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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    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.

    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

    Summary

    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.

    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.

    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.
    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.

    Conclusions

    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).
    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.
    Remote sensing of sun-induced fluorescence to improve modeling of diurnal courses of gross primary production (GPP)
    Damm, A. ; Elbers, J.A. ; Erler, A. ; Giolis, B. ; Hamdi, K. ; Hutjes, R.W.A. ; Kosvancova, M. ; Meroni, M. ; Migliettas, F. ; Moersch, A. ; Moreno, J. ; Schickling, A. ; Sonnenschein, R. ; Udelhoven, T. ; Linden, S. van der; Hostert, P. ; Rascher, U. - \ 2010
    Global Change Biology 16 (2010)1. - ISSN 1354-1013 - p. 171 - 186.
    koolstofcyclus - primaire productie - remote sensing - fluorescentie - spectroscopie - planten - fotosynthese - modelleren - carbon cycle - primary production - remote sensing - fluorescence - spectroscopy - plants - photosynthesis - modeling - light-use efficiency - induced chlorophyll fluorescence - photochemical reflectance index - net primary production - eddy covariance - photosynthetic efficiency - leaf senescence - photosystem-ii - carbon-dioxide - boreal forest
    Terrestrial gross primary production (GPP) is an important parameter to explore and quantify carbon fixation by plant ecosystems at various scales. Remote sensing (RS) offers a unique possibility to investigate GPP in a spatially explicit fashion; however, budgeting of terrestrial carbon cycles based on this approach still remains uncertain. To improve calculations, spatio-temporal variability of GPP must be investigated in more detail on local and regional scales. The overarching goal of this study is to enhance our knowledge on how environmentally induced changes of photosynthetic light-use efficiency (LUE) are linked with optical RS parameters. Diurnal courses of sun-induced fluorescence yield (FSyield) and the photochemical reflectance index of corn were derived from high-resolution spectrometric measurements and their potential as proxies for LUE was investigated. GPP was modeled using Monteith's LUE-concept and optical-based GPP and LUE values were compared with synoptically acquired eddy covariance data. It is shown that the diurnal response of complex physiological regulation of photosynthesis can be tracked reliably with the sun-induced fluorescence. Considering structural and physiological effects, this research shows for the first time that including sun-induced fluorescence into modeling approaches improves their results in predicting diurnal courses of GPP. Our results support the hypothesis that air- or spaceborne quantification of sun-induced fluorescence yield may become a powerful tool to better understand spatio-temporal variations of fluorescence yield, photosynthetic efficiency and plant stress on a global scale
    Modeling membrane protein structure through site-directed ESR spectroscopy
    Kavalenka, A.A. - \ 2009
    Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): Marcus Hemminga; J. Strancar. - [S.l. : S.n. - ISBN 9789085854241 - 119
    oppervlakte-eiwitten - moleculaire structuur - spectroscopie - paramagnetische elektronenresonantiespectroscopie - surface proteins - molecular conformation - spectroscopy - electron paramagnetic resonance spectroscopy
    Site-directed spin labeling (SDSL) electron spin resonance (ESR) spectroscopy is a
    relatively new biophysical tool for obtaining structural information about proteins. This
    thesis presents a novel approach, based on powerful spectral analysis techniques (multicomponent
    spectral simulations and evolutionary optimizations of ESR spectra) and
    modeling of the protein structure by calculating the restrictions of the conformational space
    of the attached spin label.
    First, the feasibility of the ESR spectral analysis was enhanced by speeding-up the
    spectrum optimization and by automation of the analysis routines to enable the handling of
    large sets of spectroscopic data (e.g., for the joint analysis of SDSL-ESR spectra from
    multiple sites of a spin-labeled protein). According to the testing examples a speed-up
    factor of 5-7 was achieved.
    Secondly, SDSL-ESR was used to study the topology of the long N-terminal domain
    of the photosynthetic light-harvesting complex CP29. Wild-type protein containing a single
