the present contribution global analysis is shown to have better performance than MCR-ALS in terms of the estimated mass spectra for a variety of simulated GC mass spectrometry datasets representing components that are completely co-eluting.
    Asymmetric dipping of bacteriophage M13 coat protein with increasing lipid bilayer thickness
    Stopar, D. ; Koehorst, R.B.M. ; Spruijt, R.B. ; Hemminga, M.A. - \ 2009
    Biochimica et Biophysica Acta. Biomembranes 1788 (2009)10. - ISSN 0005-2736 - p. 2217 - 2221.
    membrane-proteins - tryptophan residues - amino-acids - peptides - topology - helix - spectroscopy - orientation
    Knowledge about the vertical movement of a protein with respect to the lipid bilayer plane is important to understand protein functionality in the biological membrane. In this work, the vertical displacement of bacteriophage M13 major coat protein in a lipid bilayer is used as a model system to study the molecular details of its anchoring mechanism in a homologue series of lipids with the same polar head group but different hydrophobic chain length. The major coat proteins were reconstituted into 14:1PC, 16:1PC, 18:1PC, 20:1PC, and 22:1PC bilayers, and the fluorescence spectra were measured of the intrinsic tryptophan at position 26 and BADAN attached to an introduced cysteine at position 46, located at the opposite ends of the transmembrane helix. The fluorescence maximum of tryptophan shifted for 700 cm-1 on going from 14:1PC to 22:1PC, the corresponding shift of the fluorescence maximum of BADAN at position 46 was approximately 10 times less ( 70 cm-1). Quenching of fluorescence with the spin label CAT 1 indicates that the tryptophan is becoming progressively inaccessible for the quencher with increasing bilayer thickness, whereas quenching of BADAN attached to the T46C mutant remained approximately unchanged. This supports the idea that the BADAN probe at position 46 remains at the same depth in the bilayer irrespective of its thickness and clearly indicates an asymmetrical nature of the protein dipping in the lipid bilayer. The anchoring strength at the C-terminal domain of the protein (provided by two phenylalanine residues together with four lysine residues) was estimated to be roughly 5 times larger than the anchoring strength of the N-terminal domain
    Identification of Uranyl Surface Complexes an Ferrihydrite: Advanced EXAFS Data Analysis and CD-MUSIC Modeling
    Rossberg, A. ; Ulrich, K.U. ; Weiss, S. ; Tsushima, S. ; Hiemstra, T. ; Scheinost, A.C. - \ 2009
    Environmental Science and Technology 43 (2009)5. - ISSN 0013-936X - p. 1400 - 1406.
    transformation factor-analysis - uranium(vi) sorption - adsorption - acid - hematite - spectroscopy - goethite - u(vi)
    Previous spectroscopic research suggested that uranium(VI) adsorption to iron oxides is dominated by ternary uranyl-carbonato surface complexes across an unexpectedly wide pH range. Formation of such complexes would have a significant impact on the sorption behavior and mobility of uranium in aqueous environments. We therefore reinvestigated the identity and structural coordination of uranyl sorption complexes using a combination of U LIII-edge extended X-ray absorption fine structure (EXAFS) spectroscopy and iterative transformation factor analysis, which enhances the resolution in comparison to conventional EXAFS analysis. A range of conditions (pH, CO2 partial pressure, ionic strength) made it possible to quantify the variations in surface speciation. In the resulting set of spectral data (N = 11) the variance is explained by only two components, which represent two structurally different types of surface complexes: (1) a binary uranyl surface complex with a bidentate coordination to edges of Fe(O,OH)6 octahedra and (2) a uranyl triscarbonato surface complex where one carbonate ion bridges uranyl to the surface. This ternary type B complex differs from a type A complex where uranyl is directly attached to surface atoms and carbonate is bridged by uranyl to the surface. Both surface complexes agree qualitatively and quantitatively with predictions by a charge distribution (CD) model. According to this model the edge-sharing uranyl complex has equatorial ligands (-OH2, -OH, or one -CO3 group) that point away from the surface. The monodentate uranyl triscarbonato surface complex (type B) is relevant only at high pH and elevated pCO2. At these conditions, however, it is responsible for significant uranyl sorption, whereas standard models would predict only weak sorption. This paper presents the first spectroscopic evidence of this ternary surface complex, which has significant implications for immobilization of uranyl in carbonate-rich aqueous environments
    Modeling membrane protein structure through site-directed ESR spectroscopy
    Kavalenka, A.A. - \ 2009
    Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): Marcus Hemminga; J. Strancar. - [S.l. : S.n. - ISBN 9789085854241 - 119
    oppervlakte-eiwitten - moleculaire structuur - spectroscopie - paramagnetische elektronenresonantiespectroscopie - surface proteins - molecular conformation - spectroscopy - electron paramagnetic resonance spectroscopy
    Site-directed spin labeling (SDSL) electron spin resonance (ESR) spectroscopy is a
    relatively new biophysical tool for obtaining structural information about proteins. This
    thesis presents a novel approach, based on powerful spectral analysis techniques (multicomponent
    spectral simulations and evolutionary optimizations of ESR spectra) and
    modeling of the protein structure by calculating the restrictions of the conformational space
    of the attached spin label.
    First, the feasibility of the ESR spectral analysis was enhanced by speeding-up the
    spectrum optimization and by automation of the analysis routines to enable the handling of
    large sets of spectroscopic data (e.g., for the joint analysis of SDSL-ESR spectra from
    multiple sites of a spin-labeled protein). According to the testing examples a speed-up
    factor of 5-7 was achieved.
    Secondly, SDSL-ESR was used to study the topology of the long N-terminal domain
    of the photosynthetic light-harvesting complex CP29. Wild-type protein containing a single
    cysteine at position 108 and nine single cysteine mutants were produced, allowing to label
    different parts of the domain with a nitroxide spin label. In all cases the apoproteins were
    either solubilized in detergent, or they were reconstituted with their native pigments in
    vitro. The spin label ESR spectra were analyzed in terms of a multi-component spectral
    simulation approach. These results permit to trace the structural organization of the long Nterminal
    domain of CP29 leading to a structural model for its N-terminal domain.
    Thirdly, we proposed a novel way to translate the local structural constraints gained
    by SDSL-ESR data into a low-resolution structure of a protein by simulating the
    restrictions of the local conformational spaces of the spin label attached at different protein
    sites along the primary structure of the membrane-embedded protein. The proposed
    structural model takes into account the restricting effect of the protein backbone, amino
    acid side chains and lipid environment. We tested the sensitivity of this approach for
    artificial oligopeptides and then for membrane-embedded M13 major coat protein
    decorated with a limited number of strategically placed spin labels by employing highthroughput
    site-directed mutagenesis. We found a reasonably good agreement of the
    simulated and the experimental data taking a protein conformation close to an α-helix.
    Finally, by using an optimization algorithm we optimized the parameters of the
    protein-lipid model by improving the fit of the simulation data to the experimental
    conformational space data. The outcome of the optimization was a family of best-fit
    structures of membrane-embedded M13 protein, which not only agree with the available
    SDSL-ESR data, but also was consistent with a recent model based on site-directed
    fluorescence labeling.
    Therefore, the present method provides a challenging starting point for the
    development of a powerful methodology for the protein structure characterization, an
    alternative approach to conventional techniques.
