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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    The land of the checkpoints : Study of the daily geographies of checkpoints in the Occupied Palestinian Territories
    Rijke, Alexandra - \ 2019
    Wageningen University. Promotor(en): C. Minca, co-promotor(en): M.E. Ormond. - Wageningen : Wageningen University - ISBN 9789463951418 - 357
    cum laude

    When the Israeli state occupied the Palestinian Territories in 1967, it gradually imposed restrictions on Palestinian movement. At first easily circumvented by Palestinians, these restrictions have become an intricate, multi-layered ‘architecture of occupation’ over the last 50 years. This architecture of occupation includes the Wall, illegal Jewish settlements and an elaborate checkpoint system. As a consequence, many Palestinians and Jewish settlers have to pass through Israeli checkpoints on a daily basis. In this PhD thesis, I have analysed their experiences. I have studied the workings of the checkpoints – its rules and regulations, managers and machines – and the diverse ways in which Palestinian commuters engage with the checkpoints. I conclude that these checkpoints produce arbitrary, mutable and selective regimes of mobility, and that they should be seen as the outcome of the endless interplay between its managers, commuters, rules, material devices and procedures of control.

    Microbial treasure trove : Unravelling the potential of class 2 CRISPR–Cas systems
    Mohanraju, Prarthana - \ 2019
    Wageningen University. Promotor(en): J. van der Oost, co-promotor(en): D. Swarts. - Wageningen : Wageningen University - ISBN 9789463951258 - 318
    cum laude

    Animals are known to possess a large repertoire of immune systems with a high degree of sophistication. On the other hand, the immune systems found in bacteria and archaea appeared to be much more rudimentary. However, the ground-breaking discovery of a novel immune system, CRISPR-Cas, proved otherwise. CRISPR-Cas, is unique in being both adaptive and heritable, and it relies on small RNA molecules that specifically guide the defence system to matching invader DNA sequences. This natural defence system has been successfully repurposed into a valuable molecular technology which is a robust, efficient, easy-to-use method to precisely alter DNA sequences of living organisms. The current CRISPR-based technologies, mostly employ the Cas9 protein, for diverse biotechnological applications. Nevertheless, the natural diversity of CRISPR-Cas systems is remarkably extensive, including systems that target DNA, systems that target RNA, and systems that target both DNA and RNA. The diverse class 2 CRISPR nucleases have unique molecular features that contribute to an expansive toolbox for genome and transcriptome engineering. These nucleases differ greatly in their structure and mechanisms. These differences could be exploited as complementary applications creating numerous CRISPR-based technologies possibly with favourable specificity, efficiency and/or delivery. This thesis explores the diversity of Class 2 CRISPR–Cas systems and provides mechanistic insights into different class 2 nucleases. In addition, it describes potential applications to expand the current repertoire of CRISPR-based technologies.

    Due to the everlasting arms race between prokaryotes and their viruses, the rapid evolution of CRISPR–Cas systems has resulted in extreme structural and functional diversity. As a result, a plethora of distinct CRISPR–Cas systems are represented in genomes of most archaea and almost half of the bacteria. The key players of this system are the crRNA binding effector complexes, and the associated nuclease domains. CRISPR–Cas systems are currently grouped into two classes each of which is subdivided into three types. Class 1 systems (consisting of types I, III, and IV) use a multi-subunit protein complex to achieve interference, and class 2 systems (consisting of types II, V, and VI) utilize a single multi-domain protein, that have been repurposed for genome editing applications in a wide range of organisms. The mechanism of crRNA maturation in CRISPR–Cas12a systems was unravelled during this thesis. Unlike the type II nuclease Cas9, which utilizes a tracrRNA as well as endogenous RNaseIII for maturation of its dual crRNA/tracrRNA guides, pre-crRNA processing in the Cas12a system proceeds in the absence of tracrRNA or other Cas proteins. It was demonstrated that Cas12a nucleases possess a previously unknown RNase domain that is responsible for cleaving the pre-crRNA to generate the mature crRNAs. The typical cleavage pattern revealed that Cas12a recognizes specific secondary structures and/or motifs on its direct repeats. Furthermore, the ability to autonomously process crRNA has significant implications from a genome editing standpoint, as it provides a simple route to editing multiple genomic loci at a time (multiplex editing). Using a single customized CRISPR array up to four genes in mammalian cells ex vivo and up to three genes in mouse brain cells in vivo were shown to be edited simultaneously.

    The characterisation of a novel, diminutive type V-U1 Cas protein from Mycolicibacterium mucogenicum (MmuC2c4) was described in this thesis. Type V-U proteins are highly similar to the typical transposon-encoded TnpB-like proteins and each of them (type VU-1 to type VU-5) appear to have originated independently from distinct TnpB families. Akin to most type V proteins, MmuC2c4 was shown to recognize a 5’-TTN-3’ PAM on a double-stranded target DNA.

    The characterisation of a type II-C Cas9 orthologue of the thermophilic bacterium Geobacillus thermodenitrificans T12, ThermoCas9 is described. This is one of the first reports that provides fundamental insights into a thermophilic CRISPR–Cas9 family member. It was demonstrated that ThermoCas9 is active in vitro between 20 and 70 ℃, that the structure of its sgRNA influences its activity at elevated temperatures, it has a more stringent PAM-preference at lower temperatures, it does not tolerate extensive spacer-protospacer mismatches, and it preferentially cleaves plasmid DNA compared to linear DNA. Furthermore, ThermoCas9 was employed for pyrF gene deletion and transcriptional silencing of ldhL gene at 55 ℃ in Bacillus smithii ET 138 and for pyrF gene deletion at 37 ℃ in Pseudomonas putida. This is the first time Cas9-based bacterial genome editing and silencing tools were used at temperatures above 42 ℃.

    Four Cas12a orthologues were assessed for their salt tolerance as well as pH- and temperature stability using biochemical assays as described. Subsequently, Francisella tularensis subsp. novicida (FnCas12a) and Eubacterium eligens (EeCas12a) were applied for genome editing in a moderate thermophilic bacterium, Bacillus smithii. It is demonstrated that FnCas12a and EeCas12a are sub-optimally active in vivo at temperatures above 45 ℃. The wide growth temperature range of B. smithii ET 138 was employed for the controllable induction of Cas12a expression at temperatures below the 45 ℃ threshold. It was demonstrated that a mutant can be generated within a short span of 2-3 days. This process can be easily adapted for gene editing applications in a wide variety of both mesophilic and moderate thermophilic organisms. potential to harness the activity of anti-CRISPR (Acr) proteins for controllable bacterial genome engineering was also investigated. The Acr protein from Neisseria meningitidis (AcrIIC1Nme) was employed as an “on/off-switch” to control the activity of thermostable Cas9 orthologues from Geobacillus thermodenitrificans T12 (ThermoCas9) and Geobacillus stearothermophilus (GeoCas9). Initially, it was proven that both ThermoCas9 and GeoCas9 can introduce lethal dsDNA breaks in E. coli at 37 ℃ in a tuneable manner. Next, it was demonstrated that AcrIIC1Nme traps both tested Cas9 orthologues in a DNA-bound, catalytically inactive state. The Cas9/AcrIIC1Nme complexes can promote a transcriptional silencing effect with efficiency comparable to the catalytically “dead” ThermodCas9 and GeodCas9 variants. Finally, a single-vector, tightly controllable and highly efficient Cas9/AcrIIC1Nme-based tool for coupled silencing and targeting in E. coli was developed. This tool may serve as a basis for further developing a controllable genome editing and transcriptional regulation in model as well as non-model microorganisms.

    Furthermore, a novel biological role and mechanism for the CRISPR–Cas9 system of the pathogen Campylobacter jejuni (CjeCas9) was uncovered. It was demonstrated that upon C. jejuni infection of human cells, CjeCas9 is secreted into the cytoplasm of the infected cells and it can autonomously enter the nucleus. Inside the nucleus, it catalyses metal-dependent and sequence-independent nicking of double stranded DNA, eventually leading to cell death. Genome editing using CjeCas9 was compared with the commonly used Cas9 from Streptococcus pyogenes (SpyCas9), and the latter was shown to be superior in creating indels. It was concluded that the unique catalytic features make CjeCas9 nuclease less suitable for genome editing applications.

    In conclusion, the research described in this PhD thesis has uncovered novel molecular requirements and mechanisms of several unique Class 2 CRISPR–Cas nucleases. Besides gaining insights into their biochemical mechanism, the potential of Class 2 nucleases has been harnessed for biotechnological applications. Additionally, a unique role and mechanism of CRISPR–Cas in virulence has been elucidated. The characterisation of nucleases such as FnCas12a, EeCas12a, MmuC2c4 and ThermoCas9 opens up exciting possibilities of utilizing them as genome and transcriptome engineering tools.

    Fostering oral presentation competence in higher education
    Ginkel, Stan van - \ 2019
    Wageningen University. Promotor(en): M. Mulder, co-promotor(en): H.J.A. Biemans; J.T.M. Gulikers. - Wageningen : Wageningen University - ISBN 9789463439633 - 172
    cum laude

    Presenting is considered as a core competence of the higher educated professional. However, it remains questionable how effective learning environments fostering presentation competence should be constructed. This thesis focuses on formulating evidence-based educational design principles. Further, research questions explore effective feedback processes within the context of realistic presentation skills courses. These studies verifies the potential impact of feedback sources, such as teachers, peers and the self, on developing students’ oral presentation competence. Besides studying the quality of differing feedback sources, Virtual Reality is studied as an alternative feedback mode encouraging students’ cognition, skills and attitudes towards presenting. The constructed VR-tool, based on the principles of this thesis, is already implemented in secondary education, higher education and the corporate sector.

    The role of polycyclic aromatic hydrocarbons in developmental toxicity of petroleum substances
    Kamelia, Lenny - \ 2019
    Wageningen University. Promotor(en): I.M.C.M. Rietjens; P.J. Boogaard. - Wageningen : Wageningen University - ISBN 9789463950619 - 287
    cum laude

    REACH requires prenatal developmental toxicity (PDT) testing for substances registered in the EU at a volume of ≥100 tonnes/year. One of the consequences is that many petroleum substances (PS) will need to be tested for their potential adverse effect on prenatal development according to the current OECD 414 testing guidelines. This will involve a huge number of experimental animals and a considerable amount of resources. Therefore, the application of in vitro alternative testing strategies may reduce the animal experimentation and resources needed to study PDT potencies of PS. Furthermore, since some PS with high concentrations of polycyclic aromatic hydrocarbons (PAH) may induce PDT whilst their gas-to-liquid (GTL) analogues, which are synthetic products completely devoid of aromatics, do not induce PDT, it was hypothesized that PDT observed for some PS is caused by certain types of PAH in these products. This hypothesis was tested in the present thesis using a battery of in vitro alternative assays.

    Chapter 1 provided background information and presented the aim of the thesis. In addition, the selected test substances and in vitro alternative assays used in the present thesis were also introduced. In total, 19 samples derived from 6 PS and 2 GTL product categories were tested. These samples were selected because i) they represent a series with a systematic variation in PAH content, being substances containing a range of 3- to 7-ring PAHs including extremes regarding their PAH content (with and without PAHs) and ii) in vivo PDT data for these product categories were available, enabling in vitro-in vivo comparisons. The selected in vitro alternative assays were presented, including the embryonic stem cell test (EST), the zebrafish embryotoxicity test (ZET), and a panel of CALUX reporter gene assays. Finally, the general outline of the thesis was also provided.

    Chapter 2 assessed the applicability of the EST to evaluate in vitro embryotoxic potencies of the DMSO extracts of 9 PS (varying in their PAH content, from 5 PS categories) and 2 GTL products (containing no PAHs) as compared to their in vivo potencies. All DMSO-extracts of PS induced a concentration-dependent inhibition of ES-D3 cell differentiation into beating cardiomyocytes at non-cytotoxic concentrations, and their potency was proportional to their 3- to 7-ring PAH content. In contrast, both GTL extracts, which are completely devoid of PAHs, tested negative in the EST. When the EST results were compared to in vivo PDT data of the corresponding PS, a good correlation was found between in vitro and in vivo results (R2: 0.97). Overall, the EST showed able to evaluate the in vitro embryotoxicity of PS, within and across categories, a result for the in vitro assay that was in line with the in vivo PDT data. The results also supported the hypothesis that PAHs are the primary inducers of the PDT resulting from PS exposure.

    In Chapter 3, the role of endocrine- and dioxin-like activity in the developmental toxicity of PS extracts was investigated using a panel of Chemical Activated LUciferase gene eXpression (CALUX) assays. The same set of samples as in Chapter 2 was tested in the panel of CALUX assays that included agonist and antagonist assays for the androgen, estrogen-α, progesterone, and thyroid-β receptor, and also for the aryl hydrocarbon receptor (AhR). All DMSO-extracts of the PS showed strong AhR agonist activity and weak antiprogesterone, antiandrogen, and estrogenic activities. Only minor effects were seen for thyroid-related and antiestrogenic activity with some products. PS that are grouped in the same class induced similar luciferase expression profiles, suggesting a class specific signature of effects. None of the GTL products showed a meaningful interaction with the selected receptors, thus testing negative in all CALUX assays applied. The AhR-mediated activity of the PS correlated best (R2: 0.80) with the in vitro PDT potency of the corresponding PS as quantified previously in the EST, suggesting an important role of the AhR in mediating this effect. In conclusion, a high potential for endocrine and dioxin-like activity of some PS extracts was elucidated, which correlated with their in vitro PDT, and was driven by the type and level of PAHs present in the PS extracts. The prominent AhR-mediated activity as induced by the PS extracts tested could be one of the underlying mechanisms of PDT by these substances.

    Chapter 4 investigated the usefulness of both the EST and the AhR CALUX assay to evaluate the in vitro PDT potency of an additional series of DMSO-extracts of HFOs, heavy PS containing mainly 3- to 7-ring PAHs, and one HRBO, a highly refined mineral oil that contains no aromatics and no PAHs. All DMSO-extracts of HFOs, but not of the HRBO, resulted in inhibition of ES-D3 cell differentiation in the EST and induced AhR-mediated activity in the AhR CALUX assay, and these potencies were was shown to be proportional to the amount of 3- to 7-ring PAHs they contain. Co-exposure of ES-D3 cells (EST) or H4IIE.luc cells (AhR CALUX assay) with the selected DMSO-extracts of PS and the AhR antagonist trimethoxyflavone (TMF), successfully counteracted the PS-induced inhibition of ES-D3 cell differentiation into cardiomyocytes as well as the AhR-mediated induction of gene expression by these substances. Moreover, also for this series of PS a good concordance was obtained when comparing the EST results with available in vivo PDT data. Altogether, the resulting data corroborate the hypothesis that PS-induced PDT is induced mainly by their 3- to 7-ring PAH content and that the observed PDT is partially mediated via the AhR.

    In Chapter 5, the applicability of the ZET to evaluate developmental toxicity potency of the same set of samples as tested in Chapter 2 and 3 (DMSO-extracts of 9 PS and 2 GTL products) was investigated. All PS extracts, varying in PAH level and content, were able to inhibit the development of zebrafish embryos in a concentration-dependent manner and this potency could be associated with the amount of 3-5 ring PAHs they contain. On the contrary, DMSO-extracts of both GTL products, with no aromatics, showed no effect at all in the ZET. The potencies obtained in the ZET moderately correlated with those previously reported for the EST (R2: 0.61) and the AhR CALUX assay (R2: 0.66), while the correlation with potencies reported in in vivo studies were higher for the EST (R2: 0.85) than the ZET (R2: 0.69). Combining the results obtained from the EST (Chapter 2), AhR CALUX assay (Chapter 3), and ZET (Chapter 5) ranked and clustered the test substances in line with their in vivo potencies and chemical characteristics. It was concluded that the ZET did not outperform the EST as a stand-alone assay for testing PDT of PS but confirms the hypothesis that PAHs are the major inducers of PDT by some PS, and that the ZET is a useful addition to a battery of in vitro tests able to predict the in vivo PDT of PS.

    In Chapter 6 we combined an exogenous biotransformation system, using hamster liver microsomes, with the EST to compare the in vitro PDT potency with and without bioactivation of two model 5-ring PAHs, benzo[a]pyrene (BaP) and dibenz[a,h]anthracene (DBA), and of PAH containing PS and GTL base oil (GTLb) extracts. In the absence of bioactivation, DBA, but not BaP, inhibited the differentiation of ES-D3 cells into beating cardiomyocytes. Upon bioactivation, BaP induced in vitro PDT, while its major metabolite 3-hydroxybenzo[a]pyrene was shown to be active in the EST as well. This indicates that BaP needs metabolic activation to exert its in vitro embryotoxic effect. The PS-induced PDT in the EST was not substantially changed following bioactivation, implying that metabolism may not play a crucial role for PS to exert their in vitro PDT effects. GTL extracts tested negative in the EST, with and without bioactivation. Altogether, although some PAH constituents require metabolic activation to be able to induce PDT, some do not and this latter also appeared to hold for the (majority of) the PS constituents responsible for the in vitro PDT of these complex substances.

    Chapter 7, first presented an overview of the results and main findings, which was combined with a general discussion of the data obtained and with future perspectives for follow-up studies to be performed in the near future. It was concluded that PAHs present in PS are the major inducers of PDT caused by these substances and that this was successfully and adequately assessed using several in vitro alternative assays, including the EST, ZET, and AhR CALUX assay. The results obtained in Chapter 2, 4, and 5 of the thesis were used in a QSAR (quantitative structure activity relationship) approach to predict the in vivo PDT of a series of PS based on their PAH content. More PS extracts, ideally from different PS categories than those tested in the present thesis, should be tested to broaden the applicability domain of the proposed assay battery and the related QSAR approach for PDT testing of PS UVCBs in the future.

    How fish larvae swim: from motion to mechanics
    Voesenek, Cees J. - \ 2019
    Wageningen University. Promotor(en): J.L. van Leeuwen, co-promotor(en): F.T. Muijres; G.J.F. van Heijst. - Wageningen : Wageningen University - ISBN 9789463439015 - 238
    cum laude

    Most of the world's 34,000 known fish species are undulatory swimmers. Their body undulations are produced by fluid-structure interaction between water and the body of the fish, powered by its muscle system. Despite these complex physics, just-hatched fish larvae can already produce effective swimming motion. How they do this is not yet fully understood. With this thesis, we aim to contribute to answering this question by examining the biomechanics of swimming of early-development larval zebrafish. With novel experimental and computational techniques, we reconstructed the dynamics of the larvae from high-speed video. These analyses highlight the challenges that larval fish face during swimming, and how the larvae have evolved to solve these challenges.

    In chapter 2 we reviewed the mechanics of swimming of larval fish. We examined the functional demands on the locomotory system of fish larvae: immediately after hatching, fish need to escape predators, search and hunt for food, and migrate and disperse. These demands need to be fulfilled by the larvae while undergoing large changes in their bodies, both internal and external. Furthermore, the swimming speed and size of many larvae causes them to be in the intermediate flow regime, where the nature of the flow changes considerably with changes in size or speed. In this chapter, we integrated previous literature to gain insight into how these functional demands on the locomotory system are met with the advantages and limitations of their developing bodies and the changing hydrodynamic regime.

    In chapter 3, we analysed near-periodic swimming of zebrafish larvae with two-dimensional inverse dynamics from motion that was manually tracked from high-speed video images. We used these data to show how the intermediate flow regime affects the swimming dynamics of fish larvae. We used the Reynolds number, which indicates the relative importance of viscous forces to inertial forces, to characterise the flow regime that the larvae swim in. Furthermore, we applied the Strouhal number, a measure of the ratio of the approximate lateral tail speed to the forward swimming speed, to express changes in swimming kinematics. We found that the Strouhal number depends inversely on the Reynolds number. Fish swimming at low Reynolds numbers tend to use relatively high Strouhal numbers, indicating that their tail-beat amplitude and frequency are high. Even the larvae swimming at the highest Reynolds numbers still use relatively high Strouhal numbers (around 0.72) compared to adult fish (typically 0.2–0.3). Swimming at intermediate Reynolds numbers is associated with high drag, requiring the larvae to use high tail-beat amplitudes and frequencies (and therefore Strouhal number) to produce sufficient thrust. This mode of swimming requires relatively high-amplitude yaw torques, resulting in large angular amplitudes and an expected high energetic cost of transport: the small size of the larvae is a burden to their swimming.

    Most of the previous research on fish swimming, including our chapter 3, has been done two-dimensionally. However, fish can perform complex, three-dimensional motions to escape predators, search or hunt for food, or manoeuvre through the environment. To expand our analyses to the third dimension, we developed a method to reconstruct the 3D motion of fish from multi-camera high-speed video, described in chapter 4. With an optimisation algorithm we find the 3D position, orientation, and body curvature that best fits the high-speed video frames. We demonstrated that the method allows us to reconstruct the swimming kinematics with high accuracy, while requiring minimal manual work. In addition, we developed a novel method to calculate resultant hydrodynamic forces and torques from the reconstructed motion. The described method is a valuable tool for analysing the biomechanics of swimming, providing data for future analyses of fish swimming.

    In chapter 5, we apply this automated tracking method to analyse fast starts of zebrafish larvae five days after fertilisation. To be able to escape predators, the main functional demands on a fast start are producing sufficient speed within a narrow time frame and being able to generate a wide range of escape directions. To investigate how these demands are met, we used a five-camera high-speed video of fast-starting zebrafish larvae with unprecedented spatiotemporal resolution. From these videos, we reconstructed the 3D motion of the larvae and the resultant hydrodynamic forces and torques. Due to their undulatory swimming style, the larvae first need to bend into a C-shape before being able to produce a propulsive tail beat. For this reason, the first stage of the start is often considered ‘preparatory’. Based on the reconstructed forces and torques, we show that the first stage of the start, in addition to its preparatory role, also serves to provide most of the reorientation of the start. After this stage, the larvae unfold their bodies, moving their tails at high speeds and thus producing large propulsive forces. The turn angle produced during a start mostly depends on the amount of body curvature in the first stage, while the escape speed mainly depends on the duration of the start. This suggests that larvae are able to independently adjust the direction and speed of their escape.

    Fish larvae are able to produce these escape responses and the subsequent swimming bout immediately after hatching, despite their bodies and brains still undergoing development. To understand how this is possible, we use an advanced inverse-dynamics approach, with computational fluid dynamics and a large-amplitude beam model, to reconstruct internal mechanics from the motion of the fish in chapter 6. We compute the internal bending moments from more than 100 3D-recordings of swimming over a range of developmental stages. We show that larvae use similar bending moment patterns across development, speeds and accelerations. By varying the amplitude and duration of this pattern, the larvae can adjust their swimming speed and/or acceleration. This similarity suggests that their muscle activation patterns are also similar, which would help to explain how just-hatched larvae with limited neural capacity can produce effective swimming motion across a range of speeds and accelerations.

    In this thesis, we demonstrated that larval fish swim in a challenging hydrodynamic regime. Despite the relatively high drag, they can produce effective swimming motions to help them survive to adulthood. We developed novel methods to quantify this motion in 3D, and from it reconstructed the external and internal mechanics. With these inverse-dynamics approaches, we show that fish larvae can likely adjust their swimming in a relatively simple way, for both fast starts and continuous swimming. Thus, complex physics do not obstruct developing larvae from swimming effectively.

    Getting a grip on tree frog attachment : structures, mechanisms, and biomimetic potential
    Schöning-Langowski, Julian K.A. - \ 2019
    Wageningen University. Promotor(en): J.L. van Leeuwen, co-promotor(en): D Dodou; M. Kamperman. - Wageningen : Wageningen University - ISBN 9789463431859 - 242
    cum laude

    Tree frogs are versatile climbers that use their adhesive digital pads to attach to various substrates, even under challenging conditions. The pads are covered in mucus and can generate adhesive and frictional forces of up to several body weights per digit. For centuries, the remarkable attachment performance of tree frogs has fascinated scientists who aimed to unravel the fundamentals of tree frog attachment. Among the various mechanisms that have been discussed to explain tree frog attachment, capillary adhesion is the most commonly used one. Previous research was primarily directed at the role of the micropatterned pad surface in attachment, which resulted in the development of several tree-frog-inspired micropatterned adhesives. However, a comprehensive explanation of the mechanisms of tree frog attachment is still unavailable, and the role of internal pad structures in attachment is barely understood. In this thesis, I present an interdisciplinary analysis of the attachment apparatus of tree frogs with focus on subepidermal structures, hence contributing to the understanding of nature’s adhesive systems, and providing input for the design of biomimetic adhesives inspired by tree frogs.

    In Chapter 2, we provided a synthesis of the status quo of knowledge on tree frog attachment—ranging from the functional pad morphology to experimental findings in support of the various hypothesised mechanisms of tree frog attachment—and identified gaps in the existing knowledge. An account of the functional morphology highlights the need for an exploration of the internal pad morphology and of the chemistry of the secreted mucus in order to deepen the understanding of tree frog attachment. By revisiting current analytical models, reported data, and observations, we show that the hypothesis of wet adhesion as primary mechanism in tree frog attachment is not sufficiently supported. Van der Waals forces, which were for a long time believed to play only a minor role due to mucus covering the pad surface, may well be involved in tree frog attachment.

    In Chapter 3, we combined histochemistry and synchrotron micro-computer-tomography to characterise the internal morphology of the digital pads of the tree frog Hyla cinerea in 3D, with a focus on mechanical links between the adhesive pad surface and the internal digital skeleton. The ventral pad surface connects to the skeleton via several pathways of force transmission. A collagenous septum runs from the ventral cutis to the tip of the distal phalanx and compartmentalises the subcutaneous pad volume into a distal lymph space and a proximal space filled with mucus glands. Moreover, a collagen layer runs from the ventral cutis via interphalangeal ligaments to the middle phalanx. The fibres constituting this layer run in trajectories curved around the transverse pad-axis and form laterally separated ridges below the gland space. Using finite element analysis and numerical optimisation of a shear-loaded pad model, we show that the collagen fibres are presumably oriented along the trajectories of the maximum principal stresses, and the optimisation also results in ridge-formation, suggesting that the collagen layer is adapted towards a high stiffness during shear loading. Finally, immunohistochemical staining reveals the presence of several units of smooth muscle fibres in frog pads. These active structures may provide tree frogs with the ability to control the distribution of mechanical stresses across the ventral pad surface, hence facilitating modulation of the attachment strength.

    Chapter 4 addresses the morphology of the digital mucus glands and the chemistry of the secreted mucus. In H. cinerea, the mucus glands opening to the ventral pad surface form a macrogland and thus differ significantly in their morphology from the ones opening to the dorsal (non-adhesive) pad surface. We identified a digital mucus macrogland in min. 10 neobatrachian families that are not exclusively arboreal, indicating that the macrogland morphology is determined by generic functional requirements arising from ‘ground contact’ (e.g. lubrication and compensation of mucus loss) as well as by specific requirements for climbing and attachment. Using cryo-histochemistry as well as infrared and sum frequency generation spectroscopy, we show that—in contrast to the gland morphology—the general mucus chemistry varies only little between different body locations in the tree frogs H. cinerea and Osteopilus septentrionalis, as well as between arboreal and non-arboreal (Pyxicephalus adspersus and Ceratophrys cranwelli) frog species. This observation suggests conservation of the mucus chemistry in the course of anuran evolution and does not support a specialisation of the mucus towards attachment.

    In Chapter 5, we experimentally measured the attachment performance of the tree frogs H. cinerea and Litoria caerulea using a rotation platform setup. By analysing the effects of variations in nominal substrate roughness on attachment performance, we investigated the role of the previously proposed mechanism of mechanical interlocking in tree frog attachment. Tree frogs attach as well to nano- and microrough substrates as to a smooth substrate. Attachment performance only decreases above a nominal substrate roughness of 15 µm. These observations disagree with the expected variation of attachment performance with substrate roughness if interlocking were present, hence indicating that mechanical interlocking is negligible in tree frog attachment. Furthermore, observations of detaching frogs with our updated rotation platform setup show that tree frogs are able to withstand substantial inertial loads with only two attached limbs, suggesting that the maximum attachment performance of tree frogs is higher than reported previously.