    cysteine at position 108 and nine single cysteine mutants were produced, allowing to label
    different parts of the domain with a nitroxide spin label. In all cases the apoproteins were
    either solubilized in detergent, or they were reconstituted with their native pigments in
    vitro. The spin label ESR spectra were analyzed in terms of a multi-component spectral
    simulation approach. These results permit to trace the structural organization of the long Nterminal
    domain of CP29 leading to a structural model for its N-terminal domain.
    Thirdly, we proposed a novel way to translate the local structural constraints gained
    by SDSL-ESR data into a low-resolution structure of a protein by simulating the
    restrictions of the local conformational spaces of the spin label attached at different protein
    sites along the primary structure of the membrane-embedded protein. The proposed
    structural model takes into account the restricting effect of the protein backbone, amino
    acid side chains and lipid environment. We tested the sensitivity of this approach for
    artificial oligopeptides and then for membrane-embedded M13 major coat protein
    decorated with a limited number of strategically placed spin labels by employing highthroughput
    site-directed mutagenesis. We found a reasonably good agreement of the
    simulated and the experimental data taking a protein conformation close to an α-helix.
    Finally, by using an optimization algorithm we optimized the parameters of the
    protein-lipid model by improving the fit of the simulation data to the experimental
    conformational space data. The outcome of the optimization was a family of best-fit
    structures of membrane-embedded M13 protein, which not only agree with the available
    SDSL-ESR data, but also was consistent with a recent model based on site-directed
    fluorescence labeling.
    Therefore, the present method provides a challenging starting point for the
    development of a powerful methodology for the protein structure characterization, an
    alternative approach to conventional techniques.
    The influence of vegetation cover on the spectroscopic estimation of soil properties
    Bartholomeus, H. - \ 2009
    Wageningen University. Promotor(en): Michael Schaepman, co-promotor(en): Lammert Kooistra. - [S.l. : S.n. - ISBN 9789085854487 - 144
    bodemeigenschappen - vegetatie - spectroscopie - schatting - koolstof - landbouwgronden - ijzer - bodemchemie - geostatistiek - soil properties - vegetation - spectroscopy - estimation - carbon - agricultural soils - iron - soil chemistry - geostatistics
    Voor het bepalen van de kwaliteit van de bodem als hulpbron is er behoefte aan een regelmatige bepaling van de chemische en fysische eigenschappen, zowel in ruimte als tijd. Kwantitatieve schatting van de exacte hoeveelheid, ruimtelijke verdeling en temporele verandering van bodemeigenschappen is nog steeds een uitdaging. Het onderwerp van dit proefschrift is hoe spectrale reflectie informatie gelinkt kan worden aan bodemeigenschappen
    Primary photosynthetic processes: from supercomplex to leaf
    Broess, K. - \ 2009
    Wageningen University. Promotor(en): Herbert van Amerongen. - [S.l.] : S.n. - ISBN 9789085852988 - 124
    fotosynthese - fluorescentie - fluorescentiemicroscopie - spectroscopie - membranen - chloroplasten - fotosysteem ii - planten - photosynthesis - fluorescence - fluorescence microscopy - spectroscopy - membranes - chloroplasts - photosystem ii - plants
    This thesis describes fluorescence spectroscopy experiments on photosynthetic complexes that cover the primary photosynthetic processes, from the absorption of light by photosynthetic pigments to a charge separation (CS) in the reaction center (RC). Fluorescence spectroscopy is a useful tool in photosynthetic particles, because the latter are densely packed with fluorescence pigments like chlorophylls (Chl). The fluorescence of each pigment is affected by its environment and provide information about structure and dynamics of the photosynthetic complexes. In this thesis time-resolved fluorescence of Chl molecules is used for studying the ultrafast kinetics in membrane particles of photosystem II (PSII) (chapter 2, 3 and 4). In chapter 5 fluorescence lifetime imaging microscopy (FLIM) of is applied to study entire chloroplasts, either in the leaf or in isolated chloroplast form. The advantage of FLIM is that the interactions of the fluorescence pigments in both photosystems can be spatially resolved up to a resolution of 0.5 x 0.5 x 2 µm to indentify and quantify photosynthetic processes in their natural environment.