    The influence of vegetation cover on the spectroscopic estimation of soil properties
    Bartholomeus, H. - \ 2009
    Wageningen University. Promotor(en): Michael Schaepman, co-promotor(en): Lammert Kooistra. - [S.l. : S.n. - ISBN 9789085854487 - 144
    bodemeigenschappen - vegetatie - spectroscopie - schatting - koolstof - landbouwgronden - ijzer - bodemchemie - geostatistiek - soil properties - vegetation - spectroscopy - estimation - carbon - agricultural soils - iron - soil chemistry - geostatistics
    Voor het bepalen van de kwaliteit van de bodem als hulpbron is er behoefte aan een regelmatige bepaling van de chemische en fysische eigenschappen, zowel in ruimte als tijd. Kwantitatieve schatting van de exacte hoeveelheid, ruimtelijke verdeling en temporele verandering van bodemeigenschappen is nog steeds een uitdaging. Het onderwerp van dit proefschrift is hoe spectrale reflectie informatie gelinkt kan worden aan bodemeigenschappen
    The contributions of Dr. Alexander F.H. Goetz to imaging spectrometry
    MacDonald, J.S. ; Ustin, S.L. ; Schaepman, M.E. - \ 2009
    Remote Sensing of Environment 113 (2009)Suppl.1. - ISSN 0034-4257 - p. S2 - S4.
    aviris - spectroscopy - earth
    Hyperspectral remote sensing is the definitive optical tool for increasing knowledge and understanding of the Earth's surface. Contiguous high-resolution spectrometry provides a new dimension in mapping capability because of the potential for quantitative measurement of surface biogeochemistry. Alexander Goetz provided the vision and leadership that has produced nearly all critical developments in this field. He was among the first to recognize that spectrometry would change optical remote sensing from qualitative observations to quantitative physical measurements. His significant accomplishments over the last 25 years include development of critical image processing and atmospheric correction software, spectrometers that made it possible to move research out of the lab and into the field environment, and the development of NASA's airborne imaging spectrometer program. This special issue is dedicated to Dr. Goetz and his accomplishments
    Structural properties of a peptide derived from H+-V-ATPase subunit a
    Vermeer, L.S. ; Reat, V. ; Hemminga, M.A. ; Milon, A. - \ 2009
    Biochimica et Biophysica Acta. Biomembranes 1788 (2009)5. - ISSN 0005-2736 - p. 1204 - 1212.
    proton translocation channel - mediated cross-linking - vacuolar (h+)-atpases - transmembrane segments - magnetic-resonance - nmr-spectra - topology - domain - spectroscopy - surfaces
    The 3D structure of a peptide derived from the putative transmembrane segment 7 (TM7) of subunit a from H+-V-ATPase from Saccharomyces cerevisiae has been determined by solution state NMR in SDS. A stable helix is formed from L736 up to and including Q745, the lumenal half of the putative TM7. The helical region extends well beyond A738, as was previously suggested based on NMR studies of a similar peptide in DMSO. The pKa of both histidine residues that are important for proton transport was measured in water and in SDS. The differences that are found demonstrate that the histidine residues interact with the SDS polar heads. In detergent, circular dichroism data indicate that the secondary structure of the peptide depends on the pH and the type of detergent used. Using solid-state NMR, it is shown that the peptide is immobile in phospholipid bilayers, which means that it is probably not a single transmembrane helix in these samples. The environment is important for the structure of TM7, so in subunit a it is probably held in place by the other transmembrane helices of this subunit
    Membrane protein frustration: protein incorporation into hydrophobic mismatched binary lipid mixtures
    Stopar, D. ; Spruijt, R.B. ; Hemminga, M.A. - \ 2009
    Biophysical Journal 96 (2009)4. - ISSN 0006-3495 - p. 1408 - 1414.
    major coat protein - bacteriophage m13 - phase-transitions - acyl-chain - bilayers - fluid - phosphatidylcholines - spectroscopy - domain - solubilization
    Bacteriophage M13 major coat protein was reconstituted in different nonmatching binary lipid mixtures composed of 14:1PC and 22:1PC lipid bilayers. Challenged by this lose-lose situation of hydrophobic mismatch, the protein-lipid interactions are monitored by CD and site-directed spin-label electron spin resonance spectroscopy of spin-labeled site-specific single cysteine mutants located in the C-terminal protein domain embedded in the hydrophobic core of the membrane (I39C) and at the lipid-water interface (T46C). The CD spectra indicate an overall ¿-helical conformation irrespective of the composition of the binary lipid mixture. Spin-labeled protein mutant I39C senses the phase transition in 22:1PC, in contrast to spin-labeled protein mutant T46C, which is not affected by the transition. The results of both CD and electron spin resonance spectroscopy clearly indicate that the protein preferentially partitions into the shorter 14:1PC both above and below the gel-to-liquid crystalline phase transition temperature of 22:1PC. This preference is related to the protein tilt angle and energy penalty the protein has to pay in the thicker 22:1PC. Given the fact that in Escherichia coli, which is the host for M13 bacteriophage, it is easier to find shorter 14 carbon acyl chains than longer 22 carbon acyl chains, the choice the M13 coat protein makes seems to be evolutionary justified
    Adsorption of Anionic Surfactants in a Nonionic Polymer Brush: Experiments, Comparison with Mean-Field Theory, and Implications for Brush-Particle Interaction
    Vos, W.M. de; Biesheuvel, P.M. ; Keizer, A. de; Kleijn, J.M. ; Cohen Stuart, M.A. - \ 2009
    Langmuir 25 (2009)16. - ISSN 0743-7463 - p. 9252 - 9261.
    size-exclusion chromatography - sodium dodecyl-sulfate - aqueous-solutions - grafted polymers - hard-spheres - reflectometry - spectroscopy - monolayers - scattering - surfaces
    The adsorption of the anionic surfactants sodium dodecyl sulfate (SDS) and sodium dodecyl benzene sulfonate (SDBS) in poly(ethylene oxide) (PEO) brushes was studied using a fixed-angle optical flow-cell reflectometer. We show that, just as in solution, there is a critical association concentration (CAC) for the surfactants at which adsorption in the PEO brush starts. Above the critical micelle concentration (CMC) the adsorption is found to be completely reversible. At low brush density the adsorption per PEO monomer is equal to the adsorption of these surfactants in bulk solution. However, with increasing brush density, the number of adsorbed surfactant molecules per PEO monomer decreases rapidly. This decrease is explained in terms of excluded volume interactions plus electrostatic repulsion between the negatively charged surfactant micelles. Experimentally, a plateau value in the total adsorption is observed as a function of grafting density. The experimental results were compared to the results of an analytical self-consistent field (aSCF) model, and we found quantitative agreement. Additionally, the model predicts that the plateau value found is in fact a maximum. Both experiments and model calculations show that the adsorption scales directly with the polymerization degree of the polymers in the brush. They also show that an increase in the ionic strength leads to an increase in the adsorbed amount, which is explained as being due to a decrease in the electrostatic penalty for the adsorption of the SDS micelles. The adsorption of SDS micelles changes the interactions of the PEO brush with a silica particle. This is illustrated by atomic force microscopy (AFM) measurements of the pull-off force of a silica particle from a PEO brush: at high enough PEO densities, the addition of SDS leads to a very strong reduction in the force necessary to detach the colloidal silica particle from the PEO brush. We attribute this effect to the large amount of negative charge incorporated in the PEO brush due to SDS adsorption
    Primary photosynthetic processes: from supercomplex to leaf
    Broess, K. - \ 2009
    Wageningen University. Promotor(en): Herbert van Amerongen. - [S.l.] : S.n. - ISBN 9789085852988 - 124
    fotosynthese - fluorescentie - fluorescentiemicroscopie - spectroscopie - membranen - chloroplasten - fotosysteem ii - planten - photosynthesis - fluorescence - fluorescence microscopy - spectroscopy - membranes - chloroplasts - photosystem ii - plants
    This thesis describes fluorescence spectroscopy experiments on photosynthetic complexes that cover the primary photosynthetic processes, from the absorption of light by photosynthetic pigments to a charge separation (CS) in the reaction center (RC). Fluorescence spectroscopy is a useful tool in photosynthetic particles, because the latter are densely packed with fluorescence pigments like chlorophylls (Chl). The fluorescence of each pigment is affected by its environment and provide information about structure and dynamics of the photosynthetic complexes. In this thesis time-resolved fluorescence of Chl molecules is used for studying the ultrafast kinetics in membrane particles of photosystem II (PSII) (chapter 2, 3 and 4). In chapter 5 fluorescence lifetime imaging microscopy (FLIM) of is applied to study entire chloroplasts, either in the leaf or in isolated chloroplast form. The advantage of FLIM is that the interactions of the fluorescence pigments in both photosystems can be spatially resolved up to a resolution of 0.5 x 0.5 x 2 µm to indentify and quantify photosynthetic processes in their natural environment.

    Excitation energy transfer and charge separation in PSII membranes (chapter 2,3 and 4)

    In this thesis time-resolved fluorescence measurements of PSII containing membranes, the so called BBY particles, are performed in low-light conditions with open reaction centers. The BBY particles do not contain photosystem I (PSI) or stroma lamellae, but do support electron transfer and carry out oxygen evolution with high activity and are comparable with the grana in vivo. The fluorescence decay kinetics of the BBY particles are faster than observed in previous studies and also faster than observed for PSII in chloroplasts and thylakoid preparations. The average lifetime is 150 ps, which, together with previous annihilation experiments on light-harvesting complex II (LHCII) suggests that excitation migration from the antenna complexes contributes significantly to the overall charge separation time. This is in disagreement with the commonly applied exciton / radical-pair-equilibrium (ERPE) model that assumes that excitation energy diffusion through the antenna to the RC is much faster than the overall charge-separation time.