    Finally, I put in Chapter 6 the findings of this thesis in a wider scientific context. By integrating the outcomes of the review on tree frog attachment with the results of the experimental chapters and with insights obtained on tree-frog-inspired adhesives, I discuss the importance of the previously proposed mechanisms of tree frog attachment. I conclude that suction and mechanical interlocking are negligible. A contribution of hydrodynamic adhesion cannot be excluded, but seems to be a consequence of having a wet skin rather than a primary attachment mechanism. Whereas capillary adhesion was previously mentioned as primary adhesion mechanism, an integration of the available knowledge suggests that capillary adhesion acts together with van der Waals forces, with the latter as dominant attachment mechanism. To explore the hypothesised convergent evolution of the digital pads of tree frogs, I provide an account of what is known from this thesis and earlier works on the phylogeny of the adhesive pads. Overall, several morphological features (e.g. the micropatterned pad surface and the digital gland cluster) are widely distributed over anuran families, suggesting that the whole pad is a functional unit and raising the question if the pads evolved convergently or if they are derived from a common ancestor. In agreement with the antecedent sections, a tentative discussion of the evolutionary history of frog pads emphasises the importance of drainage, friction generation, and van der Waals forces in tree frog attachment. Based on the outcomes of this thesis, I provide suggestions for the design of tree-frog-inspired adhesives. The drainage-capabilities of frog pads render these a good model for the development of technical adhesives in a wet environment. Further promising trends are the design of fibre-reinforced micropatterned adhesives for heavy duty applications, and the creation of actuated adhesives with controllable adhesion inspired by the muscular structures found in the biological model. Finally, I present an outlook on how the field of tree frog attachment may develop in the coming years.

    Quantifying evolution in wild populations
    Ramakers, Jip Jacques Claudia - \ 2019
    Wageningen University. Promotor(en): M.E. Visser, co-promotor(en): P. Gienapp. - Wageningen : Wageningen University - ISBN 9789463439206 - 277
    cum laude

    The environment is changing and this is exerting selection pressures on wild populations. For example, the timing of phenological events such as reproduction and migration are driven by temperatures and climate change is leading to a differential shift in timing of phenology among trophic levels, in some cases leading to selection on consumer phenology. Individuals are often phenotypically plastic, meaning that they can change their phenotype (e.g. breeding time) in response to environmental conditions. This allows them to track the changing environment to some degree but ultimately a genetic change is necessary to safeguard populations from extinction in the long run. Many wild populations so far, however, could not be shown to be undergoing any genetic adaptation (e.g. a shift in their phenology) over time. Quantitative genetics, i.e. the study of the genetics of quantitative (polygenic) traits, is commonly used to identify the evolutionary parameters (genetic variation and selection) in wild populations to predict evolution, but for such predictions to be successful we need to understand the ecological factors underlying (constraints to) adaptation. In this thesis, I aimed to get an understanding of how populations are coping with environmental change and which ecological processes affect the rate of adaptation. I did this using a combined approach of field experiments to identify ecological constraints and long-term observations to make evolutionary predictions in the great tit (Parus major) and other vertebrate species.

    In the first part of my thesis (Chapter 2), I provided a broad overview of what is known about the effects of climate change on the general biology of birds. Birds are affected by climate change in several ways: they may change (1) their geographical distribution due to a shifting ‘bioclimatic envelope’, (2) advance their timing of phenological events such as breeding and migration, (3) undergo morphological changes (e.g. in body size) as an energetic adaptation, and (4) undergo demographic changes as a direct result of changes in reproductive success or survival. There has been a strong bias in the literature on phenology and therefore we still have a lot to learn about the ecological and evolutionary consequences related to these other aspects of phenotypic change. Whether observed changes in phenology are due to plasticity or due to genetic change remains an open question.

    Dutch great tits have been under increased selection for earlier laying due to increased mismatch with the caterpillar peak (the main food for their nestlings), but we see little (phenotypic) response. The lack of a response may be caused by an energetic constraint associated with breeding too early under harsh conditions, such that birds that do breed earlier may pay fitness costs. In the second part of my thesis I aimed to test whether birds were constrained to breed earlier. In Chapter 3, I used experimental food supplementation food prior to and during egg-laying to test whether females that were tricked into laying early would pay fitness costs (due to brood desertion or reduced chick-provisioning efforts) once food supplementation ceased upon the start of laying. Food supplementation was not effective at advancing laying, and any food increased, rather than decreased, fitness. Because food supplementation alone is not sufficient to test the constraints hypothesis (e.g. because it cannot distinguish whether birds are constrained by food or are just missing the essential cues to advance their breeding) we need an additional, clean manipulation of egg-laying date that does not affect the body condition of a female. In Chapter 4, I described the first results of a large-scale experiment in which great tits are genomically selected to breed early or late. Eggs produced by females from these selection lines were brought to the wild and raised by foster parents. I showed that selection lines (late vs early) did not differ in any aspect of early-life fitness (fledging success, nestling weight at fledging), but that the fitness parameters differed slightly between selection-line birds and their wild counterparts. Since only 11 birds from these fostered birds survived until breeding in 2018 (including 2 females from the early and 3 from the late selection line), we could not test whether these birds indeed bred respectively earlier or later, or whether earlier laying indeed led to higher fitness costs. I concluded that multiple years (with different environmental conditions and an increased sample size) would be needed to conclude whether birds are indeed constrained to breed earlier.

    Ultimately, breeding success in great tits is largely determined by the match of the offspring needs with the caterpillar abundance. In Chapter 5, I explored the notion that to clearly understand phenological mismatch—and to determine whether birds really are mismatched—we need a thorough, temporal description of offspring needs and food availability to quantify the amount of temporal overlap between these distributions. I found that the classical way of defining mismatch, i.e. the difference in peak dates between great tit and caterpillar phenology, outperformed a more comprehensive measure that described the temporal overlap in a model explaining variation in offspring survival and selection for laying date. I concluded that a simple measure of mismatch in highly seasonal study systems is likely to be best for describing demographic processes, and that more complex measures are likely infeasible in most practical situations.

    In the third part of my thesis, I deployed state-of-the-art quantitative genetic modelling approaches to unravel patterns of selection, genetic variation, and evolutionary response to selection in a reaction-norm context using long-term, pedigreed datasets of wild populations. Some methods to achieve this were explored in the preceding Intermezzo (Chapter 6 and 7). In Chapter 8, I investigated whether maternal effects as a form of transgenerational plasticity could affect the rate of adaptation in great tits. Using experimental and long-term data, I was able to show that the clutch size of a great tit is partly dependent on her body weight at fledgling and that it is negatively associated with the clutch size of her own mother. Such a negative maternal effect could constrain adaptation to a novel environment with selection for a larger of smaller clutch. We showed by simulation, however, that this negative maternal effect would likely have little impact on the rate of adaptation.

    Phenological changes over time do not always match evolutionary predictions; one potential reason for this discrepancy is an unrecognised environmentally induced coupling between selection and the heritability of the trait. In Chapter 9, I investigated how general such a coupling is in wild vertebrate populations, and whether such a coupling affects the expected rate of adaptation. The expectation was that if heritability and selection are negatively associated, this constrains adaptation because little genetic variation is present under strong selection and vice versa. Making use of openly available datasets (see Chapter 7), we managed to estimate environment-specific heritability and selection in 50 traits from 16 populations of 10 species. We found that heritability and selection are only rarely associated and that this association is an unlikely explanation for apparent evolutionary stasis observed in wild populations.

    Great tits respond strongly to temperature through phenotypic plasticity; this plasticity is described by a reaction norm, the linear function consisting of an elevation (the laying date in the average environment) and a slope (the sensitivity to the environment). Since different individuals have different reaction norms, selection on laying date may result in an evolutionary shift in the reaction norm. In Chapter 10, I found that individual great tits differ genetically in the elevation of the reaction norm, but not in its slope, and this reaction norm is under selection due to the advance in the caterpillar peak over time. I predicted quantitatively, however, that such evolution has been—and will be—too slow to be detected due to the high environmental variability in laying dates.

    To conclude, I investigated the evolutionary potential of populations and aimed to identify ecological constraints in adaptation. I found that there is still a lot we need to learn about the ecological and evolutionary consequences of climate change beyond the few well-known study systems, including effects on demography and population viability. Experiments aimed at unravelling the fitness costs of breeding too early are inconclusive and warrant further investigation (with more samples and multiple environments). Powerful quantitative genetic tools are available to evolutionary ecologists to quantify evolutionary trajectories but these models must be based on reality to obtain reliable predictions. I have suggested in this thesis that realistic predictions could be benefited by the integration of multiple data sources (i.e. long-term observational and experimental data) and simulations. The use of open data can aid in achieving this through the answering of novel research questions at a broad taxonomic or geographic scale. Most importantly, we need a thorough understanding of the most important components of the ecosystem of our study species. Only then can we make sense of our evolutionary predictions.

    Multi-scale monitoring and modelling of the Kapuas River Delta
    Kästner, Karl - \ 2019
    Wageningen University. Promotor(en): A.J.F. Hoitink; R. Uijlenhoet. - Wageningen : Wageningen University - ISBN 9789463434119 - 215
    cum laude
    Rivers in the humid tropics are those with the largest discharges and sediment loads of the world. Their evergreen and ever wet catchments are hotspots of biodiversity and their fertile deltas are acres of plenty for the production of rice, palm oil and rubber. At present, tropical rivers, their catchments, and deltas face growing pressure from rapid economic development and climate change, which may permanently deteriorate their ecosystem services. Yet,despite their importance and advancing degradation, relatively little is known about their physiography. This thesis reduces this gap by contributing to our fundamental understanding of tropical rivers.This thesis in particular addresses fundamental questions regarding the hydro- and morphodynamics of large sand-bedded rivers and their tidally influenced deltas: How can river and tidal discharge be effectively measured? How do the cross-section geometry and bed material change along the fluvial-tidal transition? How do these trends differ between the distributaries? How does the tide propagate up-river river? How can sediment transport be efficiently measured with acoustic instruments? How are the discharge and the sediment divided at river bifurcations? To address these questions, the author undertook a year-long journey to West Kalimantan, during which he surveyed and monitored the Kapuas River. The Kapuas River is nearly pristine and thus gives a rare insight into the hydro- and morphodynamics of a river that has not yet been restricted by either dams, dykes or groins. Findings from the survey of the Kapuas River are generalized with idealized models.
    Feel the burn: a collection of stories on hot’n’sharp DNA engineering
    Mougiakos, Ioannis - \ 2019
    Wageningen University. Promotor(en): J. van der Oost; R. van Kranenburg. - Wageningen : Wageningen University - ISBN 9789463434096 - 301
    cum laude

    The global demand on chemicals and fuels is exponentially increasing. At the same time, the excessive exploitation of fossil-based resources for the coverage of this demand has a high environmental impact, motivating the production of green chemicals and biofuels from renewable resources. Nowadays, the microbial production of green chemicals and fuels gains increasing attention, especially due to the ease in the construction of metabolically engineered microorganisms with high production capacities. This ease was achieved via the development of efficient genome engineering tools. This thesis describes the development of novel genetic tools for mesophilic and thermophilic bacteria, for metabolic engineering purposes. More specifically, here is reported: 1) the development of the first CRISPR-SpCas9-based genome engineering tools for the mesophilic bacteria Rhodobacter sphaeroides and Pseudomonas putida, as well as for the moderate thermophilic bacterium Bacillus smithii, 2) the in vitro characterization of one of the first reported thermotolerant Cas9 homologs, denoted as ThermoCas9, as well the development of the first CRISPR-ThermoCas9-based genome engineering tools for strictly thermophilic bacteria, and 3) the use of the developed tools for the metabolic exploration and exploitation of the moderate thermophilic bacterium B. smithii, towards the characterization of its acetate production pathway and the enhancement of its dicarboxylic acids productivity.

    Injecting spatial priors in Earth observation with machine vision
    Gonzalez, Diego - \ 2019
    Wageningen University. Promotor(en): D. Tuia. - Wageningen : Wageningen University - ISBN 9789463435604 - 130
    cum laude

    Remote Sensing (RS) imagery with submeter resolution is becoming ubiquitous. Be it from satellites, aerial campaigns or Unmanned Aerial Vehicles, this spatial resolution allows to recognize individual objects and their parts from above.

    This has driven, during the last few years, a big interest in the RS community on Computer Vision (CV) methods developed for the automated understanding of natural images.

    A central element to the success of \CV is the use of prior information about the image generation process and the objects these images contain: neighboring pixels are likely to belong to the same object; objects of the same nature tend to look similar with independence of their location in the image; certain objects tend to occur in particular geometric configurations; etc.

    When using RS imagery, additional prior knowledge exists on how the images were formed, since we know roughly the geographical location of the objects, the geospatial prior, and the direction they were observed from, the overhead-view prior.

    This thesis explores ways of encoding these priors in CV models to improve their performance on RS imagery, with a focus on land-cover and land-use mapping.

    Exploration of microbial systems as biocatalysts for conversion of synthesis gas to bio-based chemicals
    Diender, Martijn - \ 2019
    Wageningen University. Promotor(en): A.J.M. Stams, co-promotor(en): D.Z. Machado de Sousa. - Wageningen : Wageningen University - ISBN 9789463433914 - 204
    cum laude

    Synthesis gas (syngas) fermentation is a process capable of processing a gaseous substrate via fermentation into commodity chemicals and fuels. Gas (mainly consisting of hydrogen, carbon monoxide and carbon dioxide) fed to the fermentation process can be obtained from a wide variety of sources, including off-gases from industry, gasification of solid carbon wastes (e.g. municipal waste, lignocellulosic biomass) or gas derived from electrochemical reduction/physicochemical reduction processes.

    Current limitations of the fermentation process are the relatively poorly understood physiology and genetics of the biocatalysts involved. Therefore the work described in this thesis aimed at unravelling of the syngas metabolism of acetogenic and methanogenic strains, with main focus on carbon monoxide metabolism. In addition, the application of synthetic co-cultures for syngas fermentation was explored in order to assess if such cultivation approach could lead to broadening of the syngas fermentation product spectrum. In addition to co-cultivation proof-of-concept studies for application, new fundamental insights on the metabolism of the involved biocatalysts were obtained.

    A FAIR approach to genomics
    Koehorst, Jasper Jan - \ 2019
    Wageningen University. Promotor(en): V.A.P. Martins dos Santos, co-promotor(en): P.J. Schaap; E. Saccenti. - Wageningen : Wageningen University - ISBN 9789463433693 - 245
    cum laude

    The aim of this thesis was to increase our understanding on how genome information leads to function and phenotype. To address these questions, I developed a semantic systems biology framework capable of extracting knowledge, biological concepts and emergent system properties, from a vast array of publicly available genome information. In chapter 2, Empusa is described as an infrastructure that bridges the gap between the intended and actual content of a database. This infrastructure was used in chapters 3 and 4 to develop the framework. Chapter 3 describes the development of the Genome Biology Ontology Language and the GBOL stack of supporting tools enforcing consistency within and between the GBOL definitions in the ontology (OWL) and the Shape Expressions (ShEx) language describing the graph structure. A practical implementation of a semantic systems biology framework for FAIR (de novo) genome annotation is provided in chapter 4. The semantic framework and genome annotation tool described in this chapter has been used throughout this thesis to consistently, structurally and functionally annotate and mine microbial genomes used in chapter 5-10. In chapter 5, we introduced how the concept of protein domains and corresponding architectures can be used in comparative functional genomics to provide for a fast, efficient and scalable alternative to sequence-based methods. This allowed us to effectively compare and identify functional variations between hundreds to thousands of genomes. In chapter 6, we used 432 available complete Pseudomonas genomes to study the relationship between domain essentiality and persistence. In this chapter the focus was mainly on domains involved in metabolic functions. The metabolic domain space was explored for domain essentiality and persistence through the integration of heterogeneous data sources including six published metabolic models, a vast gene expression repository and transposon data. In chapter 7, the correlation between the expected and observed genotypes was explored using 16S-rRNA phylogeny and protein domain class content as input. In this chapter it was shown that domain class content yields a higher resolution in comparison to 16S-rRNA when analysing evolutionary distances. Using protein domain classes, we also were able to identify signifying domains, which may have important roles in shaping a species. To demonstrate the use of semantic systems biology workflows in a biotechnological setting we expanded the resource with more than 80.000 bacterial genomes. The genomic information of this resource was mined using a top down approach to identify strains having the trait for 1,3-propanediol production. This resulted in the molecular identification of 49 new species. In addition, we also experimentally verified that 4 species were capable of producing 1,3-propanediol.

    As discussed in chapter 10, the here developed semantic systems biology workflows were successfully applied in the discovery of key elements in symbiotic relationships, to improve functional genome annotation and in comparative genomics studies. Wet/dry-lab collaboration was often at the basis of the obtained results.

    The success of the collaboration between the wet and dry field, prompted me to develop an undergraduate course in which the concept of the “Moist” workflow was introduced (Chapter 9).

    Vision principles for harvest robotics : sowing artificial intelligence in agriculture
    Barth, Ruud - \ 2018
    Wageningen University. Promotor(en): E.J. van Henten, co-promotor(en): J. Hemming. - Wageningen : Wageningen University - ISBN 9789463433181 - 325
    cum laude

    The objective of this work was to further advance technology in agriculture, specifically by pursuing the research direction of agricultural robotics for harvesting in greenhouses, with the specific use-case of Capsicum annuum, also known as sweet or bell pepper. Within this scope, it was previously determined that the primary cause of agricultural robotics not yet maturing was the complexity of the tasks due to inherent variations of the crops, in turn limiting performance in harvest success and time. As a solution, it was suggested to further enhance robotic systems with sensing, world modelling and reasoning, for example by pursuing approaches like machine learning and visual servo control. In this work, we have followed this suggestion. It was identified that facilitating new levels of artificial intelligence in the domains of sensing and motion control would be one of the ways to improve upon classical mechanization. Specifically, we investigated the means of using machine learning based computer vision guided manipulation towards a basic form of world representation and autonomy. For this, in Chapter 2 we developed an eye-in-hand sensing and visual control framework for dense crops with the goal to overcome issues of occlusion and image registration that were previously introduced when sensing was performed externally from the robot manipulator. Additionally, simultaneous localization and mapping was investigated to aid in forming a world model. In Chapter 3 we aimed to reduce the requirement of annotating empirical images by providing a method to synthetically generate large sets of automatically annotated images as input for convolutional neural network (CNN) based segmentation models. An annotated dataset was created of 10,500 synthetic and 50 empirical images. In Chapter 4 we further investigated how synthetic images can be used to bootstrap CNNs for successful learning of empirical images. We provided computer vision in agriculture a pioneering machine learning based methodology for state-of-the-art plant part segmentation performance, whilst simultaneously reducing the reliance on labor intensive manual annotations. Chapter 5 explored applying a cycle consistent generative adversarial network to our dataset with the objective to generate more realistic synthetic images by translating them to the feature distribution of the empirical domain. We show that this approach can further improve segmentation performance whilst further reducing the requirement of annotated empirical images. In Chapter 6 we aimed to bring all previous chapters into practice. The objective was to estimate angles between fruit and stems from image segmentations to support visual servo control grasping in a sweet-pepper harvesting robot. Our approach calculated angles under unmodified greenhouse conditions that met the accuracy requirement of 25 degrees for 73% of the cases. Combined, the work shows a promising stepping stone towards agricultural robotics which could ensure the quality of meals and nourishment of a growing population. Furthermore, it can become an important technology for societal issues in developed nations, e.g. by solving current labor problems. It can further improve upon the quality of life and contribute to reaching an exemplary equilibrium of sustainable agricultural production.

    Creation of fibrous plant protein foods
    Dekkers, Birgit L. - \ 2018
    Wageningen University. Promotor(en): A.J. van der Goot; R.M. Boom. - Wageningen : Wageningen University - ISBN 9789463433198 - 204
    cum laude

    A transition from animal to plant-based protein is required to produce sufficient protein for the growing world population, while at the same time mitigates climate change. Especially the production of meat imposes a burden on the environment. Meat analogues, which are products that are similar to meat in its functionality, can help consumers to lower their meat consumption. The anisotropic, fibrous nature of meat is perhaps the most important characteristic of meat, which can be mimicked by structuring biopolymers, such as proteins and polysaccharides with the shear cell technology. The aim of this thesis is to obtain insight in the key mechanisms that play a role in the transformation of plant-based biopolymer blends into anisotropic/fibrous structures with shear cell technology. These two key mechanisms are the deformation of the two phases present in biopolymer blends, and the subsequent entrapment of this deformation during solidification. It was concluded that successful structure formation requires matching of the properties of the two phases. During structuring at elevated temperature, the two phases are deformed, while subsequent cooling ensures entrapment of the deformed dispersed phase(s) in the (continuous) phase. Ideally, the continuous and dispersed phase have different strength in the final product,.

    Chapter 2 presents a method to determine the water distribution in soy protein isolate (SPI) – wheat gluten (WG) blends. The concentration of water in each separate phase was directly determined with time-domain nuclear magnetic resonance relaxometry (TD-NMR), and oscillatory rheology was used to indirectly asses the water distribution by determining the viscoelastic properties of the separate phases and the blend. It was shown that water distributes unevenly in SPI-WG blends: more water was absorbed by the SPI as compared to the WG phase. This methodology was developed for SPI-WG blends at room temperature and subsequently also applied to heated and sheared samples in Chapter 3. First, water distribution in the blend after a heat and/or shear treatment was assessed with TD-NMR and the outcomes were then used to predict the viscoelastic properties of the SPI and WG phase in the blend. This yielded insight in the deformability of the two phases in the blend. The viscoelastic properties were measured under conditions that are relevant for structure formation, i.e. during and after heating and shearing. It was shown that the water distribution was hardly affected by a heat or shear treatment, whereas the viscoelastic properties of the two phases changed significantly. The viscoelastic properties of SPI and WG became more similar due to water redistribution in the blend, which allows deformation and alignment of the dispersed phase during structuring.

    Chapter 4 describes a study using a model blend that mimics soy protein concentrate (SPC). It consists of a relatively pure protein phase, soy protein isolate (SPI), and a soluble, more or less pure polysaccharide phase, pectin. This SPI-pectin blend formed fibrous materials at a similar heating temperature as SPC, being 140°C. Pectin formed the dispersed phase and was deformed when heated and sheared at optimal conditions. Chapter 5 extends the study on structure formation with SPI-pectin blends. Here, the deformation of the dispersed pectin phase and the influence of incorporated air were considered. The fibrous nature of these products appears upon tearing, and originates from detachment through or along the long side of the weak dispersed phase(s), being pectin and/or air. A model based on the rule of mixing was used to predict the mechanical anisotropy based on the volume fraction and the deformation of the weak, dispersed phase. The size and orientation of the dispersed phases, tailored by using different shear rates, were related to differences in fracture behavior when deforming the structures. Besides deformation, the strength and volume fraction of the weak phase(s) were important when composing a blend for fibrous structure formation. In Chapter 6, the behavior of the SPI and pectin phases in a blend was investigated by determining the viscoelastic properties while shearing and heating over time. A closed cavity rheometer (CCR) was used to determine these properties under similar conditions as used during fibrous structure formation. The addition of a small amount of pectin (2.2 wt.%) to a SPI dispersion (41.8 wt.%) resulted in viscoelastic behavior that changed in time during a shear treatment at elevated temperatures. Although one can clearly discern two distinct phases with SEM, the viscoelastic behavior of the SPI-pectin blend is more complex than that of a simple composite material.

    Chapter 7 demonstrates the importance of the fractionation process on the structuring potential of soy proteins. An enriched soy protein fraction was obtained through an aqueous fractionation process. Those fractions could be used to make fibrous structures when: i) the soy protein fractions were toasted, which is a dry heating step, and ii) when a concentrate (75% protein) was combined with full fat flour, in such a ratio that the protein content was similar to commercial SPC. Toasting results in decreased protein solubility, increased water holding capacity and increased viscosity of the fractions, and these changes turned out to be important for fibrous structure formation.

    Lastly, literature was reviewed to put all findings in perspective (Chapter 8). An overview is presented of all techniques that are commercially used and currently investigated to create meat-like structures. Structuring techniques are compared in their approach, being either bottom-up, which refers to assembly of structural elements that are then combined, or top-down, which refers to structuring of biopolymer blends using an overall force field. A bottom-up strategy has the potential to resemble the structure of meat most closely, by structuring the molecules including proteins into structural components (e.g. muscle cells) followed by assembly of individual structural components. A top-down strategy is more efficient in its use of resources and is better scalable, but can only create the desired structure on larger length scales. The techniques with a top-down strategy were further investigated by reviewing literature on similar processes outside this particular field of application, i.e. not meant to create fibrous structures. These insights were subsequently translated to the conditions as used in structure formation for meat analogues.

    Chapter 9 concludes with a general discussion of all results presented in this thesis. The different chapters are integrated in design rules for fibrous structure formation. Furthermore, the complexity encountered when studying material and conditions during fibrous structure formation are discussed. Then, the potential and the challenges for understanding and applying fibrous structure formation with simple shear flow are summarized.

    The overall societal goal of developing meat analogue food products is to help consumers in the transition from animal-based to a more plant-based diet. The scientific goal to obtain insight in fibrous structure formation with the shear technology as developed in this thesis is of importance, and can be the basis for developing the technology for the next generation meat analogues.

    Encapsulation of lipids to delay lipolysis and reduce food intake
    Corstens, Meinou N. - \ 2018
    Wageningen University. Promotor(en): C.G.P.H. Schroën; A.A.M. Masclee, co-promotor(en): C.C. Berton-Carabin; F.J. Troost. - Wageningen : Wageningen University - ISBN 9789463432382 - 200
    cum laude

    My PhD project aimed at developing an edible product for non-invasive weight management, and targeted a natural feedback mechanism to induce satiety: the ileal brake. In order to trigger the ileal brake mechanism, lipids and their non-absorbed metabolites need to be sensed in the ileum. We aimed at inducing this mechanism through targeted release of lipids after oral intake, for which we developed multi-layered emulsions and emulsion-alginate beads. We showed that emulsion-alginate beads control in vitro lipolysis as a function of bead size and alginate concentration, and confirmed these findings under dynamic in vitro gastrointestinal conditions (DIDGI). Moreover, ingestion of yoghurt with emulsion-alginate beads significantly reduced food intake by 6% in overweight volunteers compared to a control group, suggesting that activation of the ileal brake was achieved. These findings have important implications for the development of weight management strategies, and understanding satiety in general.

    Cryptosporidium in rivers of the world: the GloWPa-Crypto model
    Vermeulen, Lucie C. - \ 2018
    Wageningen University. Promotor(en): C. Kroeze; G.J. Medema, co-promotor(en): N. Hofstra. - Wageningen : Wageningen University - ISBN 9789463438209 - 236
    cum laude

    Diarrhoeal disease is very common around the world. Knowing more about the global burden of diarrhoeal disease and about the geographical distribution of pathogen pollution is important for decision making and water and sanitation planning. The objective of this thesis is to increase knowledge on the sources, fate and transport of Cryptosporidium in rivers worldwide using spatially explicit modelling. I present the Global Waterborne Pathogen model for Cryptosporidium (GloWPa-Crypto), the first global model of waterborne pathogen emissions to and concentrations in rivers. The model is used to provide information on pathogen concentrations in data-sparse regions, identify hotspot regions, identify the relative contribution of different sources, and in scenario analysis to study the impacts of global change or management strategies. Furthermore, the model can be applied in the analysis of risk, burden of disease and health-based treatment targets, and make a valuable contribution in meeting the Sustainable Development Goals.