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

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


    Photosynthesis in plant leaves (Chapter 5)

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

    General conclusions

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



















    Physical interactions among plant MADS-box transcription factors and their biological relevance
    Nougalli Tonaco, I.A. - \ 2008
    Wageningen University. Promotor(en): Sacco de Vries; Gerco Angenent, co-promotor(en): Richard Immink. - [S.l.] : S.n. - ISBN 9789085048299 - 150
    planten - transcriptiefactoren - genexpressie - transcriptie - petunia hybrida - arabidopsis thaliana - fluorescentie - spectroscopie - dna-bindende eiwitten - bloemen - technieken - plantenontwikkeling - genregulatie - transcriptieregulatie - plants - transcription factors - gene expression - transcription - petunia hybrida - arabidopsis thaliana - fluorescence - spectroscopy - dna binding proteins - flowers - techniques - plant development - gene regulation - regulation of transcription
    The biological interpretation of the genome starts from transcription, and many different signaling pathways are integrated at this level. Transcription factors play a central role in the transcription process, because they select the down-stream genes and determine their spatial and temporal expression. In higher eudicot species around 2000 specific transcription factors are present, which can be classified into families based on conserved common domains. The MADS-box transcription factor family is an important family of transcription regulators in plants and genetic studies revealed that members of this family are involved in various developmental processes, like floral induction, floral organ formation and fruit development. In contrast to this wealth of information concerning MADS-box gene functions, the molecular mode of action of the encoded proteins is far from completely understood. Biochemical and yeast η-hybrid experiments performed in the past showed that MADS-box proteins are able to interact mutually, and based on these findings a hypothetical quaternary model has been proposed as molecular working mechanism. According to this model two MADS-box protein dimers assemble into a higher order complex, which binds DNA and regulates target gene expression. Although, this molecular mechanism sounds plausible, it still lacks evidence from in vivo studies. In this study we investigated physical interactions among members of the Petunia hybrida and Arabidopsis thaliana MADS-box transcription factor families in living plant cells. For this purpose, sophisticated micro-spectroscopy techniques have been implemented and in addition, some novel fluorescent-protein-based tools were developed. The first chapter gives an introduction about the dynamic transcriptional process and describes our current knowledge about transcriptional regulation in eukaryotes. The central question of this chapter is how transcription factors are able to find their specific binding sites (ci's-elements) within the huge genome. The various mechanisms, such as "looping" and "sliding", that have been proposed are discussed, as well as the relevance of direct interactions between transcription factors for the control of gene expression.
    In a first attempt to detect protein interactions in living cells, we transiently expressed combinations of petunia MADS-box transcription factors labeled with different color variants of the Green Fluorescent Protein (GFP) in leaf protoplasts (Chapter 2). Subsequently, the transfected protoplasts were analyzed by means of FRET-FLIM
    (Fluorescence Resonance Energy Transfer - Fluorescence Lifetime Imaging) to identify specific dimerization. In addition, we have obtained indirect evidence for higher-order complex formation of the petunia MADS-box proteins FLORAL BINDING PROTEIN2 (FBP2), FBP11, and FBP24 in living cells. Similar kind of analyses for Arabidopsis MADS-box proteins involved in petal and stamen development revealed clear differences in interaction affinities in vivo and furthermore, many homodimers were identified that could not be detected by yeast-based systems in the past (Chapter 3). This result demonstrated the robustness of the FRET-FLIM approach. Based on our observations, we hypothesize that 'partner selectivity' plays an important role in complex formation at particular developmental stages. To study differences in interaction affinity and selectivity and the consequences for complex formation in more detail, a novel method was developed (Chapter 4). The technique, designated "Competition-FRET", allows the verification of competition effects between proteins, and furthermore, it may provide information about the formation of higher-order complexes between different proteins under study. The developed method was implemented to investigate in depth the preference for homo- or heterodimer interactions of the Arabidopsis MADS-box proteins AGAMOUS (AG) and SEPALLATA3 (SEP3).
    The detection of interactions in living cells by FRET as it has been done in the studies described above demands a sophisticated microscopy set-up, and therefore, we decided to test and implement an alternative and theoretically simple technique (Chapter 5). This method for the in vivo detection of protein-protein interaction is called BiFC (Bimolecular Fluorescence Complementation), or "Split-YFP". In this system, a fluorescent molecule is split into two inactive domains and these two non-fluorescent parts are fused to the proteins under study. Only upon interaction of the two protein partners the two non-fluorescent parts of the fluorescent molecule are brought into close proximity, which enables the recovery of fluorescence. We used the EYFP (Enhanced Yellow Fluorescence Protein) molecule as fluorescent molecule and were able to detect the interaction between AG and SEP3 in nuclei of Arabidopsis leaf protoplasts. Techniques like this and FRET-FLIM allow the analyses of interactions between proteins in living cells, but give no information about the size of the formed complexes. To get a first indication about the stoichiometry of protein complexes, we monitored the diffusion time of in vitro synthesized AG-EYFP and SEP3-EYFP fusion proteins by means of FCS (Fluorescence Correlation