    A simple coarse-grained method is proposed, based on the supramolecular organization of PSII and LHCII in grana membranes (C2S2M2). The proposed modelling procedure for BBY particles is only approximate and many different combinations of excitation migration time and the charge separation time can explain the observed fluorescence kinetics. However it is clear that charge transfer should be rather fast and is accompanied with a large drop in free energy.
    In chapter 3, the fluorescence kinetics of BBY particles with open RCs are compared after preferential excitation at 420 and 484 nm, which causes a difference in the initial excited-state populations of the inner and outer antenna system. The fluorescence decay is somewhat slower upon preferential excitation of chlorophyll (Chl) b, which is exclusively present in the outer antenna. Using the coarse-grained model it was possible to fit the 420 and 484 nm results simultaneously with a two-step electron transfer model and four parameters: the hopping rate between the protein-pigment complexes, the CS rate, the drop in free energy upon primary charge separation and a secondary charge separation rate. The conclusion is that the average migration time contributes ~25% to the overall trapping time. The hopping time obtained in chapter 3 is significantly faster than might be expected based on studies on trimeric and aggregated LHCII and it is concluded that excitation energy transfer in PSII follows specific pathways that require an optimized organization of the antenna complexes with respect to each other. Analysis of the composition of the BBY particles indicates that the size of the light-harvesting system in PSII is smaller than commonly found for PSII in chloroplasts and explains why the fluorescence lifetimes are smaller for the BBY’s.
    In chapter 4, four different PSII supercomplex preparations were studied. The main difference between these supercomplexes concerns the size of the outer antenna. The average lifetime of the supercomplexes becomes longer upon increasing the antenna size. The results indicate that the rate constants obtained from the coarse-grained method for BBY preparations, which is based on the supercomplex composition C2S2M2, should be slightly faster (~10%) as predicted in chapter 3. The observation that the average lifetime of the supercomplexes is relatively slow compared to what one might expect based on the measurements on BBY particles, and this will require further future studies.

    Photosynthesis in plant leaves (Chapter 5)

    With the use of femtosecond two-photon excitation TPE at 860 nm it appears to be possible to measure fluorescence lifetimes throughout the entire leaves of Arabidopsis thaliana and Alocasia wentii. It turns out that the excitation intensity can be kept sufficiently low to avoid artifacts due to singlet-singlet and singlet-triplet annihilation, while the reaction centers can be kept in the open state during the measurements. The average fluorescence lifetimes obtained for individual chloroplasts of Arabidopsis thaliana and Alocasia wentii in the open and closed state, are approximately ~250 ps and ~1.5 ns, respectively. The maximum fluorescence state correspond to a state in which all reaction centers are closed. The kinetics are very similar to those obtained for chloroplasts in vitro with the FLIM setup and to in vivo results reported in literature. No variations between chloroplasts are observed when scanning throughout the leaves of Arabidopsis thaliana and Alocasia wentii. Within individual chloroplasts some variation is detected for the relative contributions of PSI and PSII to the fluorescence. The results open up the possibility to use FLIM for the in vivo study of the primary processes of photosynthesis at the level of single chloroplasts under all kinds of (stress) conditions.

    General conclusions

    This thesis gives new insight of the kinetic processes in PSII membranes. With the use of a coarse-grained method that provides an easy way to incorporate existing knowledge and models for individual complexes, valuable conclusions can be drawn about the excitation energy transfer and the CS which hopefully contributes to an improvement of the knowledge about PSII functioning. In general it was shown that a large drop in free energy is needed in PSII membranes for all simulations with the coarse-grained method.
    The presented results on the kinetics of chloroplasts obtained in vitro and in vitro are very similar and verify that conclusions drawn from isolated chloroplasts can be extrapolated to photosynthetic processes in their natural environment.

    Increased susceptibility of ß-glucosidase from the hyperthermophile Pyrococcus furiosus to thermal inactivation at higher pressures
    Bruins, M.E. ; Meersman, F. ; Janssen, A.E.M. ; Heremans, K. ; Boom, R.M. - \ 2009
    FEBS Journal 276 (2009). - ISSN 1742-464X - p. 109 - 117.
    enzyme inactivation - escherichia-coli - proteins - stabilization - temperature - myoglobin - thermostability - denaturation - spectroscopy - aggregation
    The stability of ß-glucosidase from the hyperthermophile Pyrococcus furiosus was studied as a function of pressure, temperature and pH. The conformational stability was monitored using FTIR spectroscopy, and the functional enzyme stability was monitored by inactivation studies. The enzyme proved to be highly piezostable and thermostable, with an unfolding pressure of 800 MPa at 85 °C. The tentative pressure¿temperature stability diagram indicates that this enzyme is stabilized against thermal unfolding at low pressures. The activity measurements showed a two-step inactivation mechanism due to pressure that was most pronounced at lower temperatures. The first part of this inactivation took place at pressures below 300 MPa and was not visible as a conformational transition. The second transition in activity was concomitant with the conformational transition. An increase in pH from 5.5 to 6.5 was found to have a stabilizing effect
    8000 yr of black carbon accumulation in a colluvial soil from NW Spain
    Kaal, J. ; Martinez-Cortizas, A. ; Buurman, P. ; Criado Boado, F. - \ 2008
    Quaternary Research 69 (2008)1. - ISSN 0033-5894 - p. 56 - 61.
    solid-state c-13 - organic-matter - chemical-composition - humic acids - fractions - pyrolysis - spectroscopy - spectrometry - cambisol - fire
    Analytical pyrolysis-GC/MS and solid-state 13C NMR (nuclear magnetic resonance) were applied to the NaOH-extractable organic matter fraction of a colluvial soil from Galicia (NW Spain) that represents more than 8500 yr of accumulation. While molecular indicators of vegetation change were looked for, it seemed likely that any such signal was disturbed by the intense fire regime of the area. This conclusion was drawn from (1) the presence of three charcoal layers, (2) the high proportion of aryl C in NMR spectra (non-quantitative) and (3) the prevalence of benzenes and polycyclic aromatic hydrocarbons (PAHs) in the chromatograms (38 ± 6% of total identified peak area), also in charcoal-poor samples. If this conclusion is accurate, the area has been subjected to burning episodes for at least 8000 yr. Additionally, the results indicate that biomass burning residues (black carbon; BC) may become NaOH extractable after long periods of degradation in mineral soil. These results add to our knowledge of the long-term fate of BC in soil, which is a potential agent in the global C cycle.
    Mechanism of endocarp-imposed constraints of germination of Lannea microcarpa seeds
    Neya, O. ; Hoekstra, F.A. ; Golovina, E.A. - \ 2008
    Seed Science Research 18 (2008)01. - ISSN 0960-2585 - p. 13 - 24.
    rhus species anacardiaceae - physical dormancy - ftir microspectroscopy - desiccation tolerance - ethylene - spectroscopy - metabolism - embryos - sativa
    Lannea microcarpa, a multipurpose tree species from the dry African savanna, sheds seeds that often display inhibition of germination. The underlying mechanism was investigated using seeds processed from fully matured fruits collected from natural stands in Burkina Faso. Germination of fresh seeds was variable (16¿28%), while they did not germinate after drying and rehydration. Mechanical scarification of the endocarp at the proximal end of the seeds increased germination to 83¿94%. Scarification on the distal end led to delayed radicle emergence through the produced hole in c. 40% of the seeds. The endocarp was permeable to water and respiratory gases. Increased water content in scarified seeds was associated with radicle extension during germination. Intact and scarified non-germinated seeds displayed a moderate rate of respiration with respiratory quotient (RQ) values of c. 1. Respiration increased and RQ decreased to c. 0.7 with radicle emergence. Ethylene evolution peaked in both intact and scarified seeds at the beginning of incubation and then decreased to low values. Inhibition of ethylene production by 1¿5 mM 2-amino-ethoxyvinylglycine (AVG) caused only a partial decrease of germination of the scarified seeds. Intact non-germinated seeds gradually lost viability during incubation at 30°C, but could be rescued by delayed scarification before day 15 of incubation. It is concluded that radicle emergence in dry L. microcarpa seeds is inhibited only mechanically. The mechanical properties of the endocarp are attributed to irreversible structural changes of the lignin¿hemicellulose complex, which occur during drying.
