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
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 - 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
University. Promotor(en): Cees Buisman, co-promotor(en): J. Woisetschläger; E.C. Fuchs. - Wageningen : Wageningen University - ISBN 9789462577039 - 223 p.
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 - 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
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

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.

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
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

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 <Q(2)
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 - 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.
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