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

    Imaging spectroscopy : applications in agriculture
    Zedde, H.J. van de; Brakel, R.P. van - \ 2007
    spectroscopie - kwaliteitscontroles - monitoring - sensorische evaluatie - voedselinspectie - tomaten - patates frites - beeldvormende spectroscopie - spectroscopy - quality controls - monitoring - sensory evaluation - food inspection - tomatoes - chips (French fries) - imaging spectroscopy
    Imaging Spectroscopy is the study of light as a function of spatial distribution and wavelength that has been transmitted, emitted, reflected or scattered from an object. This allows us to derive information about the spatial relation of the chemistry of the object. Imaging spectroscopy is suited for the following tasks: • Quality control: detection of latent defects in agri-products, e.g. vegetables and fruit. • Quantification of compounds: carotenes, proteins, sugars, moisture etc. In this poster the following two applications are discussed: 1) Measuring of compounds in tomatoes and 2) Detection and classification of latent defects in French Fries
    Structure-rheology relations in sodium caseinate containing systems
    Ruis, H.G.M. - \ 2007
    Wageningen University. Promotor(en): Erik van der Linden, co-promotor(en): Paul Venema. - [S.l.] : S.n. - ISBN 9789085046486 - 125
    natriumcaseïnaat - reologische eigenschappen - afschuifkracht - gelering - emulsies - structuur - verzuring - spectroscopie - licht - verstrooiing - sodium caseinate - rheological properties - shear - gelation - emulsions - structure - acidification - spectroscopy - light - scattering
    The general aim of the work described in this thesis was to investigate structure-rheologyrelations for dairy related products, focusing on model systems containing sodium caseinate. The acid inducedgelationof sodium caseinate, of sodium caseinate stabilized emulsions, and the effect of shear on the structure formation was characterized. Special attention was given to the sol-gel transition point, which was defined by a frequency independent loss tangent. It was shown that the sol-gel transition point is completely controlled by the pH and the temperature, independent of the concentration sodium caseinate or the applied shear rate. Considering sodium caseinate solutions, increase of the temperature of acidification caused a decrease of the critical pH forgelationand a more dense gel structure. The formed gels were not in thermodynamicequilibrium,however, due to the slow kinetics of the system they were stable on the time scale of the experiment. At the gel point we have strong indications that the structure can not be characterized by a single fractal dimension. During the acid inducedgelationof sodium caseinate stabilized emulsions a single sol-gel transition was observed. Addition of an excess of sodium caseinate to the emulsion resulted in two sol-gel transitions upon acidification. Application of shear during the acidification of the emulsions showed a decreasing radius of the aggregates formed at thegelpointwith increasing shear rate. The aggregates formed becamemore densedue to the application of shear while the network that was formed by the aggregates became less compact. No shear induced alignment was observed of emulsion droplets dispersed in water or ina sodiumcaseinatesolution, while emulsion droplets dispersed in axanthansolution did align in a shear field. Addition of sodium inhibited the string formation of the emulsion droplets
    Distance constraints from site-directed spectroscopy as a tool to study membrane protein structure
    Vos, W.L. - \ 2007
    Wageningen University. Promotor(en): Herbert van Amerongen, co-promotor(en): Marcus Hemminga. - [S.l.] : S.n. - ISBN 9789085046257 - 106
    oppervlakte-eiwitten - moleculaire structuur - spectroscopie - surface proteins - molecular conformation - spectroscopy
