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
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