    Adsorption of the protein bovine serum albumin in a planar poly(acrylic acid) brush layer as measured by optical reflectometry
    Vos, W.M. de; Biesheuvel, P.M. ; Keizer, A. de; Kleijn, J.M. ; Cohen Stuart, M.A. - \ 2008
    Langmuir 24 (2008)13. - ISSN 0743-7463 - p. 6575 - 6584.
    spherical polyelectrolyte brushes - electrostatic interactions - charge regulation - aqueous-solution - complexes - spectroscopy - chloride) - particles
    The adsorption of bovine serum albumin (BSA) in a planar poly(acrylic acid) (PAA) brush layer has been studied by fixed-angle optical reflectometry. The influence of polymer length, grafting density, and salt concentration is studied as a function of pH. The results are compared with predictions of an analytical polyelectrolyte brush model, which incorporates charge regulation and excluded volume interactions. A maximum in adsorption is found near the point of zero charge (pzc) of the protein. At the maximum, BSA accumulates in a PAA brush to at least 30 vol %. Substantial adsorption continues above the pzc, that is, in the pH range where a net negatively charged protein adsorbs into a negatively charged brush layer, up to a critical pH value. This critical pH value decreases with increasing ionic strength. The adsorbed amount increases strongly with both increasing PAA chain length and increasing grafting density. Experimental data compare well with the analytical model without having to include a nonhomogeneous charge distribution on the protein surface. Instead, charge regulation, which implies that the protein adjusts its charge due to the negative electrostatic potential in the brush, plays an important role in the interpretation of the adsorbed amounts. Together with nonelectrostatic interactions, it explains the significant protein adsorption above the pzc.
    Retrieval of chlorophyll concentration from leaf reflectance spectra using wavelet analysis
    Blackburn, G.A. ; Ferwerda, J.G. - \ 2008
    Remote Sensing of Environment 112 (2008)4. - ISSN 0034-4257 - p. 1614 - 1632.
    hyperspectral data - vegetation - calibration - prospect - pigment - spectroscopy - indexes - models - red
    The dynamics of foliar chlorophyll concentrations have considerable significance for plant¿environment interactions, ecosystem functioning and crop growth. Hyperspectral remote sensing has a valuable role in the monitoring of such dynamics. This study focussed upon improving the accuracy of chlorophyll quantification by applying wavelet analysis to reflectance spectra. Leaf-scale radiative transfer models were used to generate very large spectral data sets with which to develop and rigorously test refinements to the approach and compare it with existing spectral indices. The results demonstrated that by decomposing leaf spectra, the resultant wavelet coefficients can be used to generate accurate predictions of chlorophyll concentration, despite wide variations in the range of other biochemical and biophysical factors that influence leaf reflectance. Wavelet analysis outperformed predictive models based on untransformed spectra and a range of spectral indices. The paper discusses the possibilities for further refining the wavelet approach and for extending the technique to the sensing of a variety of vegetation properties at a range of spatial scales.
    Water content of acacia honey dertermined by two established methods and by optothermal window
    Szopos, S. ; Doka, O. ; Bicanic, D.D. ; Ajtony, Z. - \ 2008
    Acta Chimica Slovenica 55 (2008)2. - ISSN 1318-0207 - p. 273 - 276.
    The major objective of the research study described here was to explore the potential of the optothermal window (OW) technique as a new approach towards a simple, rapid determination of water content in honey. Water, major component of foods, influences their physical and chemical properties. Single mode RLT-1480-40G laser diode and the standard addition method were used to calibrate the response of the OW detector at analytical wavelength of 1478 nm and to determine water content of Acacia honey. The performance of the OW method was compared to that of well established gravimetry and refractometry; the values obtained by the three different methods are practically the same
    Practical, reliable and inexpensive assay of lycopene in tomato products based on the combined use of light emitting diode (LED) and the optothermal window
    Bicanic, D.D. ; Cuypers, R. ; Luterotti, S. ; Sporec, M. ; Zoppi, A. ; Vugec, J. - \ 2008
    Acta Chimica Slovenica 55 (2008)2. - ISSN 1318-0207 - p. 468 - 473.
    performance liquid-chromatography - quantification - spectroscopy
    Light emitting diode (LED) combined with the concept of optothermal window (OW) is proposed as a new approach (LED-OW) to detect lycopene in a wide range of tomato-based products (tomato juice, tomato ketchup, tomato passata and tomato puree). Phytonutrient lycopene is a dominant antioxidant in these products while beta-carotene is present in significantly lower quantities. Therefore for all practical reasons the interfering effect of beta-carotene at 502 nm analytical wavelength can be neglected. The LED-OW method is low-cost and simple, yet accurate and precise. The major attributes of the new method are its rapid speed of response and the fact that no preparation whatsoever of the sample is needed before the analysis. The lycopene found in tomato products studied here varies from 8 mg/100 g to 60 mg/100 g fresh product. Results obtained by LED-OW method were compared to the outcome of conventional, time consuming spectrophotometric methods and the correlation was very good (R = 0.98). Precision of the LED-OW instrumental setup ranged from 0.5 to 7.4%; the RSD achieved for lycopene-richest samples (= 40 mg/100 g) did not exceed 1.7%. Repeatability of analysis by LED-OW was found to vary between 0.7 and 7.1%.
    Assessment of near infrared and "software sensor" for biomass monitoring and control
    Soons, Z.I.T.A. ; Streefland, M. ; Straten, G. van; Boxtel, A.J.B. van - \ 2008
    Chemometrics and Intelligent Laboratory Systems 94 (2008)2. - ISSN 0169-7439 - p. 166 - 174.
    analytical technology pat - bordetella-pertussis - fermentation processes - growth-rate - calibration - design - online - chemometrics - spectroscopy - toxin
    Spectroscopic instrumentation is often seen as promising for process analytical technology (PAT) to enhance control of manufacturing (bio)pharmaceuticals. The interpretation of near infrared spectra is challenging due to the large number of wavelengths recorded and the overlapping absorbance features of near infrared spectroscopy. This work applies a controlled random search procedure to select an optimal window of wavelengths giving a good calibration model for biomass concentrations during cultivation of Bordetella pertussis, the causative agent of whooping cough. The proposed wavelengths selection procedure outperforms the traditional calibration procedures. In the second half of the paper, the near infrared based predictions are compared with the estimations obtained from a software sensor for biomass and specific growth rate based in standard measurements of oxygen consumption. Both methods estimate the exponential biomass growth properly. The near infrared predictions depend on the quality of the training dataset, which needs to encompass all possible sources of temporary disturbances like pH and dissolved oxygen. If the training dataset does not comprise such disturbances, then the accuracy and robustness of the near infrared predictions are less favorable than those of the software sensor. Although near infrared has the potential to provide more information than just biomass, the software sensor is the preferred choice for feedback control of biomass and specific growth rate
    Alkyl-Functionalized Oxide-Free Silicon Nanoparticles: Synthesis and Optical Properties
    Rosso-Vasic, M. ; Spruijt, E. ; Lagen, B. van; Cola, L. de; Zuilhof, H. - \ 2008
    Small 4 (2008)10. - ISSN 1613-6810 - p. 1835 - 1841.