    Membrane proteins are involved in nearly every process in the living cell. Their scientific importance cannot be overstated, and they account for nearly 60% of all prescribed drugs. Despite being an abundant and important class of proteins, high-resolution structural data on membrane proteins are relatively scarce. X-ray diffraction and NMR spectroscopy are routinely applied nowadays for the determination of structures of water-soluble proteins. However, for membrane proteins that require an amphipathic environment, there is not yet a well-defined strategy for obtaining the structure. For this reason, techniques based on site-directed labeling are being developed to study membrane proteins in their natural environment. In this work, we use two techniques based on the dipole-dipole interaction between two labels, electron spin resonance (ESR) and fluorescence (or Förster) resonance energy transfer (FRET) to obtain low-resolution (0.3-3 nm) distance information on the structure of membrane peptides. FRET is used to study the conformation of a reference membrane protein, i.e. M13 major coat protein, in fully hydrated vesicles. The FRET-derived distance constraints are used to refine the set of high-resolution structures that is available in the protein databank. We show that the coat protein adopts an extended conformation that is not very different from the conformation in the phage particle. In a separate part of this work, we use the FRET approach to monitor the conformation of the coat protein under conditions of hydrophobic mismatch. Although it was suggested that transmembrane protein domains can adapt their backbone conformation to different conditions of hydrophobic stress and that M13 coat protein is a flexible protein that can adapt to a multitude of environments, we show that the conformation of the coat protein in fact is similar under different conditions of hydrophobic mismatch. A parallel approach, based on ESR spin labeling, is used to study the conformation of a peptide that is derived from the crucial proton translocating domain of vacuolar ATPase. First we present a method to enhance the analysis for the determination of distances between two spin labels based on matrix-assisted laser desorption/ionization - time of flight mass spectrometry. Secondly, we use the data from the ESR experiments to study the structure of the peptide. Based on the combined results from the ESR experiments, molecular dynamics simulations and circular dichroism studies we conclude that the peptide forms a dynamica-helix when bound to SDS micelles. We discuss these findings in the light of the current models for proton translocation in the vacuolar ATPase.
    Quantitative remote sensing of Norway spruce (Picea abies (L.) Karst.): spectroscopy from needles to crowns to canopies
    Malenovsky, Z. - \ 2006
    Wageningen University. Promotor(en): Michael Schaepman, co-promotor(en): Jan Clevers; P. Cudlin. - - 141
    picea abies - remote sensing - spectroscopie - kroondak - bergbossen - dennennaalden - schaalverandering - picea abies - remote sensing - spectroscopy - canopy - mountain forests - pine needles - scaling
    Mountain ecosystems represent nearly one fourth of the Earth's land surface, and provide (ecosystem) services to a significant part of the world's human population. As was noted in the 1992 United Nations Conference on Environment and Development (UNCED) inRio de Janeiro(Agenda 21), these ecosystems are experiencing rapid degradation due to environmental and human impact at the local scale having, however, a global spread. This work contributes to the spatial monitoring of mountain forest ecosystems dominated byNorwayspruce trees ( Picea abies (L.) Karst.) through developing new quantitative approaches using optical hyperspectral remote sensing.