    The art of being small : brain-body size scaling in minute parasitic wasps
    Woude, Emma van der - \ 2017
    Wageningen University. Promotor(en): M. Dicke, co-promotor(en): H.M. Smid. - Wageningen : Wageningen University - ISBN 9789463436564 - 231
    brain - insects - neurons - scaling - cognitive development - vespidae - parasitoid wasps - cum laude - hersenen - insecten - neuronen - schaalverandering - cognitieve ontwikkeling - vespidae - sluipwespen

    Haller’s rule states that small animals have relatively larger brains than large animals. This brain-body size relationship may enable small animals to maintain similar levels of brain performance as large animals. However, it also causes small animals to spend an exceptionally large proportion of energy on the development and maintenance of energetically expensive brain tissue. The work that is presented in this thesis reveals how the smallest animals face the challenge to maintain ecologically required levels of cognitive performance, while being limited by small numbers of neurons and a restricted energy balance. Developing into a small adult has cognitive costs for the parasitic wasp Nasonia vitripennis, and relative brain size is strongly constrained in this species. The extremely small parasitic wasp Trichogramma evanescens forms an exception to Haller’s rule by showing isometric brain-body size scaling. Miniaturized insect species may apply this strategy to avoid the excessive energetic costs of relatively large brains, thereby achieving smaller brain and body sizes than would be possible in the situation that is described by Haller’s rule. This brain-scaling strategy does not result in affected memory performance of small T. evanescens compared to larger individuals, and appears to be facilitated by a large flexibility in the size of neural components, rather than in their number or structural complexity. Maintaining neural complexity may the underlying mechanism that maintains the cognitive abilities of the smallest brains, possibly at the cost of reduced longevity as a consequence of the small size of neuronal cell bodies. This strategy could form the art of being small.

    Rural livelihoods and agricultural commercialization in colonial Uganda: conjunctures of external influences and local realities
    Haas, Michiel A. de - \ 2017
    Wageningen University. Promotor(en): E.H.P. Frankema, co-promotor(en): N.B.J. Koning. - Wageningen : Wageningen University - ISBN 9789463436281 - 250
    cum laude - livelihoods - livelihood strategies - communities - rural areas - farmers - history - colonies - colonialism - income - gender - social inequalities - food crops - cash crops - uganda - east africa - middelen van bestaan - strategieën voor levensonderhoud - gemeenschappen - platteland - boeren - geschiedenis - kolonies - kolonialisme - inkomen - geslacht (gender) - sociale ongelijkheden - voedselgewassen - marktgewassen - uganda - oost-afrika

    The economic history of Sub-Saharan Africa is characterized by geographically and temporally dispersed booms and busts. The export-led ‘cash-crop revolution’ in parts of Sub-Saharan Africa during the colonial era is a key example of an economic boom. This thesis examines how external influences and local realities shaped the nature, extent and impact of the ‘cash-crop revolution’ in colonial Uganda, a landlocked country in central east Africa, where cotton and coffee production for global markets took off following completion of a railway to the coast. The thesis consists of five targeted ‘interventions’ into contemporary debates of comparative African development. Each of these five interventions is grounded in the understanding that the ability of rural Africans to respond to and benefit from trade integration during the colonial era was mediated by colonial policies, resource endowments and local institutions.

    The first chapter reconstructs welfare development of Ugandan cash-crop farmers. Recent scholarship on historical welfare development in Sub-Saharan Africa has uncovered long-term trends in standards of living. How the majority of rural dwellers fared, however, remains largely elusive. This chapter presents a new approach to reconstructing rural living standards in a historical context, building upon the well-established real wage literature, but moving beyond it to capture rural realities, employing sub-national rural survey, census, and price data. The approach is applied to colonial and early post-colonial Uganda (1915–70), and yields a number of findings. While an expanding smallholder-based cash-crop sector established itself as the backbone of Uganda’s colonial economy, farm characteristics remained largely stagnant after the initial adoption of cash crops. Smallholders maintained living standards well above subsistence level, and while the profitability of cash crops was low, their cultivation provided a reliable source of cash income. At the same time, there were pronounced limits to rural welfare expansion. Around the time of decolonization, unskilled wages rose rapidly while farm incomes lagged behind. As a result, an urban–rural income reversal took place. The study also reveals considerable differences within Uganda, which were mediated to an important extent by differential resource endowments. Smallholders in Uganda’s banana regions required fewer labour inputs to maintain a farm income than their grain-farming counterparts, creating opportunities for additional income generation and livelihood diversification.

    The second chapter zooms in on labour migration which connected Belgian-controlled Ruanda-Urundi to British-controlled Buganda, the central province of Uganda on the shores of Lake Victoria. The emergence of new labour mobility patterns was a key aspect of economic change in colonial Africa. Under conditions of land abundance and labour scarcity, the supply of wage labour required either the ‘pull’ forces of attractive working conditions and high wages, or the ‘push’ forces of taxation and other deliberate colonial interventions. Building upon primary sources, I show that this case diverges from the ‘conventional’ narrative of labour scarcity in colonial Africa. I argue that Ruanda-Urundi should be regarded as labour abundant and that migrants were not primarily ‘pushed’ by colonial labour policies, but rather by poverty and limited access to agricultural resources. This explains why they were willing to work for low wages in Buganda. I show that African rural employers were the primary beneficiaries of migrant labour, while colonial governments on both sides of the border were unable to control the course of the flow. As in the first chapter, this chapter highlights that the effects of trade integration on African rural development were uneven, and mediated by differences in resource endowments, local institutions and colonial policies.

    The third chapter zooms out of the rural economy, evaluating the broader opportunity structures faced by African men and women in Uganda, and discussing the interaction of local institutions and colonial policies as drivers of uneven educational and occupational opportunities. The chapter engages with a recent article by Meier zu Selhausen and Weisdorf (2016) to show how selection biases in, and Eurocentric interpretations of, parish registers have provoked an overly optimistic account of European influences on the educational and occupational opportunities of African men and women. We confront their dataset, drawn from the marriage registers of the Anglican Cathedral in Kampala, with Uganda’s 1991 census, and show that trends in literacy and numeracy of men and women born in Kampala lagged half a century behind those who wedded in Namirembe Cathedral. We run a regression analysis showing that access to schooling during the colonial era was unequal along lines of gender and ethnicity. We foreground the role of Africans in the spread of education, argue that European influences were not just diffusive but also divisive, and that gender inequality was reconfigured rather than eliminated under colonial rule. This chapter also makes a methodological contribution. The renaissance of African economic history in the past decade has opened up new research avenues to study the long-term social and economic development of Africa. We show that a sensitive treatment of African realities in the evaluation of European colonial legacies, and a critical stance towards the use of new sources and approaches, is crucial.

    The fourth chapter singles out the role of resource endowments in explaining Uganda’s ‘cotton revolution’ in a comparative African perspective. Why did some African smallholders adopt cash crops on a considerable scale, while most others were hesitant to do so? The chapter sets out to explore the importance of factor endowments in shaping the degrees to which cash crops were adopted in colonial tropical Africa. We conduct an in-depth case study of the ‘cotton revolution’ in colonial Uganda to put the factor endowments perspective to the test. Our empirical findings, based on an annual panel data analysis at the district-level from 1925 until 1960, underscore the importance of Uganda’s equatorial bimodal rainfall distribution as an enabling factor for its ‘cotton revolution’. Evidence is provided at a unique spatial micro-level, capitalizing on detailed household surveys from the same period. We demonstrate that previous explanations associating the variegated responses of African farmers to cash crops with, either the role of colonial coercion, or the distinction between ‘forest/banana’ and ‘savannah/grain’ zones, cannot explain the widespread adoption of cotton in Uganda. We argue, instead, that the key to the cotton revolution were Uganda’s two rainy seasons, which enabled farmers to grow cotton while simultaneously pursuing food security. Our study highlights the importance of food security and labour seasonality as important determinants of uneven agricultural commercialization in colonial tropical Africa.

    The fifth and final chapter further investigates the experience of African smallholders with cotton cultivation, providing a comparative explanatory analysis of variegated cotton outcomes, focusing in particular on the role of colonial and post-colonial policies. The chapter challenges the widely accepted view that (i) African colonial cotton projects consistently failed, that (ii) this failure should be attributed to conditions particular to Africa, which made export cotton inherently unviable and unprofitable to farmers, and that (iii) the repression and resistance often associated with cotton, all resulted from the stubborn and overbearing insistence of colonial governments on the crop per se. I argue along three lines. Firstly, to show that cotton outcomes were diverse, I compare cases of cotton production in Sub-Saharan Africa across time and space. Secondly, to refute the idea that cotton was a priori unattractive, I argue that the crop had substantial potential to connect farmers to markets and contribute to poverty alleviation, particularly in vulnerable, marginal and landlocked areas. Thirdly, to illustrate how an interaction between local conditions and government policies created conducive conditions for cotton adoption, I zoom in on the few yet significant ‘cotton success stories’ in twentieth century Africa. Smallholders in colonial Uganda adopted cotton because of favourable ecological and marketing conditions, and policies had an auxiliary positive effect. Smallholders in post-colonial Francophone West Africa faced much more challenging local conditions, but benefitted from effective external intervention and coordinated policy. On a more general level, this chapter demonstrates that, from a perspective of rural development, colonial policies should not only be seen as overbearing and interventionist, but also as inadequate, failing to aid rural Africans to benefit from new opportunities created by trade integration.

    Amphibious anthropology : engaging with maritime worlds in Indonesia
    Pauwelussen, Annet P. - \ 2017
    Wageningen University. Promotor(en): Leontine Visser, co-promotor(en): Gerard Verschoor. - Wageningen : Wageningen University - ISBN 9789463430654 - 208
    cum laude

    This thesis explores how people live amphibiously in dynamic land-sea environments. It is based on eighteen months of ethnographic fieldwork (2011 – 2013) in the Makassar Strait maritime region in Indonesia: a complex and amphibious land-sea interface. In Western science little attention is given to how people live at sea. There is a general land bias, by which people are seen as primarily belonging to the land. Yet people do live at sea, or rather: in these dynamic land-sea environments. Engaging with these mobile and sea-based ways of life of maritime people provides not only a fuller understanding of how people relate to their environment, but , essentially, it also enables a critical reflection of land-biased assumptions in science and society.

    Anthropology, with its qualitative research methods is particularly suitable to do such in-depth and long-term engagement with other worlds. The research on which the thesis is based was carried out as a mobile ethnography, following people seawards, travelling with them for days to visit close family on faraway islands or joining them on their fishing and diving trips, including illegal fishers using bombs and cyanide poison on coral reefs. Also followed were the practices of marine conservation staff, as they organised field trips to fishing communities. These travels – described in the thesis – show how islands and marine spaces that are remote from the land, turn out to be regional hubs of oversees trade and family relations. From a sea-based perspective the Makassar Strait is a continuity of relations and movements flanked by land masses. This inverts the land-based perspective of the sea as an extension of the land by putting the sea centre stage.

    The Makassar Strait figures in this thesis as an active and moving world – or worlds – of human-marine relations to learn from and theorise about the notion of ontological flow: fluidity of being and moving in relation. Flow is both movement as a pattern of activity – the flowing – and that what flows; elements, matter and meaning in motion. The notion of worlds in flow has infused recent ontological debates in anthropological theory in which reality is assumed contingent, fluid and multiple – thereby revitalising the philosophical work of earlier thinkers, among whom Michel Serres and Gilles Deleuze. This way of thinking complexity and ontological fluidity is central to literature that has emerged out of the cross-fertilisation of Science and Technology Studies (STS), anthropology and philosophy. Despite differences, these studies share the objective to follow, engage with and translate how, in practice, material and semiotic realities come to be and matter – instead of developing a way to ‘access reality better’.

    The concept of ‘amphibiousness’ is mobilised to refer to living in and moving between different worlds that can intermingle but that cannot be reduced to each other. The concept is used to describe the human capacity to live in different worlds at the same time. This amphibious capacity is further elaborated 1) in terms of living in a hybrid land-water interface, 2) in terms of being able to move along with different understandings of the world, of reality, and 3) It refers to the methodology of the anthropologist who also needs to move in these worlds bodily and cognitively, to develop a sensitivity to and understanding of these different worlds. Amphibiousness captures the anthropological engagement with flow, multiplicity and otherness by way of moving between worlds in order to explore the moving interface between worlds, realities or ways of life that partly interact. The research question: How to grasp flow – the fluctuations of and between bodies, things or worlds in the making - conceptually and methodologically without reducing its vital mobility and fluidity? is elaborated in a methodological Chapter 2, and three research chapters (Chapter 3, Chapter 4, and Chapter 5) that each focus from a different angle on human-marine relations.

    The research exposes fundamentally different, and sometimes conflicting, ways in which people understand and experience their relation to the sea. These were not just different perspectives on one maritime reality, or world. These were inherently different understandings of reality, and different ways in which this reality is put into practice, in which worlds – plural – are being created and sustained. In anthropology we speak of ontological difference, because it concerns with (radically) different notions of wat exists, what is real, what matters and what entities participate in the reproduction of the world.

    Although these worlds are different – they cannot be reduced to each another - they are also not separated in any clear-cut way. They do flow into each other, as people, objects and ideas can amphibiously move in between. It is argued in this thesis that such amphibious translation is essential for more effective and equal collaboration in marine conservation. International environmental organisations insufficiently acknowledge (radically) different ways of doing and thinking human-marine relations. Disregarding these undermines the viability of conservation programs as it repeatedly leads to clashes between different ways in which maritime worlds are understood and organised in practice. To be effective, marine conservation needs to become amphibious; attentive to fundamentally different ways of understanding and experiencing the relationship between people and the sea, as well as the mobile practices of trade, fishing, travel and family affiliations through which these worlds are shaped beyond the borders of marine reserves.

    Chapter 2 intends to answer the question how to grasp environmental otherness – radically different ways of understanding and experiencing human-marine relations – in and through ethnography. Chapter 3 serves to provide some empirical grounding to show the relevancy and urgency of a paradigmatic shift in conservation thinking, finding ways to engaging mobile maritime people like the Bajau. The solution to the ‘participation problem’ in conservation will not lie in developing ways to make local people participate more in Western conservation schemes. What is needed is an ontological shift in conservation thinking itself. Chapter 4 describes a conservation outreach project that attempts to educate and convert local people into coral protectors. Both coral and the sea-dwelling Bajau people appear to be amphibious beings, moving between a changeable land-water interface, and between different, fluidly interwoven ontological constellations. Failure of conservation organisations to recognise the ontologically ambiguous nature of ‘coral’ and ‘people’ translates to a breakdown of outreach goals. Chapter 5 provides a case study of a dangerous and destructive fishing practice (cyanide fishing) by which fishers dive beyond the limits of what their body can take – and spirits allow, a practice that generates feeling of both fear and enjoyment as they experience a process of becoming permeable to fluids, spirits and currents penetrating or leaking out of their bodies. This chapter exposes how cyanide fishing sustains as a way of life, involving and producing affective relations.

    In Chapter 6 it is concluded how ontological multiplicity is of a heuristic and political relevance to social science, and anthropology in particular because it allows us to engage with radical difference – or the real on different terms – instead of explaining it away in our own terms. Engaging with such radical different is important because it allows to see the realities that systematically escape (scholarly) attention, yet affect the world nonetheless. This requires translation – the practice of relating different worlds, reals, repertoires or ways of life and bringing them into interaction – which is a process of, and a condition for, dialogue. The notion of amphibiousness has practical and political value, in particular for reconsidering conservation and development outreach and how it may be reframed as a process involving ontological dialogue. Providing room for ambiguity, thinking with amphibiousness furthermore encourages suspension of the (Western) tendency to explain the Other, to fix what does not add up.

    River export of nutrients to the coastal waters of China: the MARINA model to assess sources, effects and solutions
    Strokal, Maryna - \ 2016
    Wageningen University. Promotor(en): Carolien Kroeze, co-promotor(en): S. Luan; Lin Ma. - Wageningen : Wageningen University - ISBN 9789462579729 - 226
    cum laude - nutrients - rivers - coastal water - models - eutrophication - coastal areas - water pollution - china - voedingsstoffen - rivieren - kustwateren - modellen - eutrofiëring - kustgebieden - waterverontreiniging - china

    Rivers export increasing amounts of nitrogen (N) and phosphorus (P) to the coastal waters of China. This causes eutrophication problems that can damage living organisms when oxygen levels drop and threaten human health through toxic algae. We know that these problems result from human activities on land such as agriculture and urbanization. However, the relative importance of these human activities for river export of nutrients to Chinese seas is not well studied. There are two important issues that need further investigation: the relative importance of upstream pollution on downstream impacts and the relative importance of typical sources of nutrients in Chinese rivers that are often ignored in existing modeling studies.

    My PhD thesis, therefore, aims to better understand trends in river export of nutrients to the coastal waters of China by source from sub-basins, and the associated coastal eutrophication. To this end, I developed the MARINA model: Model to Assess River Inputs of Nutrients to seAs. For this, I used the existing Global NEWS-2 model (Nutrient Export from WaterSheds) as a starting point.

    I formulated five sub-objectives to achieve the main objective:

    To analyze the original Global NEWS-2 model for river export of nutrients and the associated coastal eutrophication (Chapter 2);

    To develop a sub-basin scale modeling approach to account for impacts of upstream human activities on downstream water pollution, taking the Pearl River as an example (Chapter 3);

    To quantify the relative share of manure point sources to nutrient inputs to rivers at the sub-basin scale (Chapter 4);

    To quantify the relative share of sources to river export of nutrients at the sub-basin scale (Chapter 5);

    To explore optimistic futures to reduce river export of nutrients and coastal eutrophication in China (Chapter 6).

    The study area includes rivers draining roughly 40% of China. This includes the most densely populated areas, and areas with intensive economic activities. The rivers include the Yangtze (Changjiang), Yellow (Huanghe), Pearl, Huai, Hai and Liao. In the MARINA model, the drainage areas of the large Yangtze, Yellow and Pearl rivers are divided into up-, middle- and downstream sub-basins. The principle of the sub-basin approach of MARINA is that nutrients from human activities are transported by tributaries to outlets of sub-basins and then to the river mouth (coastal waters) through the main channel. The model takes into account nutrients that are partly lost or retained during transport towards the river mouth. The model quantifies river export of nutrients by source from sub-basins for 1970, 2000 and 2050.

    The main six findings of the MARINA results for China are:

    Finding 1: Dissolved N and P export by Chinese rivers increased by a factor of 2-8 between 1970 and 2000;

    Finding 2: The potential for coastal eutrophication was low in 1970 and high in 2000 in China;

    Finding 3: Most dissolved N and P in Chinese seas is from middlestream and downstream human activities;

    Finding 4: Manure point sources are responsible for 20-80% of dissolved N and P in Chinese rivers;

    Finding 5: In the future, river export of nutrients may increase in the Global Orchestration (GO) scenario of the Millennium Ecosystem Assessment. Current policy plans (CP scenario) may not sufficient to avoid this increase;

    Finding 6: In optimistic scenarios (OPT-1 and OPT-2), the potential for coastal eutrophication is low in 2050, mainly as a result of assumed full implementation of: (1) high recycling rates of animal manure (OPT-1 and OPT-2), and (2) high efficiencies of nutrient removal in sewage systems (OPT-2, see Figure 1).

    Figure 1. Illustration of future scenarios for coastal water quality in China. GO is Global Orchestration of the Millennium Ecosystem Assessment and assumes environmental actions that are either absent or ineffective in reducing water pollution. CP is based on GO, but incorporates the “Zero Growth in Synthetic Fertilizers after 2020” policy. OPT-1 and OP-2 are optimistic scenarios that assume high nutrient use efficiencies in agriculture (OPT-1, OPT-2) and sewage (OPT-2).

    My PhD thesis reveals novel insights for effective environmental policies in China. It shows the importance of manure point sources in water pollution by nutrients. Clearly, managing this source will likely reduce coastal eutrophication in the future. Furthermore, the implementation of advanced technologies is essential when dealing with urban pollution. My PhD thesis may also be useful for other world regions with similar environmental problems as in China. The new, sub-basin scale MARINA model is rather transparent and thus can be applied to other large, data-poor basins that may benefit from the allocation of effective management options. With this I hope to contribute to future availability of sufficiently clean water for next generations, not only in China, but also in other world regions.

    The neurotoxin BMAA in aquatic systems : analysis, occurrence and effects
    Faassen, E.J. - \ 2016
    Wageningen University. Promotor(en): Marten Scheffer, co-promotor(en): Miguel Lurling. - Wageningen : Wageningen University - ISBN 9789462577855 - 194
    cum laude - neurotoxins - aquatic environment - urban areas - effects - environmental impact - daphnia magna - elisa - water quality - analytical methods - aquatic ecology - neurotoxinen - aquatisch milieu - stedelijke gebieden - effecten - milieueffect - daphnia magna - elisa - waterkwaliteit - analytische methoden - aquatische ecologie

    Eutrophication is a major water quality issue and in many aquatic systems, it leads to the proliferation of toxic phytoplankton species. The neurotoxin β-N-methylamino-L-alanine (BMAA) is one of the compounds that can be present in phytoplankton. BMAA has been suggested to play a role in the neurodegenerative diseases Alzheimer’s disease, Parkinson’s disease and amyotrophic lateral sclerosis, although this hypothesis still needs to be confirmed. It is expected that the main human exposure pathways to BMAA are through direct contact with BMAA containing phytoplankton and through ingestion of BMAA contaminated food, such as fish and shellfish. However, reports on the occurrence of BMAA in aquatic systems have been conflicting and the cause of these reported differences was heavily debated. The use of different analytical methods seems to play a crucial role in the observed discrepancies, but initially, there was little consensus on which method produced most reliable results. The objectives of the work presented in this thesis therefore were to find out what has caused the differences in published results on BMAA concentrations, and to identify and produce reliable data on the presence of BMAA in aquatic systems. In addition, I aimed to determine the effect of BMAA exposure on a key species in many freshwater ecosystems, the grazer Daphnia magna.

    The performances of different analytical techniques were compared, and LC-MS/MS analysis, either preceded by derivatisation or not, was found to produce most reliable results. LC-FLD and ELISA should not be used for BMAA analysis, as both methods risk misidentifying BMAA or overestimating its concentrations due to their low selectivity. When reviewing literature on the presence of BMAA in aquatic systems, it was found that the observed discrepancies in results could be explained by the use of unselective analytical methods in some studies, and by severe reporting deficiencies in others. When only studies that used appropriate analytical techniques and that correctly reported their work were taken into account, it was shown that BMAA could be present in phytoplankton and higher aquatic organisms, in concentrations of µg/g dry weight or lower. These results are in agreement with our findings of BMAA in cyanobacterial scums from Dutch urban waters. In a 2008 screening, BMAA was found to be present in 9 out of 21 analysed cyanobacterial scums, at concentrations ranging from 4 to 42 µg/g dry weight. When this screening was repeated 8 years later with 52 similar samples, BMAA was detected below the quantification limit in one sample and quantified in another sample at 0.6 µg/g dry weight.

    In order to perform the work presented in this thesis, sensitive and selective analytical methods, mostly based on LC-MS/MS analysis without derivatisation, were developed. This resulted in a standard operating procedure for the underivatised LC-MS/MS analysis of BMAA in cyanobacteria. Also, a CYANOCOST initiated workshop was given, in which a group of scientists from 17 independent laboratories evaluated LC-MS/MS based methods in different matrices. A bound BMAA from found in the supernatant was the most abundant fraction in the positive samples that were tested: cycad seed, seafood and exposed D. magna. In addition, it was found that the deuterated internal standard used for quantification was not a good indicator for the release of BMAA from bound forms, resulting in unprecise quantification of total BMAA.

    BMAA was found to reduce survival, somatic growth, reproduction and population growth in D. magna. Animals did not adapt to BMAA exposure: exposed animals born from exposed mothers had a lower brood viability and neonate weight than animals exposed to BMAA, but born from unexposed mothers. In addition, D. magna was shown to take up BMAA from the growth medium and to transfer it to its offspring. D. magna therefore might be an important vector for BMAA transfer along the pelagic food chain, but whether BMAA plays a role in preventing zooplankton from controlling cyanobacterial blooms needs further investigation.

    Although BMAA research has much progressed between the start of this thesis’ work and its completion, some important questions still require an answer. Most urgently, it should be determined whether BMAA is indeed involved in the neurological diseases mentioned above, and if so, which doses trigger the onset of these diseases. Human exposure pathways should then be more systematically quantified, and it might be prudent to investigate if the occurrence of BMAA is restricted to aquatic systems, or whether sources from terrestrial systems contribute to BMAA exposure as well.

    Feed sources for livestock : recycling towards a green planet
    Zanten, H.H.E. van - \ 2016
    Wageningen University. Promotor(en): Imke de Boer, co-promotor(en): Paul Bikker; Bastiaan Meerburg. - Wageningen : Wageningen University - ISBN 9789462578050 - 251
    cum laude - livestock - livestock feeding - feeds - resources - food wastes - leftovers - recycling - greenhouse gases - environmental impact - innovations - sustainable animal husbandry - animal production - vee - veevoeding - voer - hulpbronnen - voedselafval - etensresten - recycling - broeikasgassen - milieueffect - innovaties - duurzame veehouderij - dierlijke productie

    Production of food has re-emerged at the top of the global political agenda, driven by two contemporary challenges: the challenge to produce enough nutritious food to feed a growing and more prosperous human population, and the challenge to produce this food in an environmentally sustainable way. Current levels of production of especially animal-source food (ASF), pose severe pressure on the environment via their emissions to air, water, and soil; and their use of scarce resources, such as land, water, and fossil energy. The livestock sector, for example, is responsible for about 15% of the global anthropogenic emissions of greenhouse gases and uses about 70% of global agricultural land.

    Many proposed mitigation strategies to feed the world sustainably, therefore, focus primarily on reducing the environmental impact of the livestock sector, so-called production-side strategies. Other strategies focus on changing consumption patterns by reducing consumption of ASF, or on shifting from ASF with a higher environmental impact (e.g. beef) to ASF with a lower environmental impact (e.g. pork or chicken), so called consumption-side strategies.

    Most of the environmental impact of production of ASF is related to production of feed. One production-side strategy to reduce the environmental impact is the use of products that humans cannot or do not want to eat, such as co-products, food-waste, and biomass from marginal lands for livestock feed (referred to as ‘leftover streams’ in this thesis). This strategy is effective, because feeding leftover streams to livestock transforms an inedible food stream into high-quality food products, such as meat, milk, and eggs.

    Two production-side strategies that use leftover streams as livestock feed were explored in this thesis: replacing soybean meal (SBM) in diets of growing pigs with either rapeseed meal (RSM) or with waste-fed larvae meal. Replacing SBM with RSM in growing-pig diets was assessed because RSM became increasingly available following an increase in bio-energy production in the EU. In this strategy, therefore, the RSM content in pig diets increased at the expense of SBM. SBM is an ingredient associated with a high environmental impact. It was expected, therefore, that replacing SBM with RSM in pig diets would lead to a decrease in the environmental impact of pork production. Replacing SBM with waste-fed larvae meal was assessed because recent developments show the environmental benefits of rearing insects as livestock feed. Insects have a low feed conversion ratio (kg feed/kg product) and can be consumed completely, without residual materials, such as bones or feathers. The nutritional value of insects is high, especially as a protein source for livestock. Insect-based feed products, therefore, can replace conventional feed ingredients, such as SBM. Altogether this strategy suggests that waste-fed larvae meal might become an important alternative feed source in the future.

    To gain insight into the status quo of the environmental impact of both mitigation strategies, replacing SBM with RSM or with waste-fed insects, we first used the attributional life cycle assessment (ALCA) method. Based on the ALCA method, results showed that each mitigation strategy was promising. Replacing SBM with RSM in growing pig diets hardly changed either global warming potential (GWP) or energy use (EU), but decreased land use (LU) up to 16% per kg body weight gain. As expected, feed production had the largest environmental impact, responsible for about 50% of the GWP, 60% of the EU, and 77% of the total LU. Feed production in combination with feed intake, were the most sensitive parameters; a small change in both these two parameters changed the results. Replacing SBM with waste-fed larvae meal in growing-pig diets showed that EU hardly changed, but GWP (29%) and LU (54%) decreased per kg body weight gain. Based on ALCA results, each mitigation strategy, therefore, seems to offer potential to reduce the environmental impact of pork production. An ALCA, however, has two disadvantages: it does not account for product-packages and it does not consider feed-food competition.

    The first disadvantage of ALCA was that the complexity of dealing with product-packages is not fully considered. ‘Product-package’ refers to a multiple-output situation. During the processing of sugar beet, for example, beet-pulp and molasses are produced in addition to sugar. Sugar, beet-pulp, and molasses together form a ‘package of products’ because they cannot be produced independently from each other. An ALCA does not account for the fact that the production volume of the co-product(s) depends on the demand for the determining product (e.g. sugar), which results in the limited availability of co-products. Increasing the use of co-products in animal feed, consequently, results in reducing use of a co-product in another sector, requiring them to be replaced with a different product. The environmental impact of increasing the use of a co-product or food-waste, therefore, depends on the net environmental impact. The net environmental impact refers to the environmental benefits of using the product in its new application minus the environmental cost of replacing the product in its old application.