    hydrogen-terminated silicon - porous silicon - surface functionalization - nanocrystals - hydrosilylation - monolayers - luminescence - spectroscopy - photoluminescence - nanoclusters
    Highly monodisperse silicon nanoparticles (1.57 ± 0.21 nm) are synthesized with a covalently attached alkyl monolayer on a gram scale. Infrared spectroscopy shows that these silicon nanoparticles contain only a few oxygen atoms per nanoparticle. XPS spectra clearly show the presence of unoxidized Si and attached alkyl chains. Owing to the relatively efficient synthesis (yields 100-fold higher than of those previously reported) the molar extinction coefficient can be measured: max = 1.7 × 10-4 M-1cm-1, only a factor of 4 lower than that of CdS and CdSe nanoparticles of that size. The quantum yield of emission ranges from 0.12 (C10H21-capping) to 0.23 (C16H33-capping). UV/Vis absorption and emission spectroscopy show clear vibrational progressions (974 ± 14 cm-1; up to five vibrational bands visible at room temperature), resembling bulk SiC phonons, which support the monodispersity observed by TEM. This was also confirmed by time-resolved fluorescence anisotropy measurements, which display a strictly monoexponential decay that can only be indicative of monodisperse, ball-shaped nanoparticles
    Physical interactions among plant MADS-box transcription factors and their biological relevance
    Nougalli Tonaco, I.A. - \ 2008
    Wageningen University. Promotor(en): Sacco de Vries; Gerco Angenent, co-promotor(en): Richard Immink. - [S.l.] : S.n. - ISBN 9789085048299 - 150
    planten - transcriptiefactoren - genexpressie - transcriptie - petunia hybrida - arabidopsis thaliana - fluorescentie - spectroscopie - dna-bindende eiwitten - bloemen - technieken - plantenontwikkeling - genregulatie - transcriptieregulatie - plants - transcription factors - gene expression - transcription - petunia hybrida - arabidopsis thaliana - fluorescence - spectroscopy - dna binding proteins - flowers - techniques - plant development - gene regulation - regulation of transcription
    The biological interpretation of the genome starts from transcription, and many different signaling pathways are integrated at this level. Transcription factors play a central role in the transcription process, because they select the down-stream genes and determine their spatial and temporal expression. In higher eudicot species around 2000 specific transcription factors are present, which can be classified into families based on conserved common domains. The MADS-box transcription factor family is an important family of transcription regulators in plants and genetic studies revealed that members of this family are involved in various developmental processes, like floral induction, floral organ formation and fruit development. In contrast to this wealth of information concerning MADS-box gene functions, the molecular mode of action of the encoded proteins is far from completely understood. Biochemical and yeast η-hybrid experiments performed in the past showed that MADS-box proteins are able to interact mutually, and based on these findings a hypothetical quaternary model has been proposed as molecular working mechanism. According to this model two MADS-box protein dimers assemble into a higher order complex, which binds DNA and regulates target gene expression. Although, this molecular mechanism sounds plausible, it still lacks evidence from in vivo studies. In this study we investigated physical interactions among members of the Petunia hybrida and Arabidopsis thaliana MADS-box transcription factor families in living plant cells. For this purpose, sophisticated micro-spectroscopy techniques have been implemented and in addition, some novel fluorescent-protein-based tools were developed. The first chapter gives an introduction about the dynamic transcriptional process and describes our current knowledge about transcriptional regulation in eukaryotes. The central question of this chapter is how transcription factors are able to find their specific binding sites (ci's-elements) within the huge genome. The various mechanisms, such as "looping" and "sliding", that have been proposed are discussed, as well as the relevance of direct interactions between transcription factors for the control of gene expression.
    In a first attempt to detect protein interactions in living cells, we transiently expressed combinations of petunia MADS-box transcription factors labeled with different color variants of the Green Fluorescent Protein (GFP) in leaf protoplasts (Chapter 2). Subsequently, the transfected protoplasts were analyzed by means of FRET-FLIM
    (Fluorescence Resonance Energy Transfer - Fluorescence Lifetime Imaging) to identify specific dimerization. In addition, we have obtained indirect evidence for higher-order complex formation of the petunia MADS-box proteins FLORAL BINDING PROTEIN2 (FBP2), FBP11, and FBP24 in living cells. Similar kind of analyses for Arabidopsis MADS-box proteins involved in petal and stamen development revealed clear differences in interaction affinities in vivo and furthermore, many homodimers were identified that could not be detected by yeast-based systems in the past (Chapter 3). This result demonstrated the robustness of the FRET-FLIM approach. Based on our observations, we hypothesize that 'partner selectivity' plays an important role in complex formation at particular developmental stages. To study differences in interaction affinity and selectivity and the consequences for complex formation in more detail, a novel method was developed (Chapter 4). The technique, designated "Competition-FRET", allows the verification of competition effects between proteins, and furthermore, it may provide information about the formation of higher-order complexes between different proteins under study. The developed method was implemented to investigate in depth the preference for homo- or heterodimer interactions of the Arabidopsis MADS-box proteins AGAMOUS (AG) and SEPALLATA3 (SEP3).
    The detection of interactions in living cells by FRET as it has been done in the studies described above demands a sophisticated microscopy set-up, and therefore, we decided to test and implement an alternative and theoretically simple technique (Chapter 5). This method for the in vivo detection of protein-protein interaction is called BiFC (Bimolecular Fluorescence Complementation), or "Split-YFP". In this system, a fluorescent molecule is split into two inactive domains and these two non-fluorescent parts are fused to the proteins under study. Only upon interaction of the two protein partners the two non-fluorescent parts of the fluorescent molecule are brought into close proximity, which enables the recovery of fluorescence. We used the EYFP (Enhanced Yellow Fluorescence Protein) molecule as fluorescent molecule and were able to detect the interaction between AG and SEP3 in nuclei of Arabidopsis leaf protoplasts. Techniques like this and FRET-FLIM allow the analyses of interactions between proteins in living cells, but give no information about the size of the formed complexes. To get a first indication about the stoichiometry of protein complexes, we monitored the diffusion time of in vitro synthesized AG-EYFP and SEP3-EYFP fusion proteins by means of FCS (Fluorescence Correlation

    Spectroscopy). From these experiments described in Chapter 6, we could speculate that SEP3 is present as a dimer and also as a higher order complex, whilst AG on its own is able to assemble into larger complexes. The diffusion time of the product formed upon co-translation of both AG and SEP3, suggests that a multimenc protein complex with a high molecular weight is formed upon interaction between AG and SEP3. Even though FCS is a powerful technique, these interpretations should be taken cautiously, mainly because these experiments were done in vitro instead of in living cells. Finally, in the last chapter we discuss the various methods that have been implemented and developed to monitor protein-protein interactions and complex formation of MADS-box transcription factors in living plant cells. Furthermore, we made a first step to monitor interactions in intact tissues under endogenous expression levels, and the preliminary results obtained from these in planta FRET-FLIM measurements are discussed.

    Imaging spectroscopy : applications in agriculture
    Zedde, H.J. van de; Brakel, R.P. van - \ 2007
    spectroscopie - kwaliteitscontroles - monitoring - sensorische evaluatie - voedselinspectie - tomaten - patates frites - beeldvormende spectroscopie - spectroscopy - quality controls - monitoring - sensory evaluation - food inspection - tomatoes - chips (French fries) - imaging spectroscopy
    Imaging Spectroscopy is the study of light as a function of spatial distribution and wavelength that has been transmitted, emitted, reflected or scattered from an object. This allows us to derive information about the spatial relation of the chemistry of the object. Imaging spectroscopy is suited for the following tasks: • Quality control: detection of latent defects in agri-products, e.g. vegetables and fruit. • Quantification of compounds: carotenes, proteins, sugars, moisture etc. In this poster the following two applications are discussed: 1) Measuring of compounds in tomatoes and 2) Detection and classification of latent defects in French Fries
    Negative compressibility and non-equivalence of two statistical ensembles in the escape transition of a polymer chain
    Skvortsov, A.M. ; Klushin, L.I. ; Leermakers, F.A.M. - \ 2007
    Journal of Chemical Physics 126 (2007). - ISSN 0021-9606 - p. 024095 - 024095.
    atomic-force microscopy - spectroscopy - elasticity - surface
    An end-tethered polymer chain compressed between two pistons undergoes an abrupt transition from a confined coil state to an inhomogeneous flowerlike conformation partially escaped from the gap. This phase transition is first order in the thermodynamic limit of infinitely long chains. A rigorous analytical theory is presented for a Gaussian chain in two ensembles: (a) the H-ensemble, in which the distance H between the pistons plays the role of the independent control parameter, and (b) the conjugate f-ensemble, in which the external compression force f is the independent parameter. Details about the metastable chain configurations are analyzed by introducing the Landau free energy as a function of the chain stretching order parameter. The binodal and spinodal lines, as well as the barrier heights between the stable and metastable states in the free energy landscape, are presented in both ensembles. In the loop region for the average force with dependence on the distance H (i.e., in the H-ensemble) a negative compressibility exists, whereas in the f-ensemble the average distance as a function of the force is strictly monotonic. The average fraction of imprisoned segments and the lateral force, taken as functions of the distance H or the average H, respectively, have different behaviors in the two ensembles. These results demonstrate a clear counterexample of a main principle of statistical mechanics, stating that all ensembles are equivalent in the thermodynamic limit. The authors show that the negative compressibility in the escape transition is a purely equilibrium result and analyze in detail the origin of the nonequivalence of the ensembles. It is argued that it should be possible to employ the escape transition and its anomalous behavior in macroscopically homogeneous, but microscopically inhomogeneous, materials.