    A common denominator for all experiments described and performed throughout this work is spectroscopy, used in combination with ecological reasoning and physically based bottom-up scaling approaches. The spectral information acquired at the level of leaves (needles) is scaled up to the level of tree crowns and then to the level of forest canopies by means of radiative transfer modelling. This up-scaling method is based fully on cause-effect relations of vegetation-photon interaction allowing for its subsequent numerical inversion. We have employed radiative transfer models to develop an inversion routine for the retrieval of quantitative forest canopy biochemical (concentration of chlorophyll) and biophysical (leaf area index) parameters based on hyperspectral data acquired by theAirborne Imaging Spectroradiometer (AISA)Eagle.

    The starting point of this work was the calibration and validation of the leaf radiative transfer model PROSPECT (leaf optical PROperties SPECTra) for Norway spruce needles at wavelengths ranging from 450-1000 nm. Simultaneously, an investigation on the variability in hemispherical-directional reflectance, transmittance and absorptance of sunlit spruce needle samples was carried out for environmental stress resistant and stress resilient spruce crowns. Recalibration of the PROSPECT chlorophyll and dry matter specific absorption coefficients kab (l) and km (l) resulted in close agreement of the PROSPECT simulated needle optical properties with the spectral measurements of three investigated needle age-classes. The root mean square error (RMSE) between simulated and measured needle reflectance, transmittance, and absorptance signatures was 1.74%, 1.53%, and 2.91%, respectively. Testing the adjusted PROSPECT model for total chlorophyll concentration, dry matter content, and leaf water content retrieved simultaneously from laboratory based spectrometer measurements of independent needle samples showed an improved performance.

    When comparing sunlit needles of primary shoots of the two environmental stress response classes, significant quantitative differences were discovered at red edge (710-715 nm) and green (540-565 nm) wavelengths with respect to the variability in needle optical properties. These differences are related to the changes in the concentration of the foliar pigments, which proved to be significantly lower for needles of stress resilient trees. High variability in qualitative spectral characteristics was found at wavelengths relating to far-red (740 nm) and green (530 nm) fluorescence emissions. No significant spectral variation was found within the near infrared wavelengths of the tested needles. Consequently, we conclude that sunlit needle samples of a specific age-class collected from a randomly selected branch within two tested crown parts were representative for both of them, but they are optically different if collected from stress resistant or stress resilient crowns.

    The needle optical properties were up-scaled to the crowns and to the canopies by the 3-dimensional Discrete Anisotropic Radiative Transfer (DART) model. A detailed sensitivity analysis investigating the effect of woody elements introduced into the DART model on the nadir bidirectional reflectance factor (BRF) was performed at a very high spatial resolution (0.4 m) before its direct use for the Norway spruce canopy. The sensitivity analysis was performed separately for both sunlit and shaded parts of the simulated forest canopy and it was validated against BRF measurements at the same spatial resolution acquired over the simulated forest stand by the AISA sensor. Results showed a nadir BRF for the Norway spruce canopy modelled as pure foliage to be similar to the one for foliage including only robust woody constituents (i.e., trunks and branches of first order). The incorporation of small woody parts in DART caused the nadir canopy reflectance to decrease in the near-infrared (NIR) about 4%, in the red edge about 2%, and in the green bands less than 1%. These findings stressed the importance of including fine woody elements in radiative transfer based retrievals of the forest canopy properties at very high spatial resolution, especially if the NIR wavelengths are exploited.

    The coupled radiative transfer models PROSPECT and DART were employed to develop and test the sensitivity of a robust chlorophyll estimating optical index for a heterogeneous coniferous forest canopy. A newly proposed index named 'Area under curve Normalized to Maximal Band depth between 650-725nm' (ANMB 650-725 ) is based on the continuum removal method applied on reflectance spectra. The approach is taking advantage of the fine spectral resolution and sampling interval of hyperspectral images to isolate the chlorophyll absorption feature between 650 and 725 nm. The results, obtained from simulated hyperspectral data with a pixel size of0.9 m, showed a strong linear relationship of the ANMB 650-725 with spruce crown C ab concentration (r 2 = 0.9798) and an insensitivity for varying canopy structural features such as LAI and canopy closure. Chlorophyll concentration retrieval using the ANMB 650-725 index remained stable also after introduction of the spectral information of epiphytic lichen ( Pseudevernia sp.) and an increased sensor noise (signal to noise ratio equal to five).