    A consequential theoretical framework was developed to account for product-packages. The results, based on the consequential framework, contradicted standard ALCA results. The consequential LCA (CLCA) method we used for replacing SBM with RSM showed an increased GWP (up to 15%), EU (up to 12%), and LU (up to 10%) per kg body weight gain. Moreover, this CLCA method showed that replacing SBM with waste-fed larvae meal increased GWP (60%) and EU (90%), but decreased LU (73%) per kg body weight gain.

    Accounting for product-packages increased the net environmental impact of each strategy, replacing SBM with RSM or with waste-fed larvae meal. The difference in results between ALCA and CLCA was especially large in the strategy with waste-fed larvae meal. The difference was caused mainly by the use of food-waste. Food-waste fed to larvae was used initially to produce bio-energy via anaerobic digestion. In CLCA, the environmental impact related to replacing the bio-energy function of food-waste with fossil-energy was included. The net environmental impact became negative, because environmental benefits of replacing SBM with waste-fed larvae meal were less than environmental costs related to the marginal energy source, i.e. fossil energy, replacing the bio-energy. Results of the indirect environmental impact, however, are situation specific: if the marginal energy source were wind or solar energy, the net environmental impact of using waste-fed larvae meal might be positive. Waste-fed larvae meal, therefore, appears to be an interesting mitigation strategy only when energy from wind and solar energy are used more dominantly than energy from fossil sources.

    If results were based solely on ALCA, then these potentially negative impacts would have been overlooked. Consideration of the environmental consequences of product-packaging, therefore, is essential to determine total environmental costs. If policy makers or the feed industry want to assess the net environmental impact of a potential mitigation strategy, then we recommend to perform a CLCA instead of an ALCA. The framework developed in this thesis can be used to perform such an assessment.

    The second disadvantage of an LCA was that it does not take into account feed-food competition, e.g. competition for land between humans and animals. Most LCA studies focus on the total amount of land required to produce one kg ASF. LCA studies do not account for competition for land between humans and animals, or so-called feed-food competition. In other words, they do not include, differences in the consumption of human-edible products by various livestock species or differences in the suitability of land used for feed production as land to cultivate food-crops directly. Given the global constraints on land, it is more efficient to grow food directly for human consumption rather than for livestock. To address the contribution of livestock to a future sustainable food supply, a measure for land use efficiency was developed, called the land use ratio (LUR). The LUR accounts for plant productivity, efficiency of converting human-inedible feed into ASF, and suitability of land for crop cultivation. The LUR also has a life-cycle perspective.

    Results of the LUR illustrated that dairy cows on sandy soil, laying hens, and pig production systems in the Netherlands have a LUR >1.0. In terms of protein produced per m2, therefore, it is more efficient to use these soils for livestock production to produce crops for direct human consumption than to produce feed for livestock. Only dairy cows on peat soil produce human digestible protein (HDP) more efficiently than crops do, because peat is not suitable for crop production. The LUR allows identification of livestock production systems that are able to produce HDP more efficiently than crops do. Livestock systems with a LUR<1.0, such as dairy on peat, have an important role to play in future sustainable nutrition supply.

    Results of the LUR showed that livestock production systems using mainly co-products, food-waste, and biomass from marginal land, can produce human digestible protein more efficiently than crop production systems do. The availability of those leftover streams, however, is limited and, therefore, the amount of ASF produced based only on leftover streams is also limited. Because LUR is a ratio, LUR results do not give an indication of how much ASF can be produced based on livestock systems that feed mainly on leftover streams.

    The third, and last, mitigation strategy, therefore, focused on the amount of ASF that can be consumed by humans, when livestock are fed only on leftover steams, also referred to as “default livestock”. The calculation of the amount of ASF was based on the assumption that a vegan diet was consumed in principle. The resulting co-products and food-waste were fed to pigs and, biomass from grazing land was fed to ruminants. Results showed that in total 21 g animal source protein per person per day could be produced by feeding livestock entirely on leftovers.

    Considering feed-food crops and feeding food-waste made an important contribution to the 21 g of protein that could be produced from default livestock. Considering feed-food crops implies that choices have to be made between different crops, based on their contribution to feed and food production. Oil production from soy cultivation, for example, resulted in the co-product SBM. Results showed that considering feed-food crops can affect the final protein production from pork. The practice of feeding food-waste to livestock is currently prohibited due to problems of food safety but the practice shows potential in extensively reducing the environmental impact of livestock production. Considering feed-food crops and feeding food-waste are examples of mitigation strategies that currently can be implemented to reduce further the environmental impact of the livestock sector.

    On average, it is recommended to consume about 57 g of protein from ASF or plant-origin per person per day. Only ASF from default livestock does not fulfil the current global protein consumption of 32 g per person per day, but about one third of the protein each person needs can be produced without any competition for land between feed and food production. To feed the world more sustainably, by requiring livestock production systems with a LUR <1.0, however, a paradigm shift is needed. Global average consumption of ASF should decrease to about 21 g of protein per person per day. Innovations are needed, moreover, to overcome problems of food safety and technical concerns related to collecting the leftover streams. This applies, in particular to food-waste, which is currently unused in livestock production but which presents a valuable strategy in mitigating environmental impacts caused by livestock production. Livestock systems should change their focus, furthermore, from increasing productivity per animal towards increasing protein production for humans per ha. By using leftover streams optimally, the livestock sector is able to produce a crucial amount of protein, while still avoiding competition for land between feed and food crops. Livestock, therefore, can make an important contribution to the future nutrition supply.

    To tweet or not to tweet : the role of personality in the social networks of great tits : the role of personality in the social networks of great tits
    Snijders, L. - \ 2016
    Wageningen University. Promotor(en): Marc Naguib, co-promotor(en): Kees van Oers. - Wageningen : Wageningen University - ISBN 9789462576940 - 237
    cum laude - parus major - personality - communication between animals - social structure - vocalization - bird song - social behaviour - animal behaviour - behavioural biology - parus major - persoonlijkheid - communicatie tussen dieren - sociale structuur - vocalisatie - vogelzang - sociaal gedrag - diergedrag - gedragsbiologie

    To tweet or not to tweet: The role of personality in the social networks of great tits
    By: Lysanne Snijders

    Project video:

    When mentioning social networks it is easy to think of online networks for people, such as Facebook and Twitter. But many animals also have social networks. In proximity networks they encounter each other physically and in communication networks they connect to each other by using signals. Their position in such social networks is important. It can influence the likelihood of finding new food, acquiring novel foraging techniques, rising in social status and acquiring a mate. However, having many contacts can also be risky as it increases the likelihood of encountering infectious diseases, social stress or ending up in a fight.
    As social network position can be so significant, it is essential that we know what determines it. A likely key factor is personality. Individuals consistently differ in how risk-prone (pro-active) and risk-averse (re-active) they tend to behave. As making face-to-face contact is not without risk, bolder individuals might have more social contacts.

    An ideal model to study this hypothesis is the great tit. A common garden bird. There are well established methods to quantify personality differences in great tits and with the newest tracking technologies we can now also monitor their face-tot-face contacts. What makes the great tit even more interesting is that they like to breed in nest boxes and so we can also study potential fitness effects of specific network positions. Additionally, great tits are songbirds, which makes them also ideal to answer a second question: Do individuals that are shy to approach others, use communication instead? Since communication is often a less risky connection strategy than face-to-face contact.

    In this PhD thesis I reveal how and when personality explains why some birds are better connected than others. In wild territorial populations pro-active males were better connected to other males and were most likely to approach a rival. In contrast, when removing the risk of fights during male-to-male spatial associations, via a video-playback experiment in captivity, the re-active males appeared to be most social. When confronted with the life-size video image of a novel conspecific, they spent the most time associating with it. When lowering the risks associated with spatial associations the social preferences of re-active individuals might thus increase. No relationship was found between social network position in the wild and reproductive success, an important fitness component.
    Wild male great tits that were less likely to approach a rival, sang more actively at dawn. Dawn song is the peak time for male great tit singing activity and operates as a large communication network. Since a prime function of singing at dawn is territory advertisement, these birds might thus try to prevent rival territory intrusions by singing more fiercely at dawn. No direct links were found between personality and an individual’s place in the communication network, however pro-active birds vocalized most actively during territory intrusions and increased their singing activity significantly during the fertile period of their mate.
    Communication networks and proximity networks can influence each other via song, by attracting or repulsing conspecifics to come close. For example, the vocal response of an intruded male to its rival significantly influenced whether female neighbours would come close to the intrusion site and if male neighbours would stay away.

    What determines the place in a social network? By knowing this we learn more about how groups function and how different social strategies in the same population can co-exist.