    FRET study of membrane proteins: determination of the tilt and orientation of the N-terminal domain of M13 major coat protein
    Nazarov, P.V. ; Koehorst, R.B.M. ; Vos, W.L. ; Apanasovich, V.V. ; Hemminga, M.A. - \ 2007
    Biophysical Journal 92 (2007)4. - ISSN 0006-3495 - p. 1296 - 1305.
    bacteriophage m13 - transmembrane domain - energy-transfer - fluorescence - dynamics - conformation - spectroscopy - modulation - peptides - micelles
    A formalism for membrane protein structure determination was developed. This method is based on steady-state FRET data and information about the position of the fluorescence maxima on site-directed fluorescent labeled proteins in combination with global data analysis utilizing simulation-based fitting. The methodology was applied to determine the structural properties of the N-terminal domain of the major coat protein from bacteriophage M13 reconstituted into unilamellar DOPC/DOPG (4:1 mol/mol) vesicles. For our purpose, the cysteine mutants A7C, A9C, N12C, S13C, Q15C, A16C, S17C, and A18C in the N-terminal domain of this protein were produced and specifically labeled with the fluorescence probe AEDANS. The energy transfer data from the natural Trp-26 to AEDANS were analyzed assuming a two-helix protein model. Furthermore, the polarity Stokes shift of the AEDANS fluorescence maxima is taken into account. As a result the orientation and tilt of the N-terminal protein domain with respect to the bilayer interface were obtained, showing for the first time, to our knowledge, an overall -helical protein conformation from amino acid residues 12¿46, close to the protein conformation in the intact phage.
    Evaluating pyrolysis-GC/MS and 13C CPMAS NMR in conjunction with a molecular mixing model of the Penido Vello peat deposit, NW Spain
    Kaal, J. ; Baldock, J.A. ; Buurman, P. ; Nierop, K.G.J. ; Pontevedra-Pombal, X. ; Martínez-Cortizas, A. - \ 2007
    Organic Geochemistry 38 (2007)7. - ISSN 0146-6380 - p. 1097 - 1111.
    soil organic-matter - polycyclic aromatic-hydrocarbons - ionization cross-sections - mass-spectrometry - state - spectroscopy - acids - alkylbenzenes - preservation - fractions
    We performed solid state 13C cross-polarization magic angle spinning (CPMAS) nuclear magnetic resonance (NMR) spectroscopy and pyrolysis¿gas chromatography/mass spectrometry (Py¿GC/MS) on the Penido Vello peat deposit located in Galicia, NW Spain. Often regarded as complementary techniques, solid state 13C NMR and Py¿GC/MS are widely used for the characterisation of organic matter. Recently, a molecular mixing model (MMM) was proposed to predict the distribution of C in biochemical components (carbohydrate, protein, lignin, lipid, char) from the 13C NMR spectral distribution, thereby allowing a quantitative comparison with Py¿GC/MS product abundances. We discuss the application of this model to a peat core, by comparing NMR-MMM results with Py¿GC/MS data. The core represents 5000 yr accumulation and ranges from fibric (at the surface) to hemic (bottom). The amounts of carbohydrates and lipids predicted by the MMM and calculated from the quantified Py¿GC/MS chromatograms are in close agreement. However, the well known low capability of the conventional Py¿GC/MS method to provide structural information on proteins from bulk soils, the poor GC amenability of polar compounds and many other possible sources of inaccuracy in Py¿GC/MS and NMR-MMM caused discrepancies with predictions made with the MMM. Also, the MMM failed to give good prediction of the C/N ratio of the peat material. Although the NMR-MMM approach does not account for molecular transitions during decomposition, this oversimplification proved to be acceptable. The MMM seems to be a useful tool for the interpretation of NMR spectral distributions in peat material.
    Determination of the degree of substitution, degree of amidation and degree of blockiness of commercial pectins by using capillary electrophoresis
    Guillotin, S.E. ; Bakx, E.J. ; Boulenguer, P. ; Schols, H.A. ; Voragen, A.G.J. - \ 2007
    Food Hydrocolloids 21 (2007)3. - ISSN 0268-005X - p. 444 - 451.
    galacturonic acid distribution - de-esterified pectins - zone-electrophoresis - quantification - endopolygalacturonase - spectroscopy - separation - behavior
    It is more and more realised that pectins are complex mixtures of many different molecules and research is directed towards the fractionation and characterisation of these pectic sub-populations. Since fractionation of pectins generally results in only low amounts of purified material, rapid characterisation methods using low amounts of samples are required. In this study, capillary electrophoresis was chosen to characterise pectins because only tiny amounts of sample are needed for the analysis. A new capillary electrophoresis (CE) protocol was developed to determine the degree of amidation, the degree of methyl-esterification (DM) and consequently the degree of substitution (DS) of pectins by analysing the pectins before and after removal of the methyl-esters. The CE results were compared with results obtained for the same pectins by using titration and Fourier transform infra-red (FTIR) spectroscopy methods. The CE method was found to be rather reliable resulting in small standard deviations for the DS and DAm. The CE method had the advantage of being rapid due to the limited sample preparation and automation of the analysis. In addition, CE was used successfully to determine the degree of blockiness of the free GalA residues over the pectic backbone.
    Red edge shift and biochemical content in grass canopies
    Mutanga, O. ; Skidmore, A.K. - \ 2007
    ISPRS Journal of Photogrammetry and Remote Sensing 62 (2007)2. - ISSN 0924-2716 - p. 34 - 42.
    kruger-national-park - vegetation indexes - absorption features - chlorophyll content - leaf reflectance - south-africa - nitrogen - spectroscopy - regression - quality
    The concentration of foliar nitrogen in tropical grass is one of the factors that explain the distribution of wildlife. Therefore, the remote sensing of foliar nitrogen contributes to a better understanding of wildlife feeding patterns. This study evaluated changes in the red edge position of the 680 nm continuum removed chlorophyll feature in the reflectance spectra of samples of Cenchus ciliaris grass grown in a greenhouse under three levels of nitrogen supply. Canopy spectral measurements from each treatment were recorded under controlled laboratory conditions over a four-week period using a GER 3700 spectroradiometer. Results indicate that the mean wavelength positions of the three fertilization treatments were statistically different. An increase in nitrogen supply yielded a shift in the red edge position to longer wavelengths. The red edge position, amplitude, slope at 713 nm and slope at 725 nm were significantly correlated to measured nitrogen concentration (bootstrapped r=0.89, -0.28, 0.63 and 0.75, respectively) even at canopy level. Based on these results, the red edge position is strongly correlated with biochemical concentration in plants compared to the other methods tested. The study provides conclusive evidence that confirms the strength of a red edge-nitrogen relationship that remains underused in remote sensing. This method is promising for estimating nutrient content in grasslands. (C) 2007 International Society for Photogrammetry and Remote Sensing, Inc. (ISPRS). Published by Elsevier B.V. All rights reserved.