    It can be concluded from this work that up-scaling procedures from needles to crowns to canopies can be successfully applied in mountain ecosystems. In particular the quantitative, physical based approaches proved to be robust and further helped to refine radiative transfer based models. In the near future, we will be seeing a number of spaceborne missions being realized (e.g., either of hyper- or super-spectral nature), where the presented up-scaling approaches can significantly contribute to increased variable retrieval accuracy. The integration of such derived products into an assessment programme for monitoring and forecasting the development of forest ecosystem services (e.g., Global Monitoring for Environment and Security (GMES)) is a logical consequence of this work.
    Spectrodirectional remote sensing : from pixels to processes
    Schaepman, M.E. - \ 2004
    Wageningen : Wageningen Universiteit - 55
    remote sensing - spectroscopie - openbare redes - remote sensing - spectroscopy - public speeches
    Uit de mest- en mineralenprogramma's : Bepalen van opbrengst, nutriëntengehalte en voederwaarde van grasland met beelden
    Schut, A.G.T. - \ 2004
    Wageningen : Plant Research International (Informatieblad / Plant Research International 398.53) - 2
    graslanden - graslandverbetering - spectroscopie - voedingswaarde - opbrengsten - voedingsstoffengehalte - reflectiefactor - voorspellen - analytische methoden - beeldvormende spectroscopie - grasslands - grassland improvement - spectroscopy - nutritive value - yields - nutrient content - reflectance - forecasting - analytical methods - imaging spectroscopy
    Beeldvormende spectroscopie is een techniek waarmee de gewasreflectie in beelden wordt vastgelegd. Met beelden kan snel en automatisch worden gemeten met een direct resultaat ter plekke. Op basis van reflectie wordt in laboratoria de samenstelling van geoogst materiaal bepaald. Door technologische ontwikkelingen is het nu mogelijk om van individuele bladeren in een veldgewas de reflectiekarakteristiek vast te leggen. Recent onderzoek aan mini-graszoden heeft aangetoond dat met beeldvormende spectroscopie goede voorspellingen gemaakt kunnen worden van opbrengst, nutriëntengehalte en voederwaarde van een grasgewas. Op basis van dit onderzoek is samen met Agrotechnology & Food Innovations B.V. een experimenteel instrument ontwikkeld, de Imspector Mobiel. In het hier gerapporteerde onderzoek is gekeken naar de mogelijkheden van deze technologie voor het nauwkeurig voorspellen van opbrengst, nutriëntengehalte en voederwaarde in het veld op veengrond in Zegveld met een heterogene zode en op zand- en kleigrond met normale zoden. Daarnaast is gekeken naar de mogelijkheid om het klaveraandeel in de drogestof en de opbrengst na beweiding te schatten
    Snelle meetmethoden als managementinstrument bij de teelt van ruwvoer
    Stienezen, M.W.J. ; Kasper, G.J. ; Holshof, G. ; Molema, G.J. ; Schut, A.G.T. ; Meuleman, J.J. ; Smits, M.C.J. - \ 2004
    Lelystad : Animal Sciences Group (PraktijkRapport / Animal Sciences Group, Praktijkonderzoek : Rundvee ) - 59
    ruwvoer (roughage) - melkveehouderij - droge stof - voedingswaarde - gewasproductie - meting - spectroscopie - agrarische bedrijfsvoering - roughage - dairy farming - dry matter - nutritive value - crop production - measurement - spectroscopy - farm management
    Quick measuring methods as management tools in the production of roughage. The most promising technique is spectroscopy, which can be applied in on-line analysis methods for measuring dry matter yield and feed value of silage and grass and which can be available for use within 5 years as a management tool in the production of roughage on dairy farms. Conceptual spectroscopy seems the best technique under the conditions mentioned for measuring feed value. The use of spectroscopy in a dotted measurement seems to be the best technique for measuring dry matter yield.
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