    Multi-population genomic prediction
    Wientjes, Y.C.J. - \ 2016
    Wageningen University. Promotor(en): Roel Veerkamp; Mario Calus. - Wageningen : Wageningen University - ISBN 9789462576193 - 267
    cum laude - dairy cattle - genomics - prediction - quantitative trait loci - genetic improvement - breeding value - selective breeding - animal breeding - animal genetics - melkvee - genomica - voorspelling - loci voor kwantitatief kenmerk - genetische verbetering - fokwaarde - selectief fokken - dierveredeling - diergenetica
    Cum laude graduation
    Ecosystem effects of bottom trawl fishing
    Denderen, P.D. van - \ 2015
    Wageningen University. Promotor(en): Adriaan Rijnsdorp, co-promotor(en): Tobias van Kooten. - Wageningen : Wageningen University - ISBN 9789462573468 - 182
    vis vangen - zeevisserij - boomkorvisserij - vismethoden - ecosystemen - milieueffect - visserijbeheer - benthos - soortenrijkdom - mariene ecologie - fishing - marine fisheries - beam trawling - fishing methods - ecosystems - environmental impact - fishery management - benthos - species richness - marine ecology - cum laude
    cum laude graduation
    The conservation and use of crop genetic resources for food security
    Khoury, C.K. - \ 2015
    Wageningen University. Promotor(en): Paul Struik, co-promotor(en): A. Jarvis. - Wageningen : Wageningen University - ISBN 9789462574427 - 302
    genetische bronnen van plantensoorten - genetische diversiteit - germplasm - landbouwontwikkeling - klimaatadaptatie - wilde verwanten - ex-situ conservering - voedselzekerheid - plant genetic resources - genetic diversity - germplasm - agricultural development - climate adaptation - wild relatives - ex situ conservation - food security - cum laude
    Cum laude graduation
    Among the factors hindering the conservation of crop genetic resources is a lack of essential information regarding this diversity. Questions include: (a) what is the status of diversity in our food systems, and where are the greatest vulnerabilities?, (b) where can genetic diversity be found that can be useful in increasing productivity and mitigating these vulnerabilities?, (c) is this genetic diversity available in the present and in the long term?, and (d) what steps are needed to improve the ability for researchers to access genetic resources critical for present and future crop improvement? This thesis aims to contribute to the knowledge required to answer these questions through an exploration of the need for, potential of, challenges and constraints regarding, and necessary steps to enhance the conservation and use of crop genetic diversity.
    Evolution, role and mechanism of prokaryotic Argonaute proteins
    Swarts, D.C. - \ 2015
    Wageningen University. Promotor(en): John van der Oost, co-promotor(en): Stan Brouns. - Wageningen : Wageningen University - ISBN 9789462572959 - 228
    eiwitten - eiwittechnologie - rna-interferentie - genexpressie - nucleasen - thermus thermophilus - pyrococcus furiosus - proteins - protein engineering - rna interference - gene expression - nucleases - thermus thermophilus - pyrococcus furiosus - cum laude
    cum laude graduation
    The hybrid nature of pig genomes : unraveling the mosaic haplotype structure in wild and commercial Sus scrofa populations
    Bosse, M. - \ 2015
    Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Hendrik-Jan Megens; Ole Madsen. - Wageningen : Wageningen University - ISBN 9789462573000 - 253
    dieren - varkens - dierveredeling - genomen - hybridisatie - sus scrofa - haplotypen - genomica - populaties - genetische variatie - animals - pigs - animal breeding - genomes - hybridization - sus scrofa - haplotypes - genomics - populations - genetic variation - cum laude
    cum laude graduation
    Tales on insect-flowering plant interactions : the ecological significance of plant responses to herbivores and pollinators
    Lucas Gomes Marques Barbosa, D. - \ 2015
    Wageningen University. Promotor(en): Marcel Dicke, co-promotor(en): Joop van Loon. - Wageningen : Wageningen University - ISBN 9789462572119 - 207
    bloeiende planten - insecten - insect-plant relaties - plant-herbivoor relaties - herbivoren - bestuivers (dieren) - trofische graden - parasitoïden - herbivoor-geinduceerde plantengeuren - flowering plants - insects - insect plant relations - plant-herbivore interactions - herbivores - pollinators - trophic levels - parasitoids - herbivore induced plant volatiles - cum laude
    cum laude graduation
    Animal deliberation : the co-evolution of technology and ethics on the farm
    Driessen, C.P.G. - \ 2014
    Wageningen University. Promotor(en): Michiel Korthals, co-promotor(en): Volkert Beekman. - Wageningen : Wageningen University - 356
    dierethiek - ethiek - veehouderij - varkenshouderij - technologie - boeren - varkens - dierlijke productie - animal ethics - ethics - livestock farming - pig farming - technology - farmers - pigs - animal production - cum laude
    cum laude graduation
    Biogenesis and signalling requirements of plant receptor-like proteins mediating resistance to fungal pathogens
    Liebrand, T.W.H. - \ 2014
    Wageningen University. Promotor(en): Pierre de Wit, co-promotor(en): Matthieu Joosten. - Wageningen : Wageningen University - ISBN 9789461738622 - 192
    solanum lycopersicum - plantenziekteverwekkende schimmels - passalora fulva - verticillium dahliae - ziekteresistentie - verdedigingsmechanismen - receptoren - pathogenesis-gerelateerde eiwitten - genetische analyse - genexpressie - solanum lycopersicum - plant pathogenic fungi - passalora fulva - verticillium dahliae - disease resistance - defence mechanisms - receptors - pathogenesis-related proteins - genetic analysis - gene expression - cum laude
    cum laude graduation
    Adaptive & heritable immunity in bacteria : on the regulation and mechanism of CRISPR defense
    Westra, E.R. - \ 2013
    Wageningen University. Promotor(en): John van der Oost; Willem de Vos, co-promotor(en): Stan Brouns. - S.l. : s.n. - ISBN 9789461735003 - 254
    bacteriën - immuniteit - immuunsysteem - verdedigingsmechanismen - rna - prokaryoten - bacteria - immunity - immune system - defence mechanisms - rna - prokaryotes - cum laude
    cum laude graduation (with distinction)
    Landscape infrastructure : urbanism beyond engineering
    Bélanger, P. - \ 2013
    Wageningen University. Promotor(en): J. Koh. - S.l. : s.n. - ISBN 9789461735270 - 441
    landschapsarchitectuur - stedelijke planning - civiele techniek - stedelijke ecologie - urbanisatie - infrastructuur - regionalisme - landscape architecture - urban planning - civil engineering - urban ecology - urbanization - infrastructure - regionalization - cum laude
    As ecology becomes the new engineering, the project of Landscape Infrastructure - a contemporary, synthetic alignment of the disciplines of landscape architecture, civil engineering and urban planning - is proposed here. Predominant challenges facing urban regions today are addressed, including changing climates, resource flows, and population mobilities. Responding to the inertia of land use zoning and overexertion of technological systems at the end of 20th century, the thesis argues for the strategic design of “infrastructural ecologies”, a synthetic landscape of living, biophysical systems that operate as urban infrastructures to shape and direct the future of urban economies into the 21st century. cum laude graduation (with distinction)
    Meiotic recombination and its implications for plant breeding
    Wijnker, T.G. - \ 2013
    Wageningen University. Promotor(en): Hans de Jong; Maarten Koornneef, co-promotor(en): R.H.G. Dirks. - S.l. : s.n. - ISBN 9789461734402 - 254
    meiose - recombinatie - homologe recombinatie - crossing over - genomica - nucleotidenvolgordes - inversie van chromosoom - haploïden - homozygoten - arabidopsis thaliana - solanaceae - plantenveredeling - meiosis - recombination - homologous recombination - crossing over - genomics - nucleotide sequences - chromosome inversion - haploids - homozygotes - arabidopsis thaliana - solanaceae - plant breeding - cum laude
    cum laude graduation (with distinction)
    Fostering argumentation-based computer-supported collaborative learning in higher education
    Noroozi, O. - \ 2013
    Wageningen University. Promotor(en): Martin Mulder, co-promotor(en): Harm Biemans. - [S.l. : s.n. - ISBN 9789461734013 - 282
    computerondersteund onderwijs - hoger onderwijs - wetenschappelijke samenwerking - discussie - leren - onderwijsmethoden - studenten - groepen - computer assisted instruction - higher education - scientific cooperation - discussion - learning - teaching methods - students - groups - cum laude
    cum laude graduation (with distinction). In collaborative settings, students of all ages need to learn to clearly explain their informed opinions and give reasons for the way in which they carry out tasks and solve problems. Engaging students in collaborative discussion and argumentation is an educational approach for preparing them to manage today’s complex issues and actively participate in knowledge societies. Despite the fact that argumentation is shaped in social conversation and also in learners’ online exchanges in daily life, learners in academic settings need to be taught to reason and argue in a way that is beneficial for knowledge sharing, domain-specific learning, and knowledge construction. Online support systems for collaboration or Computer-Supported Collaborative Learning (CSCL) environments in which learners argue in teams have been found to support the sharing, constructing, and representing of arguments with the aim of learning. This type of learning arrangement is called Argumentation-Based Computer-Supported Collaborative Learning (ABCSCL) and it is seen as a promising environment in which to facilitate collaborative argumentation and learning.
    Global rivers warming up: impacts on cooling water use in the energy sector and freshwater ecosystems
    Vliet, M.T.H. van - \ 2012
    Wageningen University. Promotor(en): Pavel Kabat, co-promotor(en): Fulco Ludwig. - S.l. : s.n. - ISBN 9789461734242 - 196
    klimaatverandering - oppervlaktewater - zoetwaterecologie - watertemperatuur - rivierafvoer - koelwater - waterorganismen - nadelige gevolgen - climatic change - surface water - freshwater ecology - water temperature - stream flow - cooling water - aquatic organisms - adverse effects - cum laude
    cum laude graduation (with distinction)
    Transnational governance through private authority : the case of the Forest Stewardship Council certification in Russia
    Tysiachniouk, M.S. - \ 2012
    Wageningen University. Promotor(en): Arthur Mol; Gert Spaargaren. - S.l. : s.n. - ISBN 9789461734327 - 352
    bosbouw - certificering - kwaliteitsnormen - bosbeleid - bosbedrijfsvoering - governance - internationale samenwerking - rusland - forestry - certification - quality standards - forest policy - forest management - governance - international cooperation - russia - cum laude
    cum laude graduation (with distinction)
    The politics of democratic governance : the implementation of the Water Framework Directive in the Netherlands
    Behagel, J.H. - \ 2012
    Wageningen University. Promotor(en): Bas Arts, co-promotor(en): Esther Turnhout. - S.l. : s.n. - ISBN 9789461734488 - 223
    kaderrichtlijn water - governance - politieke processen - democratie - besluitvorming - participatie - bestuurskunde - nederland - water framework directive - governance - political processes - democracy - decision making - participation - public administration - netherlands - cum laude
    cum laude graduation (with distinction)
    The role and evolution of fungal effectors in plant pathogenesis
    Jonge, R. de - \ 2012
    Wageningen University. Promotor(en): Pierre de Wit, co-promotor(en): Bart Thomma. - S.l. : s.n. - ISBN 9789461733917 - 148
    plantenziekteverwekkende schimmels - moleculaire plantenziektekunde - evolutie - gastheer parasiet relaties - pathogenese - genomica - immuniteit - genomen - plant pathogenic fungi - molecular plant pathology - evolution - host parasite relationships - pathogenesis - genomics - immunity - genomes - cum laude
    cum laude graduation (with distinction)
    Strength, structure and stability of polyelectrolyte complex coacervates
    Spruijt, E. - \ 2012
    Wageningen University. Promotor(en): Martien Cohen Stuart, co-promotor(en): Jasper van der Gucht. - S.l. : s.n. - ISBN 9789461733542 - 291
    elektrolyten - bindingssterkte - elektrische dubbellaag - chemische structuur - moleculaire structuur - oppervlaktespanning - electrolytes - bond strength - electrical double layer - chemical structure - molecular conformation - surface tension - cum laude
    cum laude graduation (with distinction)
    Identification of novel MONOPTEROS target genes in embryonic root initiation
    Moller, B.K. - \ 2012
    Wageningen University. Promotor(en): Sacco de Vries, co-promotor(en): Dolf Weijers. - S.l. : s.n. - ISBN 9789461732392 - 192
    plantenembryo's - wortels - plantenontwikkeling - genregulatie - arabidopsis - embryonale stamcellen - auxinen - plant embryos - roots - plant development - gene regulation - arabidopsis - embryonic stem cells - auxins - cum laude
    cum laude graduation (with distinction)
    Institutions, violent conflict, windfall gains and economic development in Africa
    Voors, M.J. - \ 2011
    Wageningen University. Promotor(en): Erwin Bulte. - [S.l.] : s.n. - ISBN 9789461731029 - 166
    ontwikkelingseconomie - economische ontwikkeling - instellingen - institutionele economie - conflict - afgewaaid fruit - oorlog - corruptie - development economics - economic development - institutions - institutional economics - conflict - windfalls - war - corruption - cum laude
    cum laude graduation (with distinction)
    Learning how to eat like a pig: facilitating vertical information transfer to reduce weaning problems in piglets
    Oostindjer, M. - \ 2011
    Wageningen University. Promotor(en): Bas Kemp, co-promotor(en): Henry van den Brand; Liesbeth Bolhuis. - [S.l.] : s.n. - ISBN 9789085859833 - 233
    biggen - zeugen - spenen - stress - leren - eten - varkensvoeding - omgevingsverrijking - aromatische stoffen - diergedrag - dierhouderij - varkenshouderij - piglets - sows - weaning - stress - learning - eating - pig feeding - environmental enrichment - flavourings - animal behaviour - animal husbandry - pig farming - cum laude
    cum laude graduation (with distinction)
    Surface evaporation and water vapor transport in the convective boundary layer
    Heerwaarden, C.C. van - \ 2011
    Wageningen University. Promotor(en): Bert Holtslag, co-promotor(en): J. Vila -Guerau de Arellano. - [S.l.] : s.n. - ISBN 9789085859130 - 156
    evaporatie - aardoppervlak - atmosfeer - grenslaag - evaporation - land surface - atmosphere - boundary layer - cum laude
    cum laude graduation (with distinction)
    Expecting the unexpected: indicators of resilience as early-warning signals for critical transitions
    Dakos, V. - \ 2011
    Wageningen University. Promotor(en): Marten Scheffer, co-promotor(en): Egbert van Nes. - S.l. : s.n. - ISBN 9789085858706 - 156
    ecosystemen - fluctuaties - verandering - klimaatverandering - indicatoren - voorspellen - ecosystems - fluctuations - change - climatic change - indicators - forecasting - cum laude
    cum laude graduation (with distinction)
    Dynamics in groundwater and surface water quality : from field-scale processes to catchment-scale models
    Velde, Y. van der - \ 2011
    Wageningen University. Promotor(en): Sjoerd van der Zee; F.C. van Geer, co-promotor(en): G.H. de Rooij. - S.l. : s.n. - ISBN 9789085858249 - 176
    hydrologie - deterministische modellen - hydrologie van stroomgebieden - innovaties - waterkwaliteit - afvoerwater - grondwater - oppervlaktewater - stroomgebieden - waterlopen - observatie - oppervlaktewaterkwaliteit - achterhoek - hydrology - deterministic models - catchment hydrology - innovations - water quality - effluents - groundwater - surface water - watersheds - streams - observation - surface water quality - achterhoek - cum laude
    cum laude graduation (with distinction)
    CRISPR-mediated antiviral defence in prokaryotes
    Jore, M.M. - \ 2010
    Wageningen University. Promotor(en): John van der Oost, co-promotor(en): Stan Brouns. - S.l. : s.n. - ISBN 9789085857815 - 154
    prokaryoten - bacteriofagen - antiviruseigenschappen - prokaryotes - bacteriophages - antiviral properties - cum laude
    cum laude graduation (with distinction)
    Surface complexation at mineral interfaces: Multisite and Charge Distribution approach
    Hiemstra, T. - \ 2010
    Wageningen University. Promotor(en): Willem van Riemsdijk. - S.l. : s.n. - ISBN 9789085857174 - 383
    bodemchemie - geochemie - adsorptie - fosfaten - ionen - organische stof - kleimineralen - kationenwisseling - soil chemistry - geochemistry - adsorption - phosphates - ions - organic matter - clay minerals - cation exchange - cum laude
    cum laude graduation (with distinction)
    Organic monolayers on oxide-free silicon : self-assembly, functionalization, patterning and electronic characterization
    Scheres, L.M.W. - \ 2010
    Wageningen University. Promotor(en): Han Zuilhof. - S.l. : s.n. - ISBN 9789085856641 - 201
    silicium - unimoleculaire films - organische verbindingen - zelf-assemblage - organische scheikunde - silicon - unimolecular films - organic compounds - self assembly - organic chemistry - cum laude
    cum laude graduation (with distinction)
    Bridging troubled waters? : everyday inter-ethnic interaction in a content of violent conflict in Kottiyar Patty, Trincomalee, Sri Lanka
    Gaasbeek, T. - \ 2010
    Wageningen University. Promotor(en): Georg Frerks; Linden Vincent. - S.l. : s.n. - ISBN 9789085856467 - 370
    rampen - conflict - oorlog - etniciteit - etnische groepen - agressief gedrag - voorlichting - irrigatie - waterbeheer - huwelijk - sociologie - sociale differentiatie - sri lanka - zuid-azië - disasters - conflict - war - ethnicity - ethnic groups - aggressive behaviour - extension - irrigation - water management - marriage - sociology - social differentiation - sri lanka - south asia - cum laude
    cum laude graduation (with distinction)
    Aquatic ecosystems in hot water : effects of climate on the functioning of shallow lakes
    Kosten, S. - \ 2010
    Wageningen University. Promotor(en): Marten Scheffer, co-promotor(en): Egbert van Nes. - S.l. : s.n. - ISBN 9789085856016 - 160
    aquatisch milieu - ecologie - meren - klimaatverandering - waterplanten - fytoplankton - biomassa - kooldioxide - voedingsstoffenbeschikbaarheid - klimaatfactoren - aquatische ecosystemen - aquatische ecologie - aquatic environment - ecology - lakes - climatic change - aquatic plants - phytoplankton - biomass - carbon dioxide - nutrient availability - climatic factors - aquatic ecosystems - aquatic ecology - cum laude
    cum laude graduation (with distinction) There is concern that a warmer climate may boost carbon emissions from lakes and promote the chance that they lose their vegetation and become dominated by phytoplankton or cyanobacteria. However, these hypotheses have been difficult to evaluate due to the scarcity of relevant field data. To explore potential climate effects we sampled 83 lakes along a latitudinal gradient of more than 6000 km ranging from Rio Grande do Norte in Brazil to the South of Argentina (5-55 oS). The lakes were selected so as to be as similar as possible in morphology and altitude while varying as much as possible in trophic state within regions. All lakes were sampled once during summer (subtropical, temperate and tundra lakes) or during the dry season (tropical lakes) between November 2004 and March 2006 by the same team. In the first chapters I address the question how climate might affect the chances for shallow lakes to be dominated by submerged plants. It has been shown that temperate lakes tend to have two contrasting states over a range of conditions: a clear state dominated by aquatic vegetation or a turbid state. The turbid state is typically dominated by phytoplankton and often characterized by poorer water quality than the clear state. The backbone of the theory explaining this pattern is a supposed positive feedback of submerged vegetation on water clarity: vegetation enhances water clarity and clearer water, in turn, promotes vegetation growth. The theory furthermore asserts that submerged vegetation coverage diminishes when nutrient concentrations increase until a critical point at which the entire vegetation disappears due to light limitation. Both aspects of the alternative state theory have been well studied in temperate shallow lakes, but the validity of the theory for warmer lakes has been questioned. In chapter 2 a graphical model is used to show how climate effects on different mechanisms assumed in the theory may affect the general predictions. An analysis of our data presented in chapter 4 reveals that submerged vegetation has similar overall effects on water clarity across our climatic gradient. Nonetheless, the results hint at differences in the underlying mechanisms between climate zones. For example, the data suggest that the positive effect of vegetation on top-down control of phytoplankton by zooplankton is lost at high densities of fish that are often found in warmer regions. The main factor explaining differences in the water clearing effect of vegetation among lakes in our data set was the concentration of humic substances. In lakes with a high concentration of humic substances vegetation did not enhance the water clarity.
    Immune responses of carp : a molecular and cellular approach to infections
    Forlenza, M. - \ 2009
    Wageningen University. Promotor(en): Huub Savelkoul; Geert Wiegertjes. - S.l. : s.n. - ISBN 9789085855125 - 212
    karper - immuniteitsreactie - immuunsysteem - experimentele infecties - moleculaire biologie - celbiologie - immuniteit - immunologie - diermodellen - vergelijkend onderzoek - carp - immune response - immune system - experimental infections - molecular biology - cellular biology - immunity - immunology - animal models - comparative research - cum laude
    cum laude graduation (with distinction)
    Regulatory and adaptive responses of Lactococcus lactis in situ
    Bachmann, H. - \ 2009
    Wageningen University. Promotor(en): Michiel Kleerebezem, co-promotor(en): J. van Hylckama. - [S.l.] : s.n. - ISBN 9789085854265 - 192
    lactococcus lactis - kaasbereiding - kazen - adaptatie - genetische regulatie - lactococcus lactis - cheesemaking - cheeses - adaptation - genetic regulation - cum laude
    cum laude graduation (with distinction)
    Physics of associative polymers : bridging time and length scales
    Sprakel, J.H.B. - \ 2009
    Wageningen University. Promotor(en): Martien Cohen Stuart; Frans Leermakers, co-promotor(en): Jasper van der Gucht. - S.l. : s.n. - ISBN 9789085853657 - 237
    polymeren - colloïden - micellen - reologische eigenschappen - oppervlakteverschijnselen - polymers - colloids - micelles - rheological properties - surface phenomena - cum laude
    cum laude graduation (with distinction)
    Physiologically based biokinetic (PBBK) models to characterize dose dependent effects, species differences, and interindividual human variation and detoxification of estragole
    Punt, A. - \ 2009
    Wageningen University. Promotor(en): Ivonne Rietjens; Peter van Bladeren, co-promotor(en): B. Schilter. - [S.l.] : s.n. - ISBN 9789085853718 - 251
    toxiciteit - soortverschillen - metabolische detoxificatie - etherische oliën - risicoschatting - carcinogenese - toxicity - species differences - metabolic detoxification - essential oils - risk assessment - carcinogenesis - cum laude
    cum laude graduation (with distinction)
    Exploring the biofluiddynamics of swimming and flight
    Lentink, D. - \ 2008
    Wageningen University. Promotor(en): Johan van Leeuwen, co-promotor(en): M.H. Dickinson; G.J.F. van Heijst. - [S.l.] : s.n. - ISBN 9789085049715 - 184
    vissen - luchtinsecten - vogels - zaden - zwemmen - vliegen - dynamica - vloeistofmechanica - diermodellen - zoölogie - engineering - fishes - aerial insects - birds - seeds - swimming - flight - dynamics - fluid mechanics - animal models - zoology - engineering - cum laude
    cum laude graduation (with distinction)
    Linking variation in plant defence to biodiversity at higher trophic levels: a multidisciplinary approach
    Poelman, E.H. - \ 2008
    Wageningen University. Promotor(en): Marcel Dicke; Louise Vet, co-promotor(en): Joop van Loon; N.M. van Dam. - [S.l.] : s.n. - ISBN 9789085049623 - 163
    brassica oleracea - cotesia - parasitoïden - verdedigingsmechanismen - hyperparasieten - trofische graden - gastheer parasiet relaties - pieris brassicae - insectenplagen - plant-herbivoor relaties - herbivoor-geinduceerde plantengeuren - brassica oleracea - cotesia - parasitoids - defence mechanisms - hyperparasites - trophic levels - host parasite relationships - pieris brassicae - insect pests - plant-herbivore interactions - herbivore induced plant volatiles - cum laude
    cum laude graduation (with distinction)
    Opposites attract?! : on the electrostatically driven co-assembly of polymers in aqueous solution
    Voets, I.K. - \ 2008
    Wageningen University. Promotor(en): Martien Cohen Stuart, co-promotor(en): Arie de Keizer. - [S.l.] : s.n. - ISBN 9789085048862 - 376
    polymeren - elektrostatische lading - micellen - fysicochemische eigenschappen - zelf-assemblage - polymers - electrostatic charging - micelles - physicochemical properties - self assembly - cum laude
    cum laude graduation (with distinction)
    The rules of the game and the game of the rules : normalization and resistance in Andean water control
    Boelens, R.A. - \ 2008
    Wageningen University. Promotor(en): Jandouwe van der Ploeg; H. Achterhuis. - [S.l.] : s.n. - ISBN 9789085048961 - 573
    irrigatiewater - irrigatiesystemen - waterbeheer - gemeenschappen - watergebruik - waterverdeling - waterbeleid - gebergten - Peru - Ecuador - Chili - Zuid-Amerika - waterrechten - andes - staat - irrigation water - irrigation systems - water management - communities - water use - water distribution - water policy - mountains - Peru - Ecuador - Chile - South America - water rights - andes - state - cum laude
    cum laude graduation (with distinction)
    Msimu wa Kupanda : targeting resources within diverse, heterogenous and dynamic farming systemes of East Africa
    Tittonell, P.A. - \ 2008
    Wageningen University. Promotor(en): Ken Giller, co-promotor(en): B. Vanlauwe; Mark van Wijk. - [S.l.] : s.n. - ISBN 9789085048077 - 320
    bedrijfssystemen - bodemvruchtbaarheid - middelentoewijzing - systeemanalyse - simulatiemodellen - kringlopen - voedingsstoffen - stikstofkringloop - organisch bodemmateriaal - kenya - uganda - afrika ten zuiden van de sahara - bodemvruchtbaarheidsbeheer - farming systems - soil fertility - resource allocation - systems analysis - simulation models - cycling - nutrients - nitrogen cycle - soil organic matter - kenya - uganda - africa south of sahara - soil fertility management - cum laude
    cum laude graduation (with distinction)
    Soil moisture dynamics and land surface-atmosphere interaction
    Teuling, A.J. - \ 2007
    Wageningen University. Promotor(en): P.A.A. Troch; Remko Uijlenhoet. - [S.l.] : s.n. - ISBN 9789085047360 - 76
    bodemwater - vocht - atmosfeer - bodemlucht - plant-water relaties - wiskundige modellen - variatie in de tijd - soil water - moisture - atmosphere - soil air - plant water relations - mathematical models - temporal variation - cum laude
    cum laude graduation (with distinction)
    Hydrogen production through biocatalyzed electrolysis
    Rozendal, R.A. - \ 2007
    Wageningen University. Promotor(en): Cees Buisman, co-promotor(en): Bert Hamelers. - [S.l.] : s.n. - ISBN 9789085047315 - 207
    waterstof - afvalwaterbehandeling - elektrolyse - biologische productie - brandstoffen - innovaties - technologie - energiebronnen - energie - biokatalyse - hydrogen - waste water treatment - electrolysis - biological production - fuels - innovations - technology - energy sources - energy - biocatalysis - cum laude
    cum laude graduation (with distinction) To replace fossil fuels, society is currently considering alternative clean fuels for transportation. Hydrogen could be such a fuel. In theory, large amounts of renewable hydrogen can be produced from organic contaminants in wastewater. During his PhD research René Rozendal has developed a new technology for this purpose: biocatalyzed electrolysis. The innovative step of biocatalyzed electrolysis is the application of electrochemically active microorganisms in combination with small input of electrical energy. Electrochemically active microorganisms are a special group of microorganisms that are able to use an electrode as electron acceptor for the oxidation of organic material. Biocatalyzed electrolysis couples this “bio-electrode” to a hydrogen generating electrode by means of a power supply. Consequently, organic contaminants in wastewater can be oxidized (i.e. the wastewater is treated), while at the same time hydrogen is generated as a valuable product. In this way biocatalyzed electrolysis can significantly increase the hydrogen yield from wastewaters compared to other technologies. Furthermore, the innovative design makes a much wider variety of wastewaters than before suitable for hydrogen production. This makes biocatalyzed electrolysis a breakthrough technology for hydrogen production from wastewaters
    Process development for gelatinisation and enzymatic hydrolysis of starch at high concentrations
    Baks, T. - \ 2007
    Wageningen University. Promotor(en): Remko Boom, co-promotor(en): Anja Janssen. - [S.l.] : s.n. - ISBN 9789085046943 - 208
    zetmeel - verwerking - hydrolyse - alfa-amylase - starch - processing - hydrolysis - alpha-amylase - cum laude
    cum laude graduation (with distinction) Enzymatic hydrolysis of starch is encountered in day-to-day life for instance in the dishwasher during removal of stains with detergents or in our mouth during chewing of starch-based foods in the presence of saliva. The reaction is also important for the (food) industry, for example for the production of beer or bio-ethanol. In industry, it is usually preceded by gelatinisation to make the starch molecules available for the enzymes. Both gelatinisation and hydrolysis are usually carried out at a starch concentrations of 30 weight-%. Increasing the starch concentration during these processes can lead to a higher productivity, lower energy consumption, lower use of water and a higher enzyme stability. However, the drawback is that the gelatinisation temperature and the viscosity increase at these conditions. By using the proper process equipment, it is possible to overcome these drawbacks and to perform the gelatinisation and hydrolysis at high starch concentrations leading to the advantages mentioned above. The purpose of this study was therefore to develop a process for gelatinisation and enzymatic hydrolysis of wheat starch at high starch concentrations (more than 40 weight-%). Besides the development of such a process, analysis methods were developed to measure the main process parameters at these conditions.
    Integrated molecular analysis of sugar metabolism of Sulfolobus solfataricus
    Brouns, S.J.J. - \ 2007
    Wageningen University. Promotor(en): Willem de Vos; John van der Oost. - [S.l.] : s.n. - ISBN 9789085047131 - 166
    arabinose - oxidoreductasen - kristaleiwitten - thermofiele bacteriën - arabinose - oxidoreductases - crystal proteins - thermophilic bacteria - cum laude
    cum laude graduation (with distinction)
    Genetical genomics in Arabidopsis: from natural variation to regulatory networks
    Keurentjes, J.J.B. - \ 2007
    Wageningen University. Promotor(en): Maarten Koornneef; Linus van der Plas, co-promotor(en): Dick Vreugdenhil. - [S.l.] : s.n. - ISBN 9789085047049 - 157
    arabidopsis - genetica - genexpressie - genetische variatie - genetische regulatie - kwantitatieve kenmerken - loci voor kwantitatief kenmerk - genexpressieanalyse - arabidopsis - genetics - gene expression - genetic variation - genetic regulation - quantitative traits - quantitative trait loci - genomics - cum laude
    cum laude graduation (with distinction)
    Diversity of the human gastrointestinal microbiota : novel perspectives from high throughput analyses
    Rajilic-Stojanovic, M. - \ 2007
    Wageningen University. Promotor(en): Willem de Vos. - [S.l.] : s.n. - ISBN 9789085046639 - 213
    darmmicro-organismen - soortendiversiteit - fylogenetica - moleculaire genetica - maagdarmziekten - intestinal microorganisms - species diversity - phylogenetics - molecular genetics - gastrointestinal diseases - cum laude
    cum laude graduation (with distinction)
    Chain stoppers in reversible supramolecular polymer solutions
    Knoben, W. - \ 2007
    Wageningen University. Promotor(en): Martien Cohen Stuart, co-promotor(en): N.A.M. Besseling. - [S.l.] : s.n. - ISBN 9789085045748 - 194
    polymeren - polymerisatie - fysische chemie - fysicochemische eigenschappen - supramoleculaire chemie - polymers - polymerization - physical chemistry - physicochemical properties - supramolecular chemistry - cum laude
    cum laude graduation (with distinction)
    The dynamics of shoreline wetlands and sediments of northern Lake Victoria
    Azza, N. - \ 2006
    Wageningen University. Promotor(en): P. Denny, co-promotor(en): J. van de Koppel; F. Kansiime. - [S.l.] : s.n. - ISBN 9789085044994 - 170
    wetlands - meren - mangroves - sediment - oost-afrika - verandering - oevers - wetlands - lakes - mangroves - sediment - east africa - change - shores - cum laude
    cum laude graduation (with distinction)
    Impact of integrated pest management farmer field schools on health, farming systems, the environment, and livelihoods of cotton growers in Southern India
    Mancini, F. - \ 2006
    Wageningen University. Promotor(en): Ariena van Bruggen, co-promotor(en): J.L.S. Jiggins; Aad Termorshuizen. - Wageningen : s.n. - ISBN 9789085043881 - 112
    geïntegreerde plagenbestrijding - gossypium - katoen - boeren - gezondheid - pesticiden - bedrijfssystemen - milieueffect - impact - levensomstandigheden - india - welzijn - integrated pest management - gossypium - cotton - farmers - health - pesticides - farming systems - environmental impact - impact - living conditions - india - well-being - cum laude
    cum laude graduation (with distinction)
    Tillering in spring wheat : a 3D virtual plant modelling study
    Evers, J.B. - \ 2006
    Wageningen University. Promotor(en): Paul Struik, co-promotor(en): Jan Vos; B. Andrieu. - Wageningen : s.n. - ISBN 9789085043775 - 159
    triticum aestivum - tarwe - plantenontwikkeling - uitstoeling - plantenmorfologie - modellen - licht - verrood licht - lichtrelaties - optische eigenschappen - bladoppervlakte-index - grondbedekking - triticum aestivum - wheat - plant development - tillering - plant morphology - models - light - far red light - light relations - optical properties - leaf area index - ground cover - cum laude
    cum laude graduation (with distinction)
    The alternative sigma factor sigmaB and the stress response of Bacillus cereus
    Schaik, W. van - \ 2005
    Wageningen University. Promotor(en): Tjakko Abee; Willem de Vos; Marcel Zwietering. - Wageningen : s.n. - ISBN 9789085041849 - 165
    bacillus cereus - stressreactie - pathogenen - voedselveiligheid - overleving - rna-polymerase - bacillus cereus - stress response - pathogens - food safety - survival - rna polymerase - cum laude
    cum laude graduation (with distinction) The bacterium Bacillus cereus is responsible for a large number of cases of foodborne illness across the world. It is also an important cause of spoilage of food, in particular of milk and dairy-products. The growth and survival of B. cereus in food or during an infection is for a large part determined by to what extent the bacterium can adapt to changes in its environment. This process is known as the stress response and the protein SigmaB has an important role in it. Stress in B. cereus leads to the rapid activation of SigmaB. Subsequently, SigmaB coordinates the transcription of a set of genes, which leads to an increased resistance to stress. For example, SigmaB contributes to the growth and survival of B. cereus at low and high temperatures. It also has a role in cellular metabolism, which may indirectly also contribute to stress resistance. The knowledge obtained on the role of SigmaB in the stress response of B. cereus may contribute to the development of new, efficient, and safe methods for the production of food.
    Functional and comparative genomics of the Archaea
    Ettema, T.J.G. - \ 2005
    Wageningen University. Promotor(en): Willem de Vos; John van der Oost. - [S.l.] : s.n. - ISBN 9789085042297 - 172
    bacteriën - transcriptie - genexpressieanalyse - bacteria - transcription - genomics - cum laude
    cum laude graduation (with distinction)
    Turbulent dispersion in the Atmospheric Convective Boundary Layer
    Dosio, A. - \ 2005
    Wageningen University. Promotor(en): Bert Holtslag; P.J.H. Builtjes, co-promotor(en): Jordi Vila-Guerau de Arellano. - [S.l.] : s.n. - ISBN 9789085041719 - 173
    atmosfeer - turbulentie - convectie - chemische samenstelling - ruimtelijke verdeling - grenslaag - atmosphere - turbulence - convection - chemical composition - spatial distribution - boundary layer - cum laude
    cum laude graduation (with distinction)
    Particle separation and fractionation by microfiltration
    Kromkamp, J. - \ 2005
    Wageningen University. Promotor(en): Remko Boom, co-promotor(en): Karin Schroen; Ruud van der Sman. - [S.l.] : s.n. - ISBN 9789085042396 - 184
    microfiltratie - membranen - deeltjes - deeltjesgrootte - simulatiemodellen - computersimulatie - microfiltration - membranes - particles - particle size - simulation models - computer simulation - cum laude
    cum laude graduation (with distinction) For the production of present-day dairy products, raw milk is often considered an entity. However, a large quality improvement could be reached if selected constituents were available. In order to achieve this, milk will have to be fractionated prior to use in dairy products. Microfiltration is an important technique for the fractionation of milk; the pore size typically being in the order of micrometers. However, due to insufficient separation caused by blockage of the filter, the potential of microfiltration is still hardly used. This instigated the Ph.D. research project of Janneke Kromkamp which aims at using microfiltration for fractionation to its fullest potential. The interaction between the different microparticles in milk and the surrounding liquid were studied at a fundamental level by means of computer simulation techniques. By coupling this information to observations on the microfiltration of milk, important new insights were obtained which can substantially improve the fractionation process. Paradoxically enough, the liquid flow was better able to fractionate particles than the membrane alone. Because the particles organise in the liquid flow, the large ones moving to the centre of the channel, the smaller ones can be separated easily. Herewith, membrane blockage, which was the biggest challenge in this thesis, is prevented. An additional advantage is that the fractionation process can be completely controlled by easily controllable process parameters. The high-quality dairy products mentioned earlier have now come within reach.
    Heterogeneity and scale in the rational design of an immobilized biocatalyst
    Roon, J.L. van - \ 2005
    Wageningen University. Promotor(en): Hans Tramper, co-promotor(en): Rik Beeftink; Karin Schroen. - [S.l.] : s.n. - ISBN 9789085042464 - 209
    katalysatoren - immobilisatie - enzymen - enzymactiviteit - synthese - antibiotica - catalysts - immobilization - enzymes - enzyme activity - synthesis - antibiotics - cum laude
    cum laude graduation (with distinction)
    Equilibrium polymers in solution and at interfaces
    Gucht, J. van der - \ 2004
    Wageningen University. Promotor(en): Gerard Fleer; Martien Cohen Stuart, co-promotor(en): N.A.M. Besseling. - [S.I.] : s.n. - ISBN 9789058089632 - 293
    polymeren - hydrofiele polymeren - evenwicht - grensvlak - waterstofbinding - reologische eigenschappen - visco-elasticiteit - polymers - hydrophilic polymers - equilibrium - interface - hydrogen bonding - rheological properties - viscoelasticity - cum laude
    cum laude graduation (with distinction)
    Impressions of Interactions: Land as a dynamic result of co-production between man and nature
    Sonneveld, M.P.W. - \ 2004
    Wageningen University. Promotor(en): J. Bouma; Tom Veldkamp. - Wageningen : s.n. - ISBN 9789058089694 - 132
    landinrichting - bodemkunde - landgebruik - boeren - bruikbare grond - bodemtypen (naar cultuur) - houding van boeren - natuur - land development - soil science - land use - farmers - soil resources - soil types (cultural) - farmers' attitudes - nature - cum laude
    cum laude graduation (with distinction)
    How do birds sing? sound analysis - mechanical modelling - muscular control
    Elemans, C.P.H. - \ 2004
    Wageningen University. Promotor(en): Johan van Leeuwen, co-promotor(en): Mees Muller; O.N. Larsen. - Wageningen : Ponsen & Looijen - ISBN 9789085041115 - 144
    duiven - streptopelia - vogels - liedjes - geluidsproductie - vibratie - mechanica - fysische modellen - spieren - zoölogie - pigeons - streptopelia - birds - songs - sound production - vibration - mechanics - physical models - muscles - zoology - cum laude
    cum laude graduation (with distinction)
    Faradaic and adsorption-mediated depolarization of electric double layers in colloids
    Duval, J.F.L. - \ 2003
    Wageningen University. Promotor(en): Martien Cohen Stuart, co-promotor(en): Herman van Leeuwen. - Wageningen : s.n. - ISBN 9789058089403 - 238
    colloïden - elektrokinetische potentiaal - oppervlakteverschijnselen - oppervlaktechemie - colloids - electrokinetic potential - surface phenomena - surface chemistry - cum laude
    cum laude graduation (with distinction)
    Self-consistent-field theory for chain molecules: extensions, computational aspects, and applications
    Male, J. - \ 2003
    Wageningen University. Promotor(en): Gerard Fleer, co-promotor(en): Frans Leermakers. - [S.l.] : s.n. - ISBN 9789058087799 - 184
    polymeren - moleculaire structuur - thermodynamica - polymers - molecular conformation - thermodynamics - cum laude
    cum laude graduation (with distinction)
    Ambition, Regulation and Reality. Complex use of land and water resources in Luwu, South Sulawesi, Indonesia
    Roth, D. - \ 2003
    Wageningen University. Promotor(en): F. von Benda-Beckmann. - [S.I.] : s.n. - ISBN 9789058088789 - 338
    cum laude - regulations - law - natural resources - land use - water resources - irrigation - conflict - politics - society - indonesia - sulawesi - regelingen - recht - natuurlijke hulpbronnen - landgebruik - watervoorraden - irrigatie - conflict - politiek - samenleving - indonesië - celebes
    In this book I present three case studies of the complex regulation of use of land and water resources in Luwu. Attention to the role of legalcomplexity -the existence of different sources and definitions of normative-legal regulation in the same socio-political space - is an important conceptual point of departure of this study. Each of the three case study sections contains specific conclusions pertaining to the issues involved. The last chapter of the book (chapter 11) is primarily a reflection on the wider meaning of the forms of complexity analyzed in the case studies for processes of regulation of resource use. In an epilogue I pay attention to the complex character of broader socio-political processes in Luwu District. 

    The state-led development of irrigation systems is an important factor in the economic and societal changes in Luwu since the colonial period. The basis of these rapid and radical changes was laid by the Dutch colonial government in the thirties of last century. Two spearheads of colonial development policy in the framework of the 'Ethical Policy' were emigration (from densely populated Java to the thinly populated 'OuterIslands' of the colonial empire) and irrigation. InNorth Luwu, both were combined in programmes for colonization (resettlement of Javanese farmers on islands outside Java) and development of large irrigation systems based on civil engineering approaches.

    These colonial development plans for Luwu were suddenly interrupted by the turbulent social and political developments in the region: the Japanese occupation, the return of the colonial power after Japanese capitulation, decolonization and theDarulIslam (DI/TII) rebellion from the early fifties until 1965. In that same year the Suharto regime came to power. After 'peace and order' had been restored in an extremely violent way, large financial donors like the World Bank supported the regime by allocating large sums of development funding. 'Pembangunan' (development) became a keyword in the political ideology of Suharto's 'New Order'. From the late sixties, the old colonial development agenda was revived. In Luwu, this led to an approach combining what was now called 'transmigration' (resettlement of farmer families from Java,BaliandLombok) with the large-scale development of irrigation systems and other infrastructure. These interventions have radically changed Luwu, and not only in a negative sense. Irrigated agriculture and improved infrastructure have considerably increased the standard of living and food security of the local population of Luwu as well as of migrants.

    At the same time, transmigration and regional migration have turned Luwu into an, in many respects, very complex society in which tensions and conflicts between the local population and migrants along lines of ethnic and religious affiliation regularly lead to violence. Because of the ethnic diversity it harbours, Luwu is often called a 'TamanMini' (MiniatureGarden), in analogy with the exhibition of the material culture of the 'recognized' ethnic groups in the archipelago established by the Suharto family. Luwu society is not only complex in a legal sense but also in a socio-cultural, political-administrative sense, as I will show in the three case studies. This high degree of complexity of Luwu society also plays an important role in issues concerning the use of natural resources.

    The first case study (see chapter 3) is an analysis of the regional history of migration of farmers from highlandSouth Sulawesito lowland Luwu. This massive migration in the second half of the twentieth century has had a great impact on current land tenure inNorth Luwu. The availability of land resources in Luwu was a strong pull factor for highland migrants in search of agricultural land. The massive and uncontrolled character of this migration and settlement inNorth Luwumade these processes politically very sensitive. Differences in ethnic and religious identity between migrants and local population are, moreover, a continuous source of tension and violent conflict. A deeper explanation of the political and social sensitivity of this migration can be found in the ways in which migration is related to wider processes of socio-economic, cultural and political-administrative change in the region. In my analysis of migration I pay special attention to the emergence and growing role of a specific 'Toraja' identity among the highland population. I pose the question whether there is a relationship between the emergence of new identities and identifications in the area and migration to lowland Luwu. ThisTorajaidentity is primarily a product of Dutch colonial and missionary politics. Both in colonial administration and mission thereexistedthe wish to unite the various population groups in highland South andCentral Sulawesiadministratively into 'GreaterToraja'. This administrative unit was intended to unite all Christianized highland groups into a 'buffer' against Islam, which had been established in lowlandSulawesimany centuries ago and was seen as a threat.

    Indonesian independence did not bring these political ambitions to an end. In the fifties they even played an important role in regional politics. Its most important manifestations were attempts to establish 'GreaterToraja' (called 'TorajaRaya') as an administrative unit at the level of a province, the struggle for autonomy of the southern highlands as 'TanaTorajaDistrict' from the languishing Luwu kingdom, and a lowland-oriented expansionism referred to as 'Lebensraum' by formerTorajapoliticians. In the latter, the high potential of lowland Luwu in terms of (irrigable) agricultural land played an important role. Massive migration to the Luwu Plain was not only seen as a solution to the social problems in the densely populated and socio-politically hierarchic highlands but also as part of a political strategy oriented towards Luwu. The first ideal died in the political realities in the region in the course of the fifties. The second ideal was realized by the actual establishment ofTanaTorajaDistrict in the fifties. The expansionism oriented towards lowland Luwu manifested itself in a rapidly increasing migration toNorth Luwuand exploitation of land in this area. I conclude that there was indeed a relation between the emergence ofTorajaidentity and migration strategies to gain access to land resources in lowland Luwu.

    The second case study (see chapters 4 to 6) is an analysis of the long-term effects of intervention in land rights in the framework of thePompenganIntegrated Area Development Project (PIADP). PIADP, a bilateral Indonesian-Dutch project for rural development, was propagated as a model for integrated rural development inIndonesia. The project had started in 1980 as thePompenganImplementation Project (PIP), an irrigation project that focused on construction and paid little attention to the social aspects of development. Under the influence of the problems that arose during implementation, of changing views of 'development' and of increasing attention to the social dimensions of processes of planned change PIP changed into the 'integrated' PIADP. The core of PIADP was intervention in land tenure through a programme for redistribution of land and resettlement of farmers.

    Notwithstanding this shift towards other core activities the project basically remained an irrigation project. Problems of land use, land rights and population density were primarily seen as a threat to local management of the future irrigation infrastructure, and land reform and farmer settlement as a solution to these problems. However, the new approach also meant a shift from a technical intervention to a much more radical, complex and socially sensitive socio-legal type of intervention. PIADP was characterized by new, social objectives originating from Dutch development policy, like creating an egalitarian structure of landownership and greater security of tenure. Thus, a growing awareness of the complexities in implementing PIP had led to even much more complex solutions to the problems, tied to ever more ambitious objectives. To reach these objectives, a 'project law' was created on the basis of Dutch donor norms and priorities as well as sections of the Indonesian 1960 Basic Agrarian Law. Existing claims to land in the project area (that is: local rights built up in the past but not by definition recognized and usually not titled by the government) were inventoried and weighed in a selection procedure for PIADP. The claim holders whose claims were recognized by the project, became 'beneficiaries' of PIADP, and qualified for land and other project facilities.