    Structure-rheology relations in sodium caseinate containing systems
    Ruis, H.G.M. - \ 2007
    Wageningen University. Promotor(en): Erik van der Linden, co-promotor(en): Paul Venema. - [S.l.] : S.n. - ISBN 9789085046486 - 125
    natriumcaseïnaat - reologische eigenschappen - afschuifkracht - gelering - emulsies - structuur - verzuring - spectroscopie - licht - verstrooiing - sodium caseinate - rheological properties - shear - gelation - emulsions - structure - acidification - spectroscopy - light - scattering
    The general aim of the work described in this thesis was to investigate structure-rheologyrelations for dairy related products, focusing on model systems containing sodium caseinate. The acid inducedgelationof sodium caseinate, of sodium caseinate stabilized emulsions, and the effect of shear on the structure formation was characterized. Special attention was given to the sol-gel transition point, which was defined by a frequency independent loss tangent. It was shown that the sol-gel transition point is completely controlled by the pH and the temperature, independent of the concentration sodium caseinate or the applied shear rate. Considering sodium caseinate solutions, increase of the temperature of acidification caused a decrease of the critical pH forgelationand a more dense gel structure. The formed gels were not in thermodynamicequilibrium,however, due to the slow kinetics of the system they were stable on the time scale of the experiment. At the gel point we have strong indications that the structure can not be characterized by a single fractal dimension. During the acid inducedgelationof sodium caseinate stabilized emulsions a single sol-gel transition was observed. Addition of an excess of sodium caseinate to the emulsion resulted in two sol-gel transitions upon acidification. Application of shear during the acidification of the emulsions showed a decreasing radius of the aggregates formed at thegelpointwith increasing shear rate. The aggregates formed becamemore densedue to the application of shear while the network that was formed by the aggregates became less compact. No shear induced alignment was observed of emulsion droplets dispersed in water or ina sodiumcaseinatesolution, while emulsion droplets dispersed in axanthansolution did align in a shear field. Addition of sodium inhibited the string formation of the emulsion droplets
    New developments in the detection and identification of processed animal proteins in feeds
    Raamsdonk, L.W.D. van; Holst, C. von; Baeten, V. ; Berben, G. ; Boix, A. ; Jong, J. de - \ 2007
    Animal Feed Science and Technology 133 (2007)1-2. - ISSN 0377-8401 - p. 63 - 83.
    bovine spongiform encephalopathy - bone meal - monoclonal-antibody - mitochondrial-dna - mass-spectrometry - pcr detection - ruminant - spectroscopy - validation - dipeptides
    It is generally accepted that the most likely route of infection of cattle with bovine spongiform encephalopathy (BSE) is by consumption of feeds containing low levels of processed animal proteins (PAPs). This likely route of infection resulted in feed bans, which were primarily aimed at ruminant feeds, and were later extended to all feeds for farmed animals. The feed bans were expected to develop into a future enforcement of the "species-to-species" ban, which prohibits only the feeding of animal-specific proteins to the same species. The species-to-species ban requires support of species-specific identification methods. In the European Union, microscopic evaluation is currently the only accepted method for the detection and characterization of PAPs in feeds, since it is possible to detect contaminations at the requested level of 1 g/kg with hardly any false negative nor positive results. This method is predominantly focused on the presence and characteristics of bone fragments, although other structures, e.g. muscle fibres, may provide circumstantial evidence of the respective animal types. Recent developments are the identification of bone fragments at the level of classes (mammal versus bird versus fish), supported by image analysis of bone characteristics. Detection of DNA and specific proteins are additional methods that can be applied for the identification of PAPs in feeds. DNA is known to be very specific for animal species and breeds, whereas proteins can also indicate the type of tissue. The latter aspect is important to differentiate between proteins that are authorised in animal nutrition from banned proteins. Improvements can be noted in recent years for both methods. For a proper application of polymerase chain reaction (PCR) to detect specific sequences of DNA, primer sets have been developed which amplify a DNA sequence shorter than approximately 100 nucleotides. Specific antibodies have been developed for protein detection of ruminant or bovine material. Recent results of various studies indicate that specific DNA and protein detection methods can detect PAPs at a contamination level of 1 g/kg. However, full validation of these methods still needs to be carried out. Other methods such as near-infrared spectroscopy (NIRS), near-infrared microscopy (NIRM), near-infrared imaging, liquid chromatography (LC) and olfactometry techniques can and will be applied for the detection of PAPs. NIRS is a non-destructive method that can be applied on-line in feed production plants. Generally, the detection limit is still too high to be applied in official control laboratories. Nevertheless, industrial application is feasible. NIRM and near-infrared imaging are techniques that allow collection of near-infrared spectra from individual particles. The level of detection is lower than 1 g/kg since it is based on the microscopic technique, in combination with the option of identification of the individual particles. LC is based on the detection and, if present, the ratio of different polypeptides. For example, carnosine is mainly present in mammals and anserine mainly found in birds. Olfactometry is based on detection of volatile non-specific agents. It is a non-destructive and fast technique. For both LC and olfactometry it appears that the presence of fish material masks the detection of proteins of land animals, even at a contamination level of 5 g/kg. Since 2003 five different proficiency studies and ring trials have been organized. The first proficiency study, allowing the participants to apply their own protocol, revealed that correct microscopic detection of 1 g/kg of mammalian PAP in the presence of 50 g fish meal/kg was realised in 0.44 of the cases. However, a bench mark study organized in the same year showed that a microscopic detection of 0.98 can be reached provided the application of an optimal protocol and a sufficient level of expertise. More recent studies showed that training, the application of a decision support system and use of an improved microscopy protocol resulted in a higher sensitivity. An attractive approach is the combination of the very low detection level of microscopy with identification by other methods. Several strategies for a combination of screening and confirmation methods are discussed in the present paper. The new developments in methodology will support current or new legislation (e.g. species-to-species ban, general application of fish meal). (c) 2006 Elsevier B.V. All rights reserved.
    Distance constraints from site-directed spectroscopy as a tool to study membrane protein structure
    Vos, W.L. - \ 2007
    Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): Marcus Hemminga. - [S.l.] : S.n. - ISBN 9789085046257 - 106
    oppervlakte-eiwitten - moleculaire structuur - spectroscopie - surface proteins - molecular conformation - spectroscopy
    Membrane proteins are involved in nearly every process in the living cell. Their scientific importance cannot be overstated, and they account for nearly 60% of all prescribed drugs. Despite being an abundant and important class of proteins, high-resolution structural data on membrane proteins are relatively scarce. X-ray diffraction and NMR spectroscopy are routinely applied nowadays for the determination of structures of water-soluble proteins. However, for membrane proteins that require an amphipathic environment, there is not yet a well-defined strategy for obtaining the structure. For this reason, techniques based on site-directed labeling are being developed to study membrane proteins in their natural environment. In this work, we use two techniques based on the dipole-dipole interaction between two labels, electron spin resonance (ESR) and fluorescence (or Förster) resonance energy transfer (FRET) to obtain low-resolution (0.3-3 nm) distance information on the structure of membrane peptides. FRET is used to study the conformation of a reference membrane protein, i.e. M13 major coat protein, in fully hydrated vesicles. The FRET-derived distance constraints are used to refine the set of high-resolution structures that is available in the protein databank. We show that the coat protein adopts an extended conformation that is not very different from the conformation in the phage particle. In a separate part of this work, we use the FRET approach to monitor the conformation of the coat protein under conditions of hydrophobic mismatch. Although it was suggested that transmembrane protein domains can adapt their backbone conformation to different conditions of hydrophobic stress and that M13 coat protein is a flexible protein that can adapt to a multitude of environments, we show that the conformation of the coat protein in fact is similar under different conditions of hydrophobic mismatch. A parallel approach, based on ESR spin labeling, is used to study the conformation of a peptide that is derived from the crucial proton translocating domain of vacuolar ATPase. First we present a method to enhance the analysis for the determination of distances between two spin labels based on matrix-assisted laser desorption/ionization - time of flight mass spectrometry. Secondly, we use the data from the ESR experiments to study the structure of the peptide. Based on the combined results from the ESR experiments, molecular dynamics simulations and circular dichroism studies we conclude that the peptide forms a dynamica-helix when bound to SDS micelles. We discuss these findings in the light of the current models for proton translocation in the vacuolar ATPase.