    The central research questions for this part of the research are: which definition of land rights has 'won', the local one based on labour invested in and boundaries created by land clearing, or the (re)definition of land rights on the basis of PIADP project law? What was the impact of the land reform programme on land use and land rights? How do various actors cope with the situation of legal complexity? How are conflicts solved and by whom? What is the role of legal institutions? Chapter 4 contains a description of the local context of PIP and PIADP and an analysis of the emergence of new developmental ambitions and objectives for PIADP. In chapter 5 I present an analysis of the implementation of the programme of land redistribution and settlement in PIADP, mainly based on my own experiences as an adviser of the land reform and settlement programme. In chapter 6 I analyze the long-term effects of this programme on security of tenure in the former project area. The analysis shows, among others, that claimants and former 'beneficiaries' of the programme have massively returned to the pre-project claim boundaries. The definition of land rights based on pre-project claims to land prove to be much stronger and to give more security of tenure than land rights defined and recognized by the government in the framework of PIADP. Further, the analysis makes clear that the government has completely withdrawn from the problems of former PIADP. Formal state-issues land titles have no value for those who hold them. Hence, coping with the continuing tensions and conflicts caused by PIADP requires a high degree of self-regulating capacity of the actors involved in the local conflicts in various ways.

    The third case study is an analysis of the role of land and water resources inKertoraharjo,avillageofBalinesetransmigrantsin theKalaenaarea inNorth Luwu(see chapters 7 to 10). Chapter 7 describes the history of settlement in the area and development of a relatively prosperous migrant society. Specifically Balinese arrangements in the fields of religion and village administration, social security and local irrigation management exist side by side with the blueprints of government administration. The diversity of areas of origin of the Balinesetransmigrantsand the different traditional norms and values (Ind.adat) introduced by these groups made the process of unification a difficult one. Chapter 8 focuses on the role of land inKertoraharjo. I analyze the differences in access to land for three status categoriesof migrants: the initialtransmigrants, their offspring and spontaneous migrants. In addition, I analyze the growing importance of cocoa cultivation next to (and sometimes instead of) irrigated agriculture since the late eighties. In an analysis of the historical development of landownership I show how Balinese landownership has spread fromKertoraharjoacross an increasingly large area stretching out across the provincial border. The growing interest in cocoa cultivation has crucially contributed to this trend. Expansion of Balinese control over land took place wholly outside the sphere of state regulation of land tenure and recognition through titling. Finally, I pay attention to the role of some forms of access to irrigated land that play an important role in strategies of economic advancement of, especially, the offspring of initialtransmigrantsand spontaneous migrants: sharecropping and pawning of land.

    Together, chapters 9 and 10 form an analysis of local irrigation management in the tertiary units of theKalaenairrigation system in which Balinese farmers own land. The technical and organizational uniformity of state-built irrigation systems in Luwu hides a high degree of ethnic and cultural diversity of the various migrant groups. What does this field of tension between standardized arrangements for local management and local diversity mean in the case of Balinese inKalaenasystem? The Balinesetransmigrantsbrought their own traditions, knowledge and practices of local irrigation management associated with the so-calledsubak, an age-old Balinese institution for irrigated rice agriculture in the broadest sense of the term (that is:subakdoes not only refer to operational and maintenance tasks but includes irrigation technical and managerial, agronomic and religious-ritual dimensions of rice agriculture). This part of the research focused on the history of local irrigation management among Balinese in the tension field formed by technology, norms and rules, and organizational arrangements based on engineering conceptions of irrigation management in the tertiary units on the one hand, and on thesubaktradition on the other. The most important research questions were: what is the role ofsubakand water users' associations in tertiary irrigation management among Balinese farmers? How are both related in the dimensions of technology, normative regulation and organizational arrangements? To what degree and in what way haveboth changed, influenced or merged in new 'hybrid' forms of local irrigation management? What is the influence of different definitions and conceptualizations of 'irrigation management' in both approaches?

    This part of the research shows that, deeply influencing each other,subakand the complex of water users' association and tertiary unit have developed in a location-specific manner. As a formal organization,subakhas become relatively marginal under the influence of the statutory introduction of the water users' associations related to the tertiary structure of the irrigation system. However, as an institution (that is: as regularized patterns of behaviour)subakcontinues to play a crucial role. Technical, normative and organizational elements ofsubakhave emerged in the world of local irrigation management formally defined by tertiary units and water users' associations. Thus, bothsubakand WUA have become 'hybrid worlds'.

    The last chapter (chapter 11) concludes the book with a reflection on the complex society that Luwu has become and its meaning for issues of resource management. The existence of a high degree of social, legal, ethno-religious and political-administrative complexity and its impact on forms of regulation, as clearly present and visible in the three case studies of this book, make approaches to regulation of natural resource use based on instrumental views of law coupled to mechanistic views of processes of development quiteprospectless. In an epilogue I finally point to the broader socio-political dimensions of Luwu District itself as a complex society in times of rapid and radical socio-political change.
    Mixed Solid-State Fermentation. Numerical modeling and experimental validation
    Schutyser, M.A.I. - \ 2003
    Wageningen University. Promotor(en): Remko Boom, co-promotor(en): Arjen Rinzema. - [S.I.] : s.n. - ISBN 9789058088482 - 165
    fermentatie - vermenging - bioreactoren - schimmels - warmteoverdracht - waterverplaatsing - deeltjes - modellen - fermentation - mixing - bioreactors - fungi - heat transfer - water transfer - particles - models - cum laude
    cum laude graduation (with distinction)
    Scatterhoarding and tree regeneration : ecology of nut dispersal in a Neotropical rainforest
    Jansen, P.A. - \ 2003
    Wageningen University. Promotor(en): Frans Bongers; Herbert Prins, co-promotor(en): Sip van Wieren. - [S.I.] : s.n. - ISBN 9789058087775
    zaadverspreiding - noten - carapa procera - knaagdieren - natuurlijke verjonging - zaadpredatie - zaadgrootte - natuurlijke selectie - tropische regenbossen - seed dispersal - nuts - carapa procera - rodents - natural regeneration - seed predation - seed size - natural selection - tropical rain forests - cum laude
    cum laude graduation (with distinction)
    Fluorescence fluctuation spectroscopy applied to living plant cells
    Hink, M. - \ 2002
    Wageningen University. Promotor(en): A.H.J. Bisseling; A.J.W.G. Visser. - S.l. : s.n. - ISBN 9789058087027 - 137
    fluorescentie-emissiespectroscopie - planteiwitten - fosfolipiden - cellen - plantenweefsels - fluorescence emission spectroscopy - plant proteins - phospholipids - cells - plant tissues - cum laude

    Keywords: Fluorescence correlation spectroscopy, photon counting histogram, intracellular, plant, AtSERK1

    In order to survive organisms have to be capable to adjust theirselves to changes in the environment. Cells, the building blocks of an organism react to these changes by sending signal molecules (for example hormones). Important biological processes like cell-division, -growth, -differentiation and - death are started after receipt of specific signal molecule that will trigger and activate other signal molecules. During evolution a complex network of signal cascades has been developed. Errors in this network may lead to disorders, diseases or even death. To study the molecules involved in this network the method, that has been used in this thesis, is both very selective as sensitive: fluorescence. After excitation using light of a specific color, a fluorescent molecule will emit light of a different color. Since most molecules are hardly fluorescent their selves, fluorescent groups can be coupled to the molecule of interest in order to distinguish it from the other molecules.

    The research described in this thesis is devoted to the application of two novel fluorescence techniques fluorescence correlation spectroscopy (FCS) and photon counting histogram analysis (PCH) to intracellular plant research. Both techniques retrieve information from the fluctuations in the fluorescence intensity that can be observed in a small volume element. The high sensitivity allows measurements under equilibrium conditions at the single-molecule detection level. Moreover, FCS-analysis can retrieve a large number of parameters, describing the time-dependent decay of the fluctuations, such as the local particle concentration, mobility of the fluorescent particles and rate constants of fast reversible reactions like triplet kinetics and protonation of the chromophore. Hence, it has been recognized that FCS has a high potential to monitor the behaviour of fluorescently labeled biomolecules in living cells at physiological relevant concentrations. Therefore, FCS could be a valuable tool in cell biology, especially in the study of molecular interactions.

    The behaviour of fluorescently labeled molecules was first studied in model biochemical systems, before applying FCS to the complex intracellular environment. The binding of a enhanced GFP labeled single chain antibody fragment (scFv-GFP) to its antigen, lipopolysacharide, present in the outer cell membrane of Ralstonia solanacearum bacteria clearly demonstrates the ability of FCS to distinguish particles on basis of the difference in diffusion coefficient.

    The diffusion coefficients of micelles loaded with a fluorescent phospholipid have been determined by FCS as well as by dynamic light scattering (DLS). The measurements of the micelle hydrodynamic volume using both techniques have been demonstrated to be equivalent. However, the concentration sensitivity of FCS is orders of magnitude higher than that of DLS and is, moreover, able to determine the extremely low critical micelle concentration by measuring the diffusion time as function of detergent concentration.

    Intracellular experiments may be complicated by the presence of autofluorescent molecules. Plant cells may contain molecules like chlorophyll, localized in the chloroplast, and pigment molecules in the vacuole that will not only fluoresce rather strongly but have broad absorption bands as well, able to absorb the fluorescence light emitted by other fluorophores. Hence, either experiments have been carried out in intracellular regions of cowpea protoplasts lacking these compartments or cell types were selected that originate from root tissue and therefore lack many pigment molecules that are responsible for intense autofluorescence. In order to achieve high signal to noise ratios (SNR) without disturbance of autofluorescence, dye depletion or cellular damage, the optimum emission wavelength of the fluorophores should lie between 560 and 610 nm and the excitation intensities in the visible range (458-514 nm) should not exceed 10 -2. The diffusion rate of synthetic fluorophores in the cytoplasm and nucleus of the plant cells was retarded by a factor 2 to 4 as compared to buffer due to the viscous intracellular environment. Moreover, FCS was able to distinguish between different types of motion: The diffusion of dyes such as rhodamine green and Cy5 did show a clear deviation from normal Brownian motion in the cytoplasm and the curves could only be fitted according to a multi-component diffusion model or an anomalous diffusion model, indicating the restricted movement of the fluorophores. One reason for this behaviour is the non-specific interactions with (large) cellular structures. The diffusion of fluorescent lipid analogues in the plant plasma membrane showed a clear deviation from Brownian motion as well, most likely caused by the presence of inhomogeneities in the plasma membrane such as microdomains.

    Green fluorescent protein (GFP) and the large number of variants available have changed microscopic research in (plant) cell biology completely. The possibility to genetically fuse the fluorescent protein moiety to the protein of interest have replaced the laborious and sometimes inefficient methods of protein labeling, purification and microinjection. On basis of their photophysical characteristics EGFP is the best fluorophore to select for single channel fluctuation spectroscopy experiments and ECFP-EYFP is the best pair to be used in dual-color based methods such as fluorescence resonance energy transfer (FRET) or dual-color fluorescence cross-correlation microscopy (FCCM). To test the applicability of FRET-FCM using ECFP and EYFP as donor-acceptor pair, fusion proteins of ECFP and EYFP having a linker of 8 or 25 alanine residues (CA 8 Y and CA 25 Y, respectively) were created. Fluorescence lifetime measurements and spectral imaging microscopy yielded FRET-efficiencies of 25% for CA 8 Y and only 8% for CA 25 Y both in vitro and in vivo . FRET-FCS measurements by autocorrelating the sensitised emission of EYFP suffered from very low fluorescence count rates. Prolonged measurement times and precise bleed-through correction were required to visualize the presence of FRET in the CA 8 Y protein. FRET measurements within the plant cells were not successful most likely due to severe scattering of the fluorescence in the plant cells, which further reduced the detected fluorescence intensity.

    In order to detect molecular interactions FRET can be used but this technique requires that the acceptor and donor molecules are in close proximity of each other. However, dual-color cross-correlation microscopy (FCCM) does not require a small distance between two fluorophores since the technique has been based upon the coincidence of intensity fluctuations in two different detection channels. This difference can be illustrated with CA 25 Y. Although some FRET occurred (E = 8%) as have been retrieved from fluorescence lifetime and spectral analysis, autocorrelation of the sensitised acceptor intensity traces did yield a FRET-FCM curve. However, using FCCM the cross-correlation curve for the CA 25 Y protein was clearly present within 2 minutes. This implies that in studies involving interactions between molecules within large complexes or across the plasma-membrane, where FRET studies might not be possible due to the relatively long distances between the molecules, dual-color FCCM is an attractive alternative.

    To study the oligomerization state and mobility of Arabidopsis thaliana somatic embryogenesis receptor kinase 1 (AtSERK1), a transmembrane protein involved in the embryogenesis of plant cells, AtSERK1 - cDNA was fused to that of ECFP or EYFP and transiently expressed in cowpea protoplasts. PCH analysis showed that 16% of the total amount of AtSERK1 fusion protein in the plasma membrane is present in dimerised form, while no evidence was found for higher oligomeric complexes. By FCCM measurements it was shown that both the monomeric as the dimerised form of fluorescent AtSERK1 diffuse in the plasma membrane according to a two-dimensional Brownian diffusion model. Although it has been shown that fluorescent lipid molecules can be restricted in their motion along the plasma membrane of cowpea protoplasts, no indication for anomalous diffusion was found for the AtSERK1 fusion proteins.

    In conclusion the application of fluorescence fluctuation techniques in living plant cells is an important asset for cell biological research. The approaches described in this thesis provide possibilities to study the dynamics of molecules at physiological relevant concentrations inside the living cell in a sensitive and selective way.

    Strawberry and beyond: a novel and comprehensive investigation of fruit maturation and ripening
    Aharoni, A. - \ 2002
    Wageningen University. Promotor(en): J.N.M. Mol; W.J. Stiekema; A.P. O'Connell. - S.l. : s.n. - ISBN 9789058087256 - 250
    fragaria - aardbeien - rijp worden - rijpen - genexpressie - genexpressieanalyse - fragaria - strawberries - ripening - maturation - gene expression - genomics - cum laude

    Functional-genomics tools such as Expressed Sequence Tags (ESTs) and whole genome sequencing, gene expression using macro and micro arrays and generation of mutant populations contributed largely to the research on model plants, mainly Arabidopsis thaliana . A substantial portion of this "tool-box" can also be utilized successfully for research on non-model plants, which are more difficult and time consuming to deal with, but allow investigations of unique biological processes such as fruit flavour biogenesis. As a first phase in a strategy to investigate strawberry fruit maturation and to identify key genes associated with fruit quality traits (in particularly aroma and flavour), we generated a collection of more than 1000 ESTs from ripe fruit cDNA library (cv. Elsanta ). Combining information on the putative identity of the ESTs and gene expression studies was subsequently used to select candidate genes for further investigation. In early studies we used RNA gel-blots to analyse levels of 50 selected genes (selected based on homology). More than 15 transcripts showed ripening - regulated expression pattern and included FaMYB1 , a member of the R2R3 MYB family of transcription factors. The FaMYB1 gene was subjected to a more profound investigation, and the results suggested it to function as repressor of late flavonoid biosynthesis genes in the ripe strawberry fruit. To perform a more comprehensive study of gene expression we constructed DNA microarrays representing 1700 strawberry cDNAs and compared gene expression both during fruit development and between receptacle and achene tissues. A major finding in this study was the identification of the SAAT gene encoding the ester-forming enzyme from strawberry. Volatile esters are major components of the aroma profiles of most fruit, including strawberry. We also generated a second, dedicated set of arrays, comprising only 384 probes selected on the basis of the first hybridisation results including mainly ripening regulated and receptacle associated cDNAs. This set was used to analyse gene expression in fruit treated with auxin and fruit under oxidative stress conditions. Taken as a whole, microarray experiments have provided us with an extensive and novel insight into the transcriptional programs active in strawberry fruit during maturation. They also led to the identification of several other flavour associated genes which are currently being characterised. As a complementary step for the large-scale analysis of gene expression using microarrays we conducted a set of experiments aimed at identifying key metabolic changes in strawberry fruit during development using a Fourier Transform Ion Cyclotron Mass Spectrometry (FTMS)-based method. The analysis identified changes in the levels of a large range of masses corresponding to known fruit metabolites and revealed novel information on the metabolic transition from immature to ripe fruit. The integration of emerging functional genomic practices will be an invaluable approach both for gene discovery and for understanding the biology of non-model plant species such as strawberry.

    The immune response of carp to blood flagellates : a model for studies on disease resistance and stress
    Saeij, J.P.J. - \ 2002
    Wageningen University. Promotor(en): W.B. van Muiswinkel; G.F. Wiegertjes. - S.l. : s.n. - ISBN 9789058086839 - 183
    karper - trypanosoma - flagellaten - bloed - immuniteitsreactie - immuniteit - macrofagen - lymfocyten - dna-sequencing - ziekteresistentie - stress - ziektemodellen - gastheer parasiet relaties - visteelt - immunologie - celbiologie - in vivo experimenten - carp - trypanosoma - flagellates - blood - immune response - immunity - macrophages - lymphocytes - dna sequencing - disease resistance - stress - disease models - host parasite relationships - fish culture - immunology - cellular biology - in vivo experimentation - cum laude

    To date, aquaculture accounts for 25% of the total world supply of (shell)fish for human consumption, a relative contribution that is expected to increase with time. The increased global demand for (shell)fish has lead to a further intensification of aquaculture with the inevitable result that fish become disposed to stress and diseases. An important factor leading to this predisposition is stress induced by aquaculture practices such as crowding, transport, handling and impaired water quality. The World Health Organisation seeks to actively stimulate prophylactic measures such as vaccination, genetic selection and the use of immunomodulation by feed additives to prevent future disease outbreaks in aquaculture. Imperative for these approaches are in vivo infection models that allow reliable, reproducible challenge experiments to monitor efficacy of new treatments. Trypanoplasma borreli and Trypanosoma carassii are both protozoan kinetoplastid extracellular blood parasites of fish. The Kinetoplastida contain a number of parasites of major importance to man, e.g.Trypanosoma brucei (sleeping sickness), Leishmania spp. (leishmaniasis), Trypanosoma cruzi (Chagas' disease). Both T. borreli and T. carassii are transmitted by blood-sucking leeches and infect cyprinids, the dominating species in freshwater aquaculture. Infection of carp with these parasites is an excellent model for comparative studies on host-parasite interactions with clear relevance to the problems faced by present day aquaculture ( chapter one ).

    Genetic selection for disease resistance can provide a major contribution to prophylaxis. One route to identify gene regions that determine susceptibility of fish to pathogens is the candidate gene approach. This approach is making use of known types of responses that have been proven important in the development of innate and acquired protective immunity. In chapter two the sequence of a candidate gene: the carp natural resistance-associated macrophage protein (NRAMP) is described. This protein is a putative metal transporter. Metals such as iron are essential nutrients for pathogens. Therefore, reducing iron availability can be an important part of the host defence strategy. Moreover, iron acts as a catalyst in the production of molecules such as hydroxyl radicals (OH·), which act as toxicants in the defence against intracellular pathogens. In chapter three the sequence of a second candidate gene: carp inducible nitric oxide synthase (iNOS) is described. Not only oxygen but also nitrogen radicals, produced by phagocytes, can act as toxicants, forming an important innate defence mechanism against pathogens. Trypanoplasma borreli or bacterial cell wall products induced iNOS expression in carp head kidney phagocytes leading to the production of high concentrations of the nitric oxide (NO) radical. The NO produced in vitro by head kidney phagocytes was cytostatic to the parasite.

    Carp challenged in vivo with T. borreli produce high amounts of NO ( chapter four ). The production of toxic molecules such as NO is potentially dangerous. In fact NO overproduction can lead to tissue damage in the host. Indeed, in vivo inhibition of NO production led to a higher rather than a lower survival of infected carp. A possible explanation for the harmful effect of NO in vivo could be the observation that, at least in vitro , NO can inhibit the proliferation of carp lymphocytes. Interestingly, in clear contrast with the effect of T. borreli , T. carassii did not induce production of NO.

    Lymphocytes are much more susceptible to the cytostatic effect of NO than phagocytes, which are mainly macrophages and neutrophilic granulocytes ( chapter five ). This difference could be ascribed to the fact that lymphocytes had lower levels of the most important cellular antioxidant glutathione (GSH). Furthermore, lymphocytes had lower levels of key enzymes involved in the maintenance of GSH compared to phagocytes.

    In chapter six we describe two sequences for carp tumour necrosis factor (TNF)a, which can be considered a third candidate gene for resistance to diseases of fish. Indeed, a polymorphism in carp TNFa2 could be associated with trypanotolerance. TNFais a cytokine produced mainly by phagocytes in response to inflammation, infection and other physiological challenges. In vitro , T. borreli could induce expression of TNFa, which mediated the production of NO by phagocytes and the proliferation of leukocytes.

    To study the exact role of phagocytes in the immune defence against T. borreli , we applied a technique to deplete carp of macrophages, in vivo ( chapter seven ). These animals became more susceptible to opportunistic bacterial infections. When infected with blood flagellate parasites, however, there was a moderate increase in parasitaemia only, demonstrating that macrophages do not play a major role in the resistance against T. borreli or T. carassii . Carp surviving an infection with T. borreli are resistant to re-infection for more than 12 months. This acquired resistance was not abrogated when the animals were depleted of macrophages.

    The major immunogenic molecules of T. borreli are proteins (probably membrane glycoproteins) and CpG DNA motifs ( chapter eight ). Carp infected with T. borreli were found to upregulate the expression of the inflammatory cytokines TNFaand interleukin (IL)-1bearly during infection. During a later phase, an upregulation of acute phase proteins (serum amyloid A, complement factor 3 and alpha-2-macroglobulin) was seen. Infection with T. borreli induced a non-specific proliferation of lymphocytes, most probably via the induction of TNFaand IL-1b, leading to the formation of parasite-aspecific antibodies. However, late during infection trypanotolerant carp do produce specific antibodies that act together with complement in lysing T. borreli .

    Stress, imposed by daily handling, severely affected resistance of carp to T. borreli ( chapter 9 ). Most likely, the effect was mediated by increased levels of cortisol. We demonstrated that, in vitro, cortisol inhibited T. borreli -induced expression of IL-1b, TNFa, SAA and iNOS thereby modulating the immune response. Cortisol also induced apoptosis of lymphocytes, but not of phagocytes. One of the first cellular metabolic changes during cortisol-induced apoptosis was a depletion of GSH. As GSH plays a major role in the protection against NO-mediated inhibition of lymphocyte proliferation, cortisol may render stressed animals more susceptible to the immunopathological effects of NO.

    In conclusion, infection of carp with blood flagellates presents an excellent model for comparative studies on host-parasite interactions. Evaluation of the modulating effects of stress on the immune response to this type of pathogens can provide information with clear relevance to the disease problems faced by intensive animal production systems.

    Oxygen diffusion in fish embryos
    Kranenbarg, S. - \ 2002
    Wageningen University. Promotor(en): J.L. van Leeuwen; J.W.M Osse; M. Muller. - S.l. : s.n. - ISBN 9789058086808 - 183
    vissen - embryo's - embryonale ontwikkeling - embryologie - zuurstof - diffusie - zuurstoftransport - zuurstofconsumptie - voedingsstoffen - beperkingen - grootte - vorm - cardiovasculair systeem - genexpressie - modellen - biofysica - fishes - embryos - embryonic development - embryology - oxygen - diffusion - oxygen transport - oxygen consumption - nutrients - constraints - size - shape - cardiovascular system - gene expression - models - biophysics - cum laude

    All vertebrate embryos pass through a developmental period of remarkably low morphological variability. This period has been called phylotypic period. During the phylotypic period, organogenesis takes place, including blood vessel development. Before the phylotypic period, the embryos rely on diffusion for the internal oxygen transport. Diffusion, however, is an efficient way of transport only over small distances. Analytical models were constructed to investigate whether physical constraints ( i.e. diffusional limitations) demand the development of an internal oxygen transport system as the embryos grow bigger. These models showed that teleost embryos are smaller than their theoretically maximum size during the phylotypic period, based on oxygen diffusion. Lack of oxygen does therefore not demand blood vessel development. Subsequently, numerical models of oxygen diffusion in a zebrafish embryo ( Danio rerio ) were developed, thereby including the realistic shape of the embryo. These models were tested and refined with oxygen micro-electrode measurements of the oxygen partial pressure profile in and around the zebrafish embryo. This numerical-experimental procedure revealed a high oxygen permeability in the yolk of the zebrafish embryo. Furthermore, lowest oxygen partial pressures were found in the head region with a gradient of posteriorly increasing oxygen partial pressures along the midline of the embryo. The three-dimensional oxygen partial pressure profile was compared with the expression pattern of the angiogenic factor ( vegf ), which is known to be expressed under hypoxic conditions. The apparent colocalization of low oxygen partial pressure and the expression of vegf suggests oxygen to play an important role in regulating blood vessel development rather than posing a direct request for its development.

    Going places, staying home : rural-urban connections and the significance of land in Buhera district, Zimbabwe
    Andersson, J.A. - \ 2002
    Wageningen University. Promotor(en): N.E. Long; van Donge. - S.l. : s.n. - ISBN 9789058085535 - 175
    arbeidsmobiliteit - migrantenarbeid - ruraal-urbane migratie - urbanisatie - plattelandsgemeenschappen - sociologie - etnografie - relaties tussen stad en platteland - stedelijke samenleving - zimbabwe - labour mobility - migrant labour - rural urban migration - urbanization - rural urban relations - urban society - rural communities - sociology - ethnography - zimbabwe - cum laude
    This book consists of four articles containing detailed ethnographic studies of people who are commonly known as migrant workers.Conventional studies on rural-urban migration and urbanisation have often examined such people in either rural or urban social situations,analysing respectively the consequences of out-migration for the rural society and its agriculture-based economy,or the adoption of urbanised life styles in cities.As a consequence, such studies have tend to reproduce common oppositions associated with the distinction between the rural and the urban,such as traditional-modern, conservative-progressive,continuity-change,peasants-workers,etc. Oppositions that,at the same time,present us with a common development perspective on the relation between the urban and the rural -i.e.that of state- directed modernisation.This thesis on migrant workers travelling back and forth between the rural district of Buhera and Harare,Zimbabwe 's capital, takes issue with such oppositions in our thinking about development.The studies show that Buhera migrants do not live in two separate -rural and urban -social worlds.Rather,it is argued that this migrant society comprises of a single cultural space,stretching different geographical spaces -i.e.Buhera society has to be understood as translocal.
    The method of enquiry adopted in the studies is best captured by the notion of travelling.Buhera migrants were followed both spatially and temporally - in their travels towards and within town,as well as back in time,to understand their history.As a consequence,it is possible to move beyond an image of a 'culture 'fragmented by mobility or moving between different - rural and urban -cultural spaces.To the Buhera migrants studied,distinctions between rural and urban social life do not seem to be important,let alone problematic.Not confined to a particular area,this society of migrants was understood as translocal,spanning different geographical spaces while at the same time constituting a single cultural space.Buhera as a geographical space remained nevertheless important,albeit not as the context of social life, constituting a cultural space or territory,but rather as a point of identification, evoking a sense of belonging.It is this 'being Buheran 'which the analyses in this book focus upon,revealing its significance for the ways in which people organise their livelihoods,thereby reproducing their Buheran identity.

    Chapter 2
    This chapter discusses the power of the state and its representatives to impose their self-produced categories of thought,arguing that this poses a major problem to the historiography of Zimbabwe,which has attributed the colonial state a dominant role in directing social change.Relying heavily on the colonial state 's own archival sources,historical analysis have often taken as unproblematic the relation between knowledge about,and control over, African societies as presented in these archival sources.This chapter challenges this hegemonic view of the colonial state in Zimbabwe,building upon the historical analysis of a rather marginal area.In the early colonial period the Buhera district was designated an African Reserve as white settlers had little interest in its dry and sandy soils.As a result of this lack of interest, historical sources on the area are largely confined to reports made by colonial officials.However,the reports do contain observations of local-level administrators that allow for a different interpretation of the state 's control over its subjects and its role in directing social change.Following the shifting biases in colonial policy discourse -from a preoccupation with the mobilisation of African labour to the modernisation of African land use -this paper shows how,with the expansion of state intervention in the area,Buhera society came to represent traditional African society.Yet,this image of Buhera in the 'controlled 'administrative order of colonial reports increasingly defied the reality of social life experienced on the ground.The historical analysis of Buhera district thus suggests a different perspective on the colonial state. Zimbabwean historiography has generally focused on areas that experienced dramatic confrontations between Europeans (settlers and administrators)and Africans -areas for which sufficient and well-classified archive material is available.Consequently,the role of the state tends to be overestimated, regional differences ignored,and the complexity of the African opposition to the colonial state oversimplified.

    Chapter 3
    In the academic debate on labour migration and urbanisation in Southern Africa the persistence of links between urban workers and people in rural areas has proved a pertinent issue.As is implied by the termlabour migrationeconomic forces have always been regarded as a major determinant of migratory behaviour.State-centred perspectives have dominated studies of rural-urban migration in Zimbabwe,where a restrictive legal regulated migration to urban centres during the colonial era in an attempt to prevent large numbers of Africans becoming permanent town dwellers.This ethnographic study of labour migrants in Harare originating from the Buhera district,however,shifts away from perspectives that reduce migratory behaviour to an effect of state intervention and/or economic forces.Such external forces are mediated by migrants 'networks that encompass both rural and urban localities.Rather than being only economically motivated, individual migrants 'participation in these networks has to be understood as an expression of a socio-cultural pattern in which rural identification and kinship ideology are of major importance.Viewing migration practices in this way observable outcomes of migrants 'socio-cultural dispositions -not only helps us to understand better the preferences that motivate economic behaviour but also challenges conventional perspectives in which the rural and urban are often viewed as distinct social worlds and the urbanisation process as part of a wider evolutionary development or transition towards a modern class society.

    Chapter 4
    Conflicts over land,a major theme in Zimbabwe 's rural history,are widely recognized as 'most serious 'in the densely populated Communal Areas. Pressure on land in these areas is considerable because of population growth and the segregationist policies of the colonial government that concentrated Africans on marginal lands.Land scarcity in the Communal Areas does not, however,mean that conflicts over land are always economically motivated.As the agricultural potential of land is often limited in Communal Areas,land cases may often be better understood as socially induced.This article on land disputes in the Murambinda area of Save Communal Land aims to elucidate the different meanings attached to land.It presents a situational analysis of a single case of land dispute and argues that land conflicts in the area are predominantly political power struggles.The litigation of land cases is dominated by village leaders (vanasabhuku)and largely takes place outside the state 's legal arena.Consequently,local state institutions responsible for land issues have a limited understanding of,and exercise little control over land issues.The findings of this study thus provide a different view in the ongoing debate on the need for tenurial reform in Zimbabwe 's Communal Areas,for they challenge the state 's administrative capacity to enforce such reform.

    Recent studies of witchcraft and sorcery in Africa,have described this domain as an all powerful and inescapable discourse.The anthropological case study presented in this chapter,however,discloses a situation in which people contest the interpretation and narratives of this domain,and challenge its applicability.Focusing on the social practices in which the witchcraft discourse is produced,the approach taken is similar to anthropological approaches that have viewed the witchcraft discourse as a device to attribute meaning in situations of existential insecurity.In a society of migrant labourers working in Harare,but originating from the rural district of Buhera,Zimbabwe,such insecurities are all too real.Many people are confronted with HIV/AIDS- related illnesses and death -euphemistically called Henry the IV (HIV). However,witchcraft accusations do not become acute because of the AIDS pandemic -for which the 'modern 'biomedical episteme has few explanations or cures -but rather,are concurrent with it.The existential insecurities which give rise to witchcraft accusations in this society,originate within the kin- based networks which span rural and urban geographical areas.In contrast with contemporary studies analysing witchcraft in so-called 'modern 'contexts such as the city,the market and state politics,this chapter thus stresses the important link between witchcraft and kinship.It analyses which social relationships are prone to witchcraft allegations,and how the discourse is contested.Thus,it identifies how the witchcraft discourse is given a place relative to other social phenomena.It is shown that this migrant society the domain of the occult is not geographically localised -in a relatively closed rural society -but translocal.Migrants in town are not free from the witchcraft of their rural kin.
    The perspective on rural-urban connections and the significance of land put forward in this thesis,is of wider significance.In the last chapter it is argued that received wisdom about the role of the land in understanding Zimbabwe 's history and contemporary politics may be limited since -as was elaborated for Buhera -it is based on the common oppositions associated with the rural- urban distinction.The discussion,which takes news reports on Zimbabwe 's political and economic crisis at the turn of the 21
    stcentury as a starting point, critically reviews two common discourses on Zimbabwe's history and current crisis.One,the dominant discourse,focuses on the rural land as the source of wealth and development.This political economy-inspired discourse situates Zimbabwe 's crisis in theruraleconomy,in the highly uneven distribution of the best agricultural land.It stresses the productive value of land.The other discourse,which may be typified as a counter-discourse,presents us with a rather different image -i.e.that of an industrializing economy in decline. Blaming the state for its economic mismanagement and focusing exclusively on economic parameters of the current crisis,this discourse is of limited use for our understanding of the current political dynamic in which non-economic values of land play such an important role.As the studies in this thesis have shown,the stress on the economic value of land has,perhaps,prevented us from understanding the socio-cultural and political value of land in Zimbabwe.
    Modelling of animal welfare : the development of a decision support system to assess the welfare status of pregnant sows
    Bracke, M.B.M. - \ 2001
    Wageningen University. Promotor(en): B.M. Spruijt; J.H.M. Metz; W.G.P. Schouten. - S.l. : s.n. - ISBN 9789058083913 - 150
    varkens - zeugen - modellen - dierenwelzijn - basisbehoeften - huisvesting, dieren - bedrijfsvoering - beoordeling - deskundigen - interviews - computer software - beslissingsondersteunende systemen - pigs - sows - models - animal welfare - basic needs - animal housing - management - assessment - experts - interviews - computer software - decision support systems - cum laude

    A computer-based decision support system for welfare assessment in pregnant sows was constructed. This system uses a description of a husbandry system as input and produces a welfare score on a scale from 0 to 10 as output. Pregnant sows were chosen as a case in search for a formalised, i.e. structured, transparent, yet flexible procedure to 'objectively' assess the overall welfare status of farm animals in relation to the housing and management system based on available (and undisputed) scientific knowledge. The procedure to construct the welfare model and to calculate welfare scores is described. Decision making is based on the needs and distress of the animal thus from the perspective of the animal.

    The sow welfare (SOWEL) model was validated using expert opinion in that there is a substantial agreement between pig welfare scientists and the model about the ranking of housing systems and, to a lesser degree, about the weighting of attributes of housing systems. The most important welfare-relevant attributes concern aspects of social contact, space, and substrate. The housing systems were roughly divided into low-, mid-, and high-welfare systems. Low-welfare systems were conventional housing in individual stalls and tethers, while high-welfare systems in our data set all provided substrate and outdoor access.

    For practical applications further development of the decision support system is recommended, as well as ongoing validation, upgrading and extending of the model, e.g. to other species. The results show that integrated welfare assessment based on available scientific knowledge is possible.

    Keywords : farm animal welfare assessment, pigs, applied ethology, housing systems, model, computer, knowledge base, expert system.

    Ecology of Drosophila aggregation pheromone: a multitrophic approach
    Wertheim, B. - \ 2001
    Wageningen University. Promotor(en): L.E.M. Vet; M. Dicke; J.C. van Lenteren. - S.l. : s.n. - ISBN 9789058084330 - 198
    drosophila melanogaster - aggregatieferomonen - dierecologie - gastheer parasiet relaties - diergedrag - trofische graden - voedselketens - aggregatie - drosophila melanogaster - aggregation - aggregation pheromones - animal ecology - animal behaviour - host parasite relationships - trophic levels - food chains - cum laude

    Many insect species use an aggregation pheromone to form groups with conspecifics in certain localities of the environment. This type of behaviour has a variety of implications for ecological interactions, both directly through the effect of the pheromone on the behaviour of con- and heterospecifics, and indirectly through the consequential aggregative distributions that may affect species interactions. The evolutionary ecology of the use of aggregation pheromone has received only little attention. Yet, these pheromones may play an intricate role in food web interactions by providing an accompanying information web.

    The aim of this thesis is to further our understanding on the ecological and evolutionary aspects of the use of aggregation pheromone in insects. By unravelling costs and benefits that arise from the use of aggregation pheromone in our ecological model organism, Drosophila melanogaster , we strive to answer why they use an aggregation pheromone and elucidate the ecological consequences of an aggregation pheromone in a food web context.

    In laboratory and field studies, we identified behaviours and interactions of the fruit fly D. melanogaster that were affected by its aggregation pheromone. The pheromone affected the distribution of adults, their eggs, competitor species and parasitoids. Moreover, a number of costs and benefits to the use of aggregation pheromone were indicated. In subsequent studies, the major hypotheses on costs and benefits were examined.

    A major benefit of using aggregation pheromone was shown to be aggregated oviposition. Aggregated oviposition enhanced the quality of the larval resource, as indicated by a higher survival of the larvae and larger size of the emerging flies. This Allee effect was characterised by a positive effect of adult density on larval fitness components, and may have arisen from the interaction between adult flies and micro-organisms (yeasts and fungi). Fungi antagonise yeast and larval development, while adults can inoculate yeast on a substrate and temper fungal growth. Larvae also tempered fungal growth, but an increased larval density did not result in an Allee effect but in competition instead.

    A major cost of using aggregation pheromone arose from an increased risk of parasitism. The parasitoid Leptopilina heterotoma uses the aggregation pheromone of adult fruit flies to localise the larval hosts, and based on this information this parasitoid can differentiate quantitatively at long range between substrates that differ in profitability. After arrival on a substrate, the pheromones no longer play a role in the host searching behaviour. A behaviour-based model was developed to predict the individual risk of parasitism for hosts in differently sized host aggregations. The functional and numerical responses of the parasitoids were combined with a flexible patch leaving decision rule for the parasitoid, to assess whether aggregation could also comprise a benefit to the hosts in terms of a diluted risk ( sensu Hamilton 1971). The model prediction reads that aggregation is not beneficial in the context of the Drosophila - Leptopilina interaction, and these predictions were supported by field data.

    In a simple spatio-temporal simulation model, the population dynamics arising from several modes of dispersal, food competition and an Allee effect were explored. The model is a first step towards a more extensive model that incorporates the responses of insects to spatially heterogeneous resources and chemical information (e.g., aggregation pheromone).

    The main conclusion from this thesis is that the aggregation pheromone of D. melanogaster plays an intricate role within a foodweb context, and that a variety of costs and benefits arise from multitrophic interactions. To understand the dynamic interactions in this and many other ecological systems, it is essential to gain more insight into the effect of aggregation pheromone on the behaviour of individuals.

    On the stability of mixed grasslands
    Schulte, R.P.O. - \ 2001
    Wageningen University. Promotor(en): P.C. Struik; E.A. Lantinga. - S.l. : s.n. - ISBN 9789058083784 - 173
    trifolium repens - weidevlinderbloemigen - graslanden - concurrentie tussen planten - gemengde weiden - planteninteractie - stabiliteit - variatie - graslandbeheer - simulatiemodellen - agro-ecologie - trifolium repens - pasture legumes - grasslands - plant competition - mixed pastures - plant interaction - stability - variation - grassland management - simulation models - agroecology - cum laude

    Recent years have seen a renewed interest in the use of white clover (Trifolium repens) in grasslands, as a more sustainable alternative to fertiliser nitrogen inputs. However, mixtures of grasses and white clover have frequently been associated with unstable and hence unreliable herbage yields. The maintenance of a stable production from mixed grasslands requires the prototyping of new grassland management strategies.

    Temporal yield fluctuations may result from intrinsic ecosystem fluctuations, from environmental fluctuations, or from both. The stability of ecosystems in isolation of their environment is defined as the intrinsic stability. The stability of systems subjected to seasonal environmental fluctuation only is defined as the extrinsic stability, while the stability of systems under a regime of both seasonal and stochastic environmental fluctuations, as measured in field experiments, is defined as the actual stability. The actual stability depends on coincidental weather events and is hence an unreliable reflection of the grassland ecosystem or of the management imposed.

    A mathematical framework is presented with which the extrinsic and intrinsic stability levels of grassland ecosystems can be deducted from their yields during a large number of years, and with which the effects of intrinsic system properties and of environmental fluctuations on the stability of their yields can be segregated. Intrinsically stable systems remain stable in the face of seasonal environmental fluctuations, but are destabilised by stochastic environmental events. Intrinsically unstable systems are instead stabilised by environmental seasonality, and may be further destabilised or stabilised by stochastic fluctuations, depending on the timing of individual environmental events.

    This framework was applied to the yield data of two long-term experiments. Regular lime applications and a grazing regime increased the extrinsic stability of grassland ecosystems, whereas fertiliser treatments only had small or inconsistent effects. It was consequently hypothesised that the extrinsic stability of ecosystems depends largely on the availability and turnover rate of nutrients.

    Vertical spatial interactions between grass species and white clover depend on the vertical distributions of their lamina and total leaf material. A mechanistic model is presented, with which the distributions of perennial ryegrass (Lolium perenne) and white clover can be accurately simulated for a wide range of sward types subjected to various management regimes. This model uses simple morphological features of both species as input variables.

    The lateral spatial heterogeneity of mixed grasslands was quantified, using data generated by the Dry Weight Rank method for botanical assessment of grasslands. The heterogeneity of the total herbage mass was highest after cutting and topping events, and under lenient grazing, and lowest under strip-grazing. Opposite responses to the grassland management were found for the heterogeneity of the white clover herbage mass.

    The performance of white clover may be compromised by infestations of creeping bentgrass (Agrostis stolonifera). A mathematical methodology, based on the Dry Weight Rank method, is presented with which the effects of niche-differentiation and direct competition between white clover and creeping bentgrass can be discriminated. The exclusion of white clover by creeping bentgrass foremost resulted from direct competition. Both species only showed niche-differentiation in response to two extreme management strategies. Whereas the clover performance was enhanced under a permanent cutting regime, creeping bentgrass prevailed under a regime of lenient grazing.

    Finally, two types of management strategies were proposed to maintain the production stability of mixed grasslands. Structural management strategies, such as lime applications, the maximisation of the grazed area, and the targeted use of mixtures of grassland species and varieties, aim to increase the extrinsic stability of ecosystems, and can be prototyped. Dynamic management strategies are required to counteract the fluctuations of the abiotic and the biotic environment, and cannot be generalised due to the individuality of each farm ecosystem.

    Additional key-words: stability, variability, ecosystem, grassland, white clover, Trifolium repens, legumes, mixtures, model, competition, methodology, dry weight rank, organic farming.

    Rethinking soil and water conservation in a changing society : a case study in eastern Burkina Faso
    Mazzucato, V. ; Niemeijer, D. - \ 2000
    Agricultural University. Promotor(en): L. Stroosnijder; N.G. Röling. - S.l. : s.n. - ISBN 9789058082503 - 380
    bodembescherming - waterbescherming - landevaluatie - duurzaamheid (sustainability) - sociale verandering - boeren - bedrijfssystemen - intensivering - Burkina Faso - soil conservation - water conservation - land evaluation - sustainability - social change - farmers - farming systems - intensification - Burkina Faso - cum laude

    Soil and water conservation is at the top of development agendas in Africa. Virtually every project related to agriculture or the environment has a soil and water conservation component to it and environmental protection plans are being drawn up by African governments in which soil and water conservation figures dominantly. This focus on soil and water conservation is due to its being perceived as a way to address both productivity and environmental sustainability questions. Land degradation and population growth are thought to be rampant in Africa and soil and water conservation helps to increase productivity to feed a growing population and does so in an environmentally sustainable way.

    Three broad approaches characterize how soil and water should be conserved. The first is a focus on capital-led intensification in the form of machinery and purchased inputs (such as mineral fertilizer and pesticides). This school of thought claims that this is the only way to obtain a fast enough increase in productivity to feed the growing population. The second approach instead focuses on "indigenous technologies", or what farmers develop, adapt, and innovate on their own account. This school claims that technologies will only be used if they are developed by and with farmers so as to take into consideration their social and environmental contexts. There is also what is called the neo-liberal approach in which it is argued that it is not enough to look at technologies, but also policies, infrastructure and markets need to be in place to stimulate the appropriate kinds of land husbandry practices.

    Despite these variegated approaches, soil and water conservation projects have, at best, had a checkered history. There is a need thus to look at the problem in a different manner than is done by studies that have lead to the above approaches. This study picks up this challenge and tries to theorize and operationalize a different approach to the study of soil and water conservation. It uses elements from previous studies but integrates them in a new way. In part 1 of the book approach, analytical framework and methods are discussed, while part 2 consists of a case study in Burkina Faso (former Upper Volta) in which the proposed approach is put into practice.

    Chapter 1 describes this approach which is based on three elements: (1) working in an interdisciplinary fashion to allow the integration of different aspects of soil and water conservation, (2) using a grounded theory methodology in which the principal element relates to starting out broad and allowing the concepts and principles to be studied to emerge from fieldwork, and (3) giving particular attention to developing a mutual relationship of trust with villagers in order to allow their opinions and views to influence the focus of the study.

    Chapter 2 presents the analytical framework that emerged out of the grounded theory methodology. It is an end-product of the research but, nonetheless, figures at the beginning of the book, as a guide to the analysis in part 2. It is presented by discussing the most influential theories that have affected the study of soil and water conservation, followed by an explanation of which elements of these theories have been used in the analytical framework. Malthus and Boserup have had a strong impact on how the land degradation problem is perceived. Both of their theories place the emphasis on population pressure as either a cause or a remedy to land degradation. Because Africa has been experiencing such strong population growth rates since the 1960s, these theories have been particularly influential in placing the emphasis on soil and water conservation technologies as a remedy to an otherwise serious land degradation problem. Neo-Malthusians argue that without outside intervention in soil and water conservation, there will be widespread death and degradation. Neo-Boserupians, instead, explain that once population pressure increases to above certain thresholds, it will act as a stimulus for populations to intensify agriculture and therefore develop better land husbandry practices. Here too, outside intervention can help stimulate this process of intensification.

    The framework resulting from this study instead, influenced by political ecology, indigenous knowledge, and social anthropological approaches, argues that the dynamics behind African agricultural systems are much more variegated than a single trend towards land degradation allows. The framework questions land degradation narratives and, rather than focus on population density as the harbinger or cure to land degradation, it focuses on the interactions of social and environmental histories of an area in order understand the dynamic landscapes that emerge as a consequence thereof. Part 2 of the book operationalizes this approach by paying attention to social historical processes that took place in the research area within the past century (chapter 4), focusing on long-term environmental change (chapter 5), looking at farmers' soil and water conservation technologies (chapter 6), understanding local economic concepts that influence allocative decisions in agriculture (chapter 7), and how social institutions, and their change over time, affect agriculture in the study region (chapter 8). The last chapter of part 2 pulls the different parts of the analysis together to explain how, in a region that is experiencing all of the trends thought to be harbingers of land degradation, no evidence of land degradation is found (chapter 9). The contents of each of these chapters will be discussed in detail below.

    The approach used in this study requires a wide variety of methods because different aspects of soil and water conservation need to be studied and because the emphasis on allowing the relevant research concepts to emerge from fieldwork requires starting out in a broad fashion. Chapter 3 presents the methods used in this study and explains the reasoning why these methods were used.

    Part 2 of the book presents the chapters that aim at answering the three main research questions: (1) what evidence is there of land degradation? (2) how do people go about conserving soil and water? (3) why do people conserve soil and water in the way that they do? Chapter 4 introduces the research area and villages and focuses on the social history of the area since the late nineteenth century. The study takes place in two villages in the eastern region of Burkina Faso and focuses on the Gourmantché system of agriculture. The emphasis on historical changes experienced in this system allows the analyses of the following chapters to be placed within a broader historical picture. Some of the major changes experienced within the last century that have significantly altered the livelihood system are an increased individualization of production and consumption in conjunction with a decline of traditional authorities, increasing cultivation in bush camps, more extensive livestock ownership among the Gourmantché, and an increased monetization and market orientation. These changes have been spurred, among others, by oppressive colonial practices and increased market integration. At the same time, population and livestock densities have risen steeply, raising the question how this has influenced the state of natural resources.

    Chapter 5 picks up on this question and conducts a multi-scale analysis of the indicators and proxies that are normally used to argue the presence of land degradation trends. Crop yields, agricultural productivity, biodiversity, and soil fertility are analyzed both spatially and temporally at the national, regional, and village levels. No evidence is found to support the land degradation narrative. Furthermore, the chapter highlights some of the weaknesses inherent in the methods used to analyze land degradation. Given the lack of evidence of land degradation, the strong population growth experienced over the last 40 years, and the relatively high rural population densities found in large parts of the country, the chapter excludes Neo-Malthusian predictions of widespread degradation and starvation. In agreement with Boserupian thinking, the evidence put forward in this chapter suggests that some form of agricultural intensification is instead taking place that allows food production to grow along with population. However, contrary to Boserup's theory, there seems to be little evidence that this form of intensification is based on high use of external inputs and increased mechanization. Neither are there any indications that certain population thresholds need to be surpassed before farmers undertake intensification or improve the environmental sustainability of their land use practices. How this intensification takes place and in what form is the topic of the chapters that follow.

    Chapter 6, takes an indigenous knowledge approach to the study of farmers' soil and water conservation technologies, but focuses not only on descriptions of the technologies as is common in indigenous knowledge studies, but also looks at farmers' theories of soil formation and degradation processes and their own roles within these processes as users of the land. It is found that Gourmantché farmers make use of an extensive repertoire of soil and water conservation practices, most of which are agronomic/biological practices that make use of management skills and biological material. Mechanical practices that make use of physical structures are used, but to a limited extent, and they seem to have declined compared to some 30 to 40 years ago. It is argued, based on stories of informants and an analysis of aerial photographs, that this is not an indication of a decline of "traditional" practices, but an adaptation of their use to changing environmental conditions.

    One of the most important points raised in this chapter is that Gourmantché farmers adapt their management practices sequentially in the course of a single growing season, as well as during the cultivation cycle of a field. This process of adaptive management has allowed farmers to maintain soil fertility or even improve it on cultivated fields relative to uncultivated land. Adaptive management involves strategic thinking and experimentation, as well as responses to changing soil fertility and unpredictable environmental and socio-economic production constraints. Thus adaptive management is a dynamic process of experimentation, fine-tuning and exploration of new opportunities.

    As was argued in the analytical framework, an absence of land degradation is not only a sign that appropriate technologies and inputs are being used in a cultivation system, but also that there is a social organization around the land that allows resources necessary for an environmentally sustainable form of agriculture to be accessed. Chapter 7 analyzes the concepts that guide economic action in order to then, in chapter 8, be able to analyze how these concepts influence access to resources for agriculture. Chapter 7 analyzes the local economy by making no a priori assumptions about the type of economy, traditional or market, that guides allocative decisions. Instead, the chapter explores the concepts guiding local economic reasoning. It was found that these concepts cannot be categorized as either purely capitalistic nor traditional. Rather, a mixture is found of market principles and social considerations. Market transactions are pervasive and livelihoods are earned not only through subsistence farming but also through incomes earned with off-farm activities and livestock husbandry. People also engage in profit making activities such as buying grain when it is cheap and reselling it when prices are high, or livestock fattening. At the same time social transactions such as gifts or interest-free loans form an important part of daily life. Even market transactions are characterized by the giving of gifts or discounts. Together, these transactions aim at a delicate balance between earning profits and establishing and maintaining social networks. An analysis of the historical development of market and social institutions does not indicate that the latter are being replaced by the former. The resulting mixture of principles that guide economic action is what we term the cultural economy.

    Chapter 8 looks at how the mixture of social and market principles affect the way in which agriculture is practiced, and in specific, how they influence the way land is conserved. The chapter highlights how social networks have changed to increasingly be used to access resources for agriculture. With the increased use of land for cultivation, borrowing of land is an option used for not over-cultivating one's own lineage land; as production units have been getting smaller, networks are increasingly used to access labor; with women's greater involvement in agriculture, their natal family ties are used to access necessary resources for conducting agriculture; as more technologies are available for cultivating, networks are used to access them; as Fulbe settle on village territories, new forms of network building are created to allow the rearing of livestock; and finally, as cash needs become greater, ways of networking to access cash are being developed. By looking at networks as a source of access to resources, the issue of accessibility is treated in a broader way than most studies on agricultural productivity and environmental sustainability that instead focus on access of resources through monetary means.

    The various analyses of the chapters 4 through 8 are drawn together in chapter 9 to explain the lack of land degradation found in the study region while the final chapter of the book draws the conclusions from this case study to a theoretical level. The most important conclusions relating to the study of soil and water conservation are (1) land degradation narratives need to be questioned by analyzing the data on which they are based; (2) while population densities can act as a stimulus to technological intensification, farmers respond to more than just population densities in order to change their agricultural practices. It is therefore necessary to study how populations adapt to changes in the social, economic and physical contexts; (3) technological intensification obtained by some African agricultural systems is based on the knowledge of crops, soils and the environment and the management skills with which this knowledge is applied. This form of intensification has obtained higher levels of productivity and environmental sustainability than approaches advocating capital-led intensification recognize; (4) there is a need for improved scientific methods for understanding the effects of farmers' practices on the environment and agricultural productivity; (5) institutional development that takes on other than capitalistic forms, can, contrary to the assumptions made by studies of capital-led intensification, lead to productive and environmentally sustainable agricultural practices; (6) social networks are not the unchanging characteristics of a traditional system but rather change as a result of people dealing with changing social, economic, and environmental contexts. As such they can be fundamental to making an agricultural system productive and environmentally sustainable; (7) people dispose of both technical as well as social means to affect agricultural performance; (8) forms of intensification in African production systems can only be understood in terms of the dynamic interplay between social and environmental histories. Consequently, there is a need for analytical frameworks that focus on this interplay between social and environmental contexts, rather than assume a simple trend towards increasing land degradation. This kind of approach reveals the dynamic and contrasting trends that can be present in different localities at different points in time. This study offers an example of such an analytical framework and how it can be operationalized, leading to innovative perspectives on African land use systems.

    The authors can be contacted at: &

    Behoudend maar buigzaam : boeren in West-Zeeuws-Vlaanderen, 1650-1850
    Cruyningen, P.J. van - \ 2000
    Agricultural University. Promotor(en): A.M. van der Woude; J. Bieleman. - S.l. : s.n. - ISBN 9789058081483 - 486
    landbouw - geschiedenis - nederland - bezit - bedrijfsontwikkeling in de landbouw - agrarische bedrijfsvoering - demografie - zeeland - zeeuws-vlaanderen - cum laude - agriculture - history - netherlands - property - farm development - farm management - demography - zeeland - zeeuws-vlaanderen

    This book deals with the ways in which farmers in West Zeeland Flanders, a region in the south west of the Netherlands, reacted to adverse economic circumstances, especially during the first half of the eighteenth century, and the effects their decisions had for society as a whole. Between 1700 and 1750, when prices for agricultural products were low, farmers extended wheat cultivation and cut down labour costs by replacing local labourers with migrant workers. Farmers who were successful in adjusting to the adverse circumstances were able to enlarge their holdings and become landowners. They became a rural elite that was able to maintain itself by way of a system of inheritance that ensured the existence of large holdings. Farm labourers, however, became impoverished, because there was not enough employment in agriculture. This caused social problems, resulting in mass emigration around the middle of the nineteenth century.

    Methane emissions from rice paddies : experiments and modelling
    Bodegom, P.M. van - \ 2000
    Agricultural University. Promotor(en): J. Goudriaan; P.A. Leffelaar; A.J.M. Stams. - S.l. : s.n. - ISBN 9789058082831 - 215
    oryza sativa - rijst - padigronden - methaan - methaanproductie - microbiologie - bodembiologie - rizosfeer - systeemanalyse - simulatiemodellen - oryza sativa - rice - paddy soils - methane - methane production - microbiology - soil biology - rhizosphere - systems analysis - simulation models - cum laude

    This thesis describes model development and experimentation on the comprehension and prediction of methane (CH 4 ) emissions from rice paddies. The large spatial and temporal variability in CH 4 emissions and the dynamic non-linear relationships between processes underlying CH 4 emissions impairs the applicability of empirical relations. Mechanistic concepts are therefore starting point of analysis throughout the thesis.