    MALDI-TOF MS evidence for the linking of flax bast fibre galactan to rhamnogalacturonan backbone
    Gur'janov, O.P. ; Gorshkova, T.A. ; Kabel, M.A. ; Schols, H.A. ; Dam, J.E.G. van - \ 2007
    Carbohydrate Polymers 67 (2007)1. - ISSN 0144-8617 - p. 86 - 96.
    linum-usitatissimum l - cell - polysaccharides - spectroscopy - degradation - transition - oligomers - pectins - walls
    Fibre-specific (1 ¿ 4)-ß-galactan extracted from bast fibre peels of developing flax (Linum usitatissimum L.) stem has been studied to elucidate its structural details. The polysaccharide was characterized by NMR and subjected to partial degradation protocols, including chemical and enzymatic approaches. The oligosaccharide fragments obtained were fractionated by gel permeation chromatography and analyzed for their molecular mass with MALDI-TOF MS. The obtained data show that this flax galactan is a complex RG-I polysaccharide with variable side chain structures. The backbone is composed of the common GalA-Rha repeats with a high degree of branching. These side chains are mainly composed of ß-1,4-linked Gal oligomers: (1) short branches of only one or two Gal residue(s); (2) long (linear) branches of up to 26 Gal residues; (3) mixed branches of between 3 and 12 Gal residues (possibly derived from longer linear side chains), that are resistant to galactanase cleavage; (4) side chains of at least 17 Gal residues, decorated with single Ara moieties. The linkage between RG backbone and galactan side chains was confirmed by the presence of fragments with (Rha-GalA)nHexm structure type. Neither chemical, nor enzymatic hydrolysis yielded oligomeric GalA residues, indicating that RG-I blocks are not interrupted by HGA regions. The polymer can be cleaved only partially by the rhamnogalacturonan hydrolase used, while the remaining part is resistant, probably due to peculiarities of side chain structure. Novel Rha-GalA oligomers were liberated by RG-hydrolase containing two or three Gal attached to Rha near the cleavage site. The native polymer is decorated by acetyl groups, with yet unknown distribution patterns. Treatment with purified and well-characterized galactanase does not change the hydrodynamic volume of flax galactan (despite considerable cleavage of Gal moieties), suggesting a complex ¿secondary¿ structure of the polymer.
    Interactive forces between co-aggregating and non-co-aggregating oral bacterial pairs
    Postollec, F. ; Norde, W. ; Vries, J. de; Busscher, H.J. ; Mei, H.C. van der - \ 2006
    Journal of Dental Research 85 (2006)3. - ISSN 0022-0345 - p. 231 - 234.
    microbial pairs - microscopy - adhesion - coaggregation - surfaces - cells - polysaccharides - spectroscopy - recognition - temperature
    The temporo-spatial development of plaque is governed by adhesive interactions between different co-aggregating bacterial strains and species. Physico-chemically, these interactions are due to attractive Lifshitz-Van der Waals and acid-base forces, and occur despite electrostatic repulsion and with a critical influence of temperature. The forces between co-aggregating and non-co-aggregating pairs have never been measured, however. The aim here, thus, is to investigate, by atomic force microscopy, whether there is a difference in interactive forces between co-aggregating and non-co-aggregating bacterial pairs at 10 degrees C, 22 degrees C, and 40 degrees C. Actinomyces naeslundii 147 was immobilized on poly-L-lysine-coated tipless AFM cantilevers, while streptococci were immobilized on poly-L-lysine-coated glass surfaces. Upon approach, a repulsive force was measured, regardless of whether a co-aggregating or non-co-aggregating pair was involved. However, upon retraction, the co-aggregating pair exhibited larger adhesive forces and energies than did the non-co-aggregating pair. Adhesive interactions between the co-aggregating pair were smallest at 40 degrees C.
    A new technique for extracting the red edge position from hyperspectral data : the linear extrapolation method
    Cho, M.A. ; Skidmore, A.K. - \ 2006
    Remote Sensing of Environment 101 (2006)2. - ISSN 0034-4257 - p. 181 - 193.
    plant leaf reflectance - chlorophyll concentration - vegetation indexes - nitrogen status - canopy scales - area index - leaves - spectroscopy - variability - stress
    There is increasing interest in using hyperspectral data for quantitative characterization of vegetation in spatial and temporal scopes. Many spectral indices are being developed to improve vegetation sensitivity by minimizing the background influence. The chlorophyll absorption continuum index (CACI) is such a measure to calculate the spectral continuum on which the analyses are based on the area of the troughs spanned by the spectral continuum. However, different values of CACI were obtained in this method because different positions of continuums were determined by different users. Furthermore, the sensitivity of CACI to agronomic parameters such as green leaf chlorophyll density (GLCD) has been reduced because the fixed positions of continuums are determined when the red edge shifted with the change in GLCD. A modified chlorophyll absorption continuum index (MCACI) is presented in this article. The red edge inflection point (REIP) replaces the maximum reflectance point (MRP) in near-infrared (NIR) shoulder on the CACI continuum. This MCACI has been proved to increase the sensitivity and predictive power of GLCD.
    A comparison of liquid chromatography, capillary electrophoresis, and mass spectrometry methods to determine xyloglucan structures in black currants
    Hilz, H. ; Jong, L.E. de; Kabel, M.A. ; Schols, H.A. ; Voragen, A.G.J. - \ 2006
    Journal of Chromatography. A, Including electrophoresis and other separation methods 1133 (2006)1-2. - ISSN 0021-9673 - p. 275 - 286.
    plant-cell walls - cultured sycamore cells - cellulose interactions - covalent linkage - fruit xyloglucan - side-chain - oligosaccharides - polysaccharides - hemicellulose - spectroscopy
    Different separation (HPAEC, RP¿HPLC, CE) and identification (MALDI¿TOF¿MS, ESI¿MSn) techniques were compared to analyse oligosaccharides obtained after incubation of xyloglucan with endo-glucanase. It was possible to analyse xyloglucan oligosaccharides with each technique. Several techniques, including off line (HPAEC¿MALDI¿TOF¿MS) or online (CE¿ESI¿MSn, RP¿HPLC¿ESI¿MSn) connection provided complementary information on xyloglucan structure. Online CE¿MS and RP¿HPLC¿MS are described for the first time in xyloglucan analysis. Advantages and disadvantages of the techniques for different purposes such as structural characterisation of oligosaccharides or oligosaccharide profiling are discussed. Black currant xyloglucans had a rather simple XXXG-type structure with galactose and fucose containing side chains.
    The folding energy landscape of apoflavodoxin is rugged. hydrogen exchange reveals non-productive misfolded intermediates.
    Bollen, Y.J.M. ; Kamphuis, M.B. ; Mierlo, C.P.M. van - \ 2006
    Proceedings of the National Academy of Sciences of the United States of America 103 (2006)11. - ISSN 0027-8424 - p. 4095 - 4100.
    azotobacter-vinelandii apoflavodoxin - protein - pathways - equilibrium - cooperativity - spectroscopy - sensitivity - topology - ensemble - dynamics
    Many native proteins occasionally form partially unfolded forms (PUFs), which can be detected by hydrogen/deuterium exchange and NMR spectroscopy. Knowledge about these metastable states is required to better understand the onset of folding-related diseases. So far, not much is known about where PUFs reside within the energy landscape for protein folding. Here, four PUFs of the relatively large apoflavodoxin (179 aa) are identified. Remarkably, at least three of them are partially misfolded conformations. The misfolding involves side-chain contacts as well as the protein backbone. The rates at which the PUFs interconvert with native protein have been determined. Comparison of these rates with stopped-flow data positions the PUFs in apoflavodoxin's complex folding energy landscape. PUF1 and PUF2 are unfolding excursions that start from native apoflavodoxin but do not continue to the unfolded state. PUF3 and PUF4 could be similar excursions, but their rates of formation suggest that they are on a dead-end folding route that starts from unfolded apoflavodoxin and does not continue all of the way to native protein. All PUFs detected thus are off the protein's productive folding route
    Structural characterization of tissue-specific galactan from flax fibers by 1H NMR and MALDI TOF mass spectrosmetry
    Gur'janov, O.P. ; Gorshkova, T. ; Kabel, M.A. ; Schols, H.A. ; Dam, J.E.G. van - \ 2006
    Russian Journal of Bioorganic Chemistry 32 (2006)6. - ISSN 1068-1620 - p. 558 - 567.
    plant-cell walls - linum-usitatissimum l - rhamnogalacturonan-i - polysaccharides - oligosaccharides - identification - spectroscopy - transition - pectins - complex
    A high-molecular-mass polysaccharide galactan (M 2000 kDa) was isolated from flax at the stage of cell wall thickening of the bast fiber development. The polymer structure was studied by 1H NMR spectroscopy and MALDI TOF mass spectrometry. It is built up of Gal (59%), Rha (15%), GalA (23%), and Ara (3%) residues. The galactan backbone consists of successively alternating monomer disaccharide units (- 4GalA1 - 2Rha1 -)n and is similar in its structure to the backbone of rhamnogalacturonan-1 (RG-I). Rhamnose residues bear in position 4 ß-(1 - 4)-galactose side chains of various lengths with a polymerization degree of up to 28 or higher. A part of the side chains have branchings.
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