    The process of CH 4 production was investigated by soil slurry incubation experiments at different temperatures and with additions of different electron donors and acceptors. Temperature influenced conversion rates and the competitiveness of microorganisms. The experiments were used to calibrate and validate a mechanistic model on CH 4 production that describes competition for acetate and H 2 /CO 2 , inhibition effects and chemolithotrophic reactions. The redox sequence leading eventually to CH 4 production was well predicted by the model, calibrating only the maximum conversion rates.

    Gas transport through paddy soil and rice plants was quantified by experiments in which the transport of SF 6 was monitored continuously by photoacoustics. A mechanistic model on gas transport in a flooded rice system based on diffusion equations was validated by these experiments and could explain why most gases are released via plant mediated transport. Variability in root distribution led to highly variable gas transport.

    Experiments showed that CH 4 oxidation in the rice rhizosphere was oxygen (O 2 ) limited. Rice rhizospheric O 2 consumption was dominated by chemical iron oxidation, and heterotrophic and methanotrophic respiration. The most abundant methanotrophs and heterotrophs were isolated and kinetically characterised. Based upon these experiments it was hypothesised that CH 4 oxidation mainly occurred at microaerophilic, low acetate conditions not very close to the root surface. A mechanistic rhizosphere model that combined production and consumption of O 2 , carbon and iron compounds with iron adsorption kinetics and diffusive transport in a rice plant and rhizosphere, confirmed this hypothesis. Oxidation of CH 4 depended on acetate and O 2 concentrations and on variables influencing competition between methanotrophs and chemical iron oxidation. Oxidation of CH 4 also depended on root growth dynamics and was intrinsically dynamic.

    The process-based concepts were simplified in a field scale model on CH 4 emissions by dividing a rice paddy into a rhizosphere compartment and a bulk soil compartment. The field scale model was validated by independent CH 4 emission measurements from fields in the Philippines, China and Indonesia in different seasons and with different inorganic and organic fertiliser additions. The model predicted CH 4 emissions well with only few generally available site-specific input parameters. A sensitivity analysis showed that the model was very sensitive to the description of substrate supply.

    The field scale model was coupled to a Geographic Information System to scale up regional CH 4 emissions from rice paddies, as was the aim of the overall project. Regional CH 4 emission estimates were however affected by the applied interpolation technique and by data resolution effects in a case study for the island of Java, Indonesia. The scaling effects were induced by the combination of a loss of information on heterogeneities and by non-linear model responses. Data availability and not model uncertainty, which was small for the field scale model developed in this thesis, limits upscaling of CH 4 emissions from rice paddies to regions.

    Variation in maintenance requirements of growing pigs in relation to body composition : a simulation study
    Knap, P.W. - \ 2000
    Agricultural University. Promotor(en): M.W.A. Verstegen; G.S. Emman. - S.l. : s.n. - ISBN 9789058081704 - 219
    varkens - groei - voedingsstoffenbehoeften - metabolisme - energie - lichaamssamenstelling - simulatiemodellen - pigs - growth - nutrient requirements - metabolism - energy - body composition - simulation models - cum laude

    Existing dynamic models for the simulation of growth metabolism in pigs were extended with routines to predict the energy requirements of protein turnover and thermoregulation. Protein turnover was modeled by distinguishing six body protein pools with different turnover rates and different growth curves. Thermoregulation was modeled by assessing minimum and maximum heat loss, and heat production, deciding by comparison of these whether the pig is cold or hot, and taking appropriate metabolic action.

    Model output compared satisfactorily with independent data. Pig populations were modeled by stochastic simulation, imposing between-animal variation on growth potential parameters and therefore on body (growth) composition. Because protein turnover, and heat production and thermal insulation, in the model depend on body (growth) composition, between-animal variation was generated in the associated energy requirements. This leads to variation in maintenance requirements as a function of variation in body composition.

    The simulated output was analysed to provide an answer on the question "to what extent can differences in maintenance requirements be attributed to differing proportions of the different organs and tissues of the body, each having different metabolic rates" ? The conclusion from this analysis is that the contribution of variation in body (growth) composition to the variation of total maintenance requirements in growing pigs is very limited, probably less than 10 % of the total variance. Experimental verification of this conclusion is desirable; the design of the required experiments is discussed, making use of the simulation results.

    Biological glasses : nature's way to preserve life
    Buitink, J. - \ 2000
    Agricultural University. Promotor(en): L.H.W. van der Plas; F.A. Hoekstra; M.A. Hemminga. - S.l. : s.n. - ISBN 9789058082398 - 202
    zaden - stuifmeel - germplasm - anhydrobiose - glazig worden - verouderen - gebruiksduur - paramagnetische elektronenresonantiespectroscopie - seeds - pollen - germplasm - anhydrobiosis - vitrification - aging - longevity - electron paramagnetic resonance spectroscopy - cum laude

    As a result of drying, the cytoplasm of desiccation-tolerant organisms, such as seed and pollen, enters into a highly viscous, solid-like, semi-equilibrium state: the glassy state. The work in this dissertation is focussed on the function and characteristics of intracellular glasses in these organisms.

    It was established that intracellular glasses are formed in both desiccation-tolerant and -intolerant pollen (chapter 1). However, desiccation-intolerant pollen loses its viability during drying before intracellular glasses are formed. This indicates that desiccation tolerance is not related with the formation of glasses during drying. Storage of cattail ( Typha latifolia ) pollen under different water contents and temperatures revealed the existence of an optimum water content for survival at a constant relative humidity (11-15%) (chapter 2). The water content corresponding to this relative humidity shifted to higher values with lower storage temperatures, and was found to be associated with the Brunauer, Emmet, and Teller monolayer value. Drying of the pollen below these water contents had detrimental effects on longevity. The water content-temperature combinations of optimal storage were found to be below the glass transition curve, indicating that optimum storage conditions are achieved when intracellular glasses are present. There was a change in ageing kinetics of cattail pollen associated with the melting of the intracellular glass. Above the glass transition temperature (T g ) the activation energy of the ageing rates increased two to three times. This suggests that the presence of glasses in the dry state improves storage stability by decreasing viscosity and, thus, ageing rate. It was concluded that T g curves might be useful for predictions of storage longevity above optimum water contents. However, they cannot be used solely to predict the precise conditions of optimum storage. Subsequently, we sought for a more direct measurement to assess the viscosity of the cytoplasm of tissues.

    For this purpose, we used electron paramagnetic resonance (EPR) spectroscopy to study the molecular mobility of the hydrophilic nitroxide spin probe 3-carboxy-proxyl (CP) that was incorporated into embryonic axes of pea seeds and cattail pollen. Using the distance between the outer extrema of the EPR spectrum (2 A zz ) as a measure of molecular mobility, a sharp increase in mobility was observed at a definite temperature during heating (chapter 3). This temperature increased with decreasing water content of the samples, and was found to be associated with the melting of the glassy state as measured by differential scanning calorimetry (DSC). Molecular mobility was found to be inversely correlated with storage stability: the higher the molecular mobility, the shorter the longevity: with decreasing water content, the molecular mobility reached a minimum, in concert with ageing rates. At very low water contents, both molecular mobility and ageing rates increased again. Minimum mobility and maximum storage stability occurred at similar water contents, suggesting that storage stability might be partially controlled by molecular mobility. To understand the nature of the changes in 2 A zz in spectra of CP in the tissues, echo detected (ED) EPR spectroscopy was employed (chapter 4). The shape of the ED EPR spectrum revealed the presence of librational motion of the spin probe, a motion typically present in glassy materials. The change in 2 A zz appeared to be the result of librational motion of the spin probe.

    With the use of saturation transfer (ST) EPR spectroscopy, a more quantitative measure of molecular mobility was acquired: the rotational correlation time (τ R ), which corresponds to the time it takes for the spin probe to rotate a radian around its axis (chapter 5). At room temperature,τ R of CP in pea embryonic axes increased during drying from 10 -11 s in de hydrated state to 10 -4 s in the dry state. At T gR was constant ataproximately10 -4 s for all water contents studied. The temperature dependence ofτ R at all water contents studied followed Arrhenius behaviour with a break at T g . The temperature effect onτ R above T g was much smaller in pea axes as found previously for sugar and polymer glasses. Thus, the melting of the intracellular glass by raising the temperature caused only a moderate increase in molecular mobility in the cytoplasm as compared to a huge increase in amorphous sugars.

    The application of saturation transfer EPR spectroscopy to biological tissues enabled a quantitative comparison between storage stability and molecular mobility in different tissues (section III). The temperature and moisture dependence of ageing rates of seeds and pollen was found to correlate with the rotational motion of CP in the cytoplasm (chapter 6-8). An increase in the temperature resulted in a faster rotational motion in the cytoplasm of cattail pollen, analogous to faster ageing rates (chapter 6). Decreasing the water content of the pollen resulted in a decrease in rotational motion until a minimum was reached, after which rotational motion slightly increased again. The water content at which this minimal rotational motion was observed increased with decreasing temperature, comparable to the pattern of ageing rate. A significant linear relationship was found between ageing rates and rotational motion in the cytoplasm of the pollen.

    We also investigated the relationship between the longevity of lettuce seeds and the molecular mobility in the cytoplasm of their radicles (chapter 7). Longevity of lettuce seeds was predicted using the viability equation of Ellis and Roberts. Increasing the temperature resulted in faster rotational motion and shorter longevity. There was a linear relationship between the logarithms of rotational motion and estimated longevity for temperatures above 5°C, which is the same temperature range for which experimental data were used to obtain the viability constants of the viability equation. Below 5°C, there was a deviation from linearity, which might stem from inaccurate predictions by the viability equation at low temperatures.

    Chapter 8 further demonstrates that there is a linear relationship between the logarithms of rotational motion in the cytoplasm of seed and pollen of several plant species and their ageing rates or longevities. This linearity suggests that cytoplasmic mobility might be an important controlling factor of ageing rates. The linear relationship between the two parameters could be used to predict lifespan of germplasm at low temperatures (at which experimental determination of longevity is practically impossible) by simply measuring theτ R values at these low temperatures (chapter 7 and 8). Based on the predictions using the linear regression between ageing rate and rotational motion of CP in pea embryonic axes, an optimum water content of storage was found. This optimum water content shifted to higher values with lowering the storage temperature, as was found previously for cattail pollen based on experimental data (chapter 2). It was predicted that the longevity of seeds at high (0.12 to 0.16 g/g) water content is much higher than previously suggested on the basis of the viability equation. The predictions show that drying germplasm too far leads to decreased longevity compared to storage of germplasm at higher water contents, suggesting that current storage protocols might have to be re-examined.

    Desiccation-tolerant organisms contain large amounts of soluble sugars. This, and the fact that sugars are excellent glass-formers has led to the suggestion that sugars play an important role in intracellular glass formation. The presence and amounts of oligosaccharides have been found to correlate with longevity. Furthermore, oligosaccharide glasses are known to increase the T g and viscosity of model sucrose glasses. This suggests that oligosaccharides might enhance the stability of intracellular glasses (chapter 9 and 10). Osmo-priming, i.e. pre-imbibition of seeds in an osmotic solution, can result in a decrease in oligosaccharide content and longevity. Priming pea seeds decreased the total oligosaccharide content in the embryonic axes (chapter 9). Despite the change in oligosaccharide:sucrose ratio, no differences in T g values were detected in the dry axes before and after priming as determined by DSC. Also no difference was found between the rotational mobility of CP in dry untreated axes and that of dry primed axes. Chapter 10 demonstrates that osmo-priming of impatiens and bell pepper seeds resulted in considerable decreases in longevity and oligosaccharide contents, while sucrose contents increased. Again, no differences in the T g curves were found between control and primed impatiens seeds. Similarly, there was no difference in rotational motion of CP in the cytoplasm between control and primed impatiens seeds and between control and primed bell pepper embryonic axes. It was concluded that oligosaccharides in seeds do not appear to affect the stability of the intracellular glassy state, and that the reduced longevity after priming is not the result of increased molecular mobility in the cytoplasm.

    To understand the nature and composition of biological glasses we investigated the molecular mobility around T g in sugars, poly-L-lysine and dry desiccation-tolerant biological systems, using ST-EPR, 1 H-NMR and FTIR spectroscopy. Two distinct changes in the temperature dependence of molecular mobility were detected in sugars and poly-L-lysine. With heating, the first change was associated with the melting of the glassy state (T g ). The second change, at which the molecular mobility abruptly increased over several orders of magnitude, was found to correspond with a critical temperature (T c ) where the dynamics of the system changed from solid-like to liquid-like. The temperature interval between T g and T c increased with increasing molecular weight of the sugars. The interval between T g and T c in biological tissues was over 50°C, implying that the stability remained high even at temperatures far above T g . A comparably high T c -T g interval was found for the molecular mobility of poly-L-lysine, suggesting that proteins rather than sugars play an important role in the intracellular glass formation. The exceptionally high T c of intracellular glasses is expected to provide excellent long-term stability to dry organisms, maintaining a slow molecular motion in the cytoplasm even at temperatures far above T g .

    Records and reputations : everyday politics of a Philippine Development NGO
    Hilhorst, D. - \ 2000
    Agricultural University. Promotor(en): D.B.W.M. van Dusseldorp; N.E. Long. - S.l. : s.n. - ISBN 9789058083166 - 261
    niet-gouvernementele organisaties - toerekenbaarheid - efficiëntie - filippijnen - politiek - plattelandsontwikkeling - non-governmental organizations - accountability - efficiency - politics - rural development - philippines - cum laude

    This study looks into the working of policies, practices and accountability of NGOs. It is based on fieldwork with one development NGO in the Cordillera of the Philippines: the Cordillera Women NGO, or CWNGO (a pseudonym). Through this study I wanted to find out why certain groups of actors form organizations that they call an NGO, and how they ascribe meanings to the organization in practice. Meaning making is central to everyday practice, since it underlies the numerous small and big, pro-active and responsive decisions and actions that together make up the organization. In addition, the study focuses on matters of everyday politics. On the one hand, this entails the way ideology was important in shaping the organization. On the other, this involves the question how NGOs acquire legitimation as a development organization vis-à-vis relevant other parties, including clients, donors and constituency. This means that I look into processes by which NGO actors convince stakeholders that a situation requires development, that NGO intervention is indispensable and appropriate, and that the NGO has no self-interest in the envisaged programme.

    The approach I developed for this rests on three pillars. Firstly, I use an actor orientation. Such an orientation starts with the premise that social actors have agency. They reflect upon their experiences and what happens around them and use their knowledge and capabilities to interpret and respond to development. An actor orientation recognizes the large range of constraints that impinge on social actors, but emphasizes that such constraints operate through people. To find out how NGOs work in a particular environment I followed their actors in their different domains of work, studying how NGO practices come about and acquire meaning, through formal manifestations and actions as well as more informal everyday operations.

    Secondly, the study focuses on how people (not just anthropologists) grapple with the relation between processes and things. In their everyday practices people have a practical awareness of the process nature of organizations and other phenomena. Yet, they simultaneously adhere to thing notions about the same. One focus of the study was how actors accommodate these different notions, how they use them strategically, and how they respond to other people's thing notions. One such a thing is the label of NGO. By most definitions, development NGOs are intermediary organizations that bring about development for poor and marginalized people. Instead I defined the name of NGO as a label claiming the organization does good for the development of others. The question then becomes why actors take on this identity and how they find recognition as the do-good organizations implied in the label. Another class of things of particular interest is representations. Through their accounts and practices NGO actors convey images about what their organization is, does and wants. Unlike the multiple realities and nitty-gritty of everyday practices, representations provide a single understanding and closure. As John Law stated, instead of asking ourselves whether a representation corresponds to reality, we should be concerned with the workability and legitimacy of a representation. Through this study, then, I wanted to see how actors compose different representations, and the contests involved in their efforts to enrol others in accepting them.

    Given my interest in issues of meanings and legitimation, discourse is important. Discourses are more or less coherent sets of references for understanding and acting upon the world around us. As was pointed out by Foucault, discourses intertwine knowledge and power. However, how discourse works, how it exactly intertwines knowledge and power is a matter for debate. This study spoke of the 'duality of discourse', following Giddens' notion of the 'duality of structure'. There are always multiple discourses and actors find room for manoeuvre to renegotiate them. The other side of the duality of discourse stipulates that discourses can indeed become powerful, although never hegemonic. The more dominant a discourse, the more it operates as a set of rules about what can and cannot be said and done and about what.

    These three pillars of my approach are elaborated in chapter 1. Chapter 2 reviews how social movement discourses are constructed and what this means for the relation between leaders and followers, as well as for power struggles in the movement. This is elaborated with a case of social resistance against hydro-electric schemes in the Chico River of the Cordillera. Chapter 3 addresses the question of how, in a situation of multiple realities, a particular discourse becomes dominant. It shows the struggles of a political movement aiming to restore its grip on development NGOs, and how women's organizations endeavoured to accommodate gender issues in a dominant political discourse. The chapter ends with a discussion of the multi-dimensional working of a powerful discourse, -as coercing, convincing and seducing-, which makes understandable why social actors submit themselves to an ideological regime that confines their room for manoeuvre.

    Chapter 4 enters the life world of village women. These women identify different meanings of development and cleverly play these out in dealing with the ensemble of development projects in their community. However, their appropriation of development interventions leads to unintended changes, in particular the erosion of the position of elder women. Chapter 5 elaborates the room for manoeuvre of NGOs. On the basis of a number of cases, it is concluded that villagers are much more decisive in the outcome of organizing processes than the NGOs. Chapter 6 provides a theoretical analysis of the concept of accountability and leads to the conclusion that transparency is a myth. A case study following a conflict in a weaving project for women shows that, instead of revealing what really happens in the localities, accounts are permeated by what happens in the accountability process.

    Chapter 7 explores how NGO actors in their everyday practices give meaning to the organization. This question turns out to be much more complex than 'management-directing-the-organization', or 'management-versus-the-rest' perspec-tives, can account for. The chapter shows how, through the symbolic use of particular locales, social networks and cultural institutions, a certain coherence nonetheless emerges. Chapter 8 gives a social analysis of successful NGO leadership. It is organized around the life history of one NGO leader, who was followed in her dealings with international arenas and funding agencies. NGO leaders appear as brokers of meaning. They enrol stakeholders to acknowledge their position, and accept their representation of situations, organizations and themselves. Chapter 9 deals with funding agencies. An extended case study is presented of the relation between CWNGO and a UN related program, which ended because the donor claimed the NGO was not efficient and was not accountable to its target group. Underlying this outcome were complex factors including organizational competition, political differences and different interpretations of 'partnership'.

    Chapter 10 is the conclusion. It outlines some implications of the study for issues of NGO everyday politics. Politics of legitimation are closely linked to accountability, which is considered a problematic issue. My analysis corroborates this. There does not seem to be a single solution or methodology to realize accountability. We shall always need to critically improvise, combine methods and make the best of them.

    Those that demand accountability, in particular donors, should acknowledge different modes of accountability instead of solely relying on formal accountability procedures. Perhaps this may bring them to invest more in trust and less in disciplining through detailed accountability demands. In particular they should invest in becoming trustworthy partners of development NGOs thereby forging the moral commitment of NGOs to live up to their promises. It was also concluded that the everyday politics of legitimation that tend to corrupt accountability also contain pressures to move towards more meaningful accountability. NGOs are vulnerable to losing their good name. The easiest way to protect one's good name is by living up to one's proclaimed standards. If they don't succeed, they risk losing their appeal for funding agencies, their legitimacy as advocates, their credibility in the eyes of the media, and eventually their status as an organization that is seen to do good for the benefit of others.

    It has been suggested that there is a tendency among development NGOs in the South to converge towards variations of Western dominated neo-liberal and liberal-democratic development agendas. On the basis of this study I find this notion an exaggeration. The future of development NGOs is likely to be much more diversified than observers of convergence expect. With or without the label of NGO, organising processes will continue to shape differential development outcomes. I expect that commitment to values which advance public and collective interests and that radically side with the poor will continue to be an important element of the ideological visions of many NGOs.

    Brushes and soap : grafted polymers and their interactions with nanocolloids
    Currie, E.P.K. - \ 2000
    Agricultural University. Promotor(en): M.A. Cohen Stuart; G.J. Fleer. - S.l. : s.n. - ISBN 9789080347069 - 209
    borstels - polymeren - colloïden - oppervlaktespanningsverlagende stoffen - brushes - polymers - colloids - surfactants - cum laude

    Layers of polymer chains end-attached to a grafting plane at high densities, so-called brushes, are a curious state of matter. The (average) monomer density within the brush is as high as in a semi-dilute polymer solution, resulting in a high osmotic pressure in the brush. Due to the grafting, however, this isotropic osmotic pressure results in an anisotropic stretching of the chains normal to the surface. This degree of stretching can be quite extensive; in this thesis PEO-chains of 700 monomers are considered which are stretched up to 20% of their total contour length, i.e. form a brush with a thickness of 50 nm, merely by the presence of similar grafted chains.

    It is evident that such extended polymer layers may strongly modify the properties of the grafting surface. To this end brushes are applied as, for instance, adsorption inhibitors or colloidal stabilisators. In this thesis we focus on the thermodynamic and structural properties of polymer brushes, both neutral and charged, and on their interactions with nanocolloids. A mean-field model is developed that describes the effect of complexes formed by polymer (or polyelectrolyte) chains and nanocolloids on the polymer conformation, and the phase behaviour of such mixtures. These two modes of investigation converge in the theoretical and experimental investigation of the interaction between neutral brushes and nanocolloids which may form complexes with the polymer chains in a bulk solution.

    A general introduction to brushes and polymer-nanocolloid complexes is presented in Chapter 1. The concepts underlying scaling and analyticalself-consistent-field (aSCF) models of brushes are briefly discussed, as are a number of technological applications of grafted polymers. The difficulties encountered in the preparation of a brush of a controlled chain length and grafting density are also considered.

    In Chapter 2 surface pressure isotherms of neutral, end-grafted chains that can adsorb to the grafting plane are modelled with the numerical Scheutjens-Fleer self-consistent-field (nSCF) model. These numerical results are compared to experimental isotherms of PS-PEO block copolymers irreversibly adsorbed at the air/water interface. Semi-quantitative agreement between the numerical and experimental isotherms is found. It is shown that for long chains the experimental and numerical isotherms obey the power law for the brush surface pressure as a function of the grafting density predicted by aSCF models.

    The predicted power law for the brush thickness is only obeyed when the experimental surface pressure isotherms also follow the aSCF power law. The adsorption/desorption transition of grafted polymers upon increasing grafting density is investigated numerically by considering the chemical potential of the grafted chains and its derivative with respect to the grafting density. It is shown that this adsorption/desorption transition is continuous, irrespective of the chain length and the adsorption strength. The behaviour of the chemical potential at large adsorption energies is reminiscent to that of a (mean-field) magnetic system approaching its critical point.

    The monomer density profiles of monodisperse and bimodal PEO-brushes are determined with neutron reflectivity and compared to profiles predicted by the nSCF model in Chapter 3. The monomer density distribution predicted by aSCF-models, namely a parabolic profile, is only found at a relatively high grafting density. At lower densities the contribution of a `tail' region at the edge of the brush to the reflectivity spectra is considerable. In this distal region, which originates from fluctuations of the extended chains, the density smoothly drops to zero. Good agreement is found between the experimental and nSCF density profiles. When short and long PEO-chains are mixed at relatively high grafting densitites a bimodal brush is formed. This biomodal density distribution is enhanced by unequal chain length ratio's and mixing ratio's at high grafting densities of such mixed layers. As expected on the basisof theoretical predictions, the long chains in the bimodal brush are additionally stretched by the presence of the shorter ones.

    In Chapter 4 the properties of annealed polyeclectrolyte brushes, consisting of grafted polyacrylic-acid (PAA) chains in contact with aqueous solution, are examined with surface pressure measurements, optical reflectivity and ellipsometry. When the ionic strength of the subphase is high and the pH relatively low, the predicted power law for the surface pressure as a function of the grafting density in the salted brush (SB) regime is found. At low ionic strength and pH, however, the PAA-chains are found to adsorb at the air/water interface.

    Due to such adsorption the predicted osmotic brush regime is not observed at the air/water interface. A novel manner to prepare brushes on a solid substrate, namely Langmuir-Blodgett deposition of PS-PAA block copolymers from an air/water interface on a hydrophobic modified silicon wafer and subsequent thermal annealing, is developed. Using this technique the average degree of dissociation of grafted PAA chains as a function of pH is measured with reflectometry. It is shown that dense grafting of the PAA-chains shifts the titration curves significantly to higher pH, as predicted by scaling models and numerical studies.

    The thickness of the PAA brushes on hydrophobic modified silicon wafers is measured with ellipsometry as a function of pH, ionic strength and grafting density. At a pH not far from the monomeric pKa, the brush thickness is theoretically predicted to initially increase with increasing ionic strength and to decrease again at high ionic strength. This non-monotonic behaviour of the brush thickness is now observed experimentally for the first time.

    The initial increase in brush thickness with increasing ionic strength is, however, experimentally less pronounced than predicted by theory.

    An analytical mean-field theory for long polymer chains that form complexes with nanocolloids is developed in the following chapters. In Chapter 5 the complexation between single polymer chains in a good solvent and surfactants in micellar aggregates is considered, using a Flory-like approach. It is shown that the number of complexed micelles on a polymer chain continuously increases with increasing surfactant concentration, in agreement with experimental evidence. The size of the coil can monotonously increase, decrease, or have a maximum as a function of the surfactant concentration. Comparison with experimental data for PEO-gels complexed with SDS shows a reasonable agreement between the predicted dependence of the gel volume on the ionic strength and experiments.

    In Chapter 6 semi-dilute solutions of complexed chains are considered. Osmotic interactions are found to strongly influence the degree of complexation in a semi-dilute solution. The degree of loading of the chains by nanocolloids decreases with increasing monomer density when the osmotic interactions between complexed particles are strong compared to those between bare monomers. If, however, the complex-monomer osmotic interactions are strong compared to both the complex-complex and monomer-monomer, phase separation into a relatively dilute phase consisting of highly loaded chains coexisting with a relatively dense phase of bare chains may occur. Such phase separation is promoted when the solvent quality decreases. If the solution is below the Theta-temperature of the bare polymer, a first-order phase transition from a bare, collapsed globule to a swollen coil with increasing particle density is predicted.

    Such a first-order phase transition is reported experimentally for collapsed polymer globules with increasing surfactant concentration. An analytical self-consistent-field theory for polymer brushes, in the presence of particles capable of complexation is presented in Chapter 7. As a monomer density gradient is present in a brush, the density of complexed particles is also predicted to vary across the brush. Roughly speaking, the complexes are predominantly located in the distal region of the brush, where the average monomer density is low. In the proximal region of the brush, close to the grafting plane, the density of complexed particles is low. Microphase separation may occur in the brush under the same conditions for which macroscopic phase separation occurs in a bulk solution.

    The overall number of complexed particles is predicted to have a maximum as a function of the grafting density. The height of the brush is found to either increase monotonously with increasing grafting density, or have a local maximum and minimum. The adsorption of the protein BSA on hydrophobic silicon wafers covered with grafted PS-PEO-chains is experimentally examined in Chapter 8. The amount of adsorbed BSA is measured with reflectometry at several grafting densities and different PEO chain lengths.

    Conventional models for the interaction between a brush and adsorbing proteins predict the adsorbed amount to decrease with increasing grafting density and chain length as the interaction between PEO and BSA in the bulk is purely repulsive. However, it is observed that the adsorbed amount has a maximum as a function of the grafting density for long chains, whereas it decreases monotonously in the case of short chains. This maximum is qualitatively understood with our aSCF model presented in Chapter 7 and indicates that some (unknown) attraction between grafted PEO and BSA may exist.

    Finally, in Chapter 9, our theoretical model is extended to complexation of polyelectrolyte chains with oppositely charged nanocolloids. In a given system (particle size, charge densities of the chain and particle) the ionic strength is the main parameter which controls complexation. At high ionic strength the attractive electrostatic interactions are suppressed and the degree of complexation is negligible. As the ionic strength decreases the attractive electrostatic interactions induce complexation. The transition from a bare polyelectrolyte to a complexed chain is predicted to be either continuous or abrupt, depending on the ratio of the charge densities and the Hamaker constant of the particles. In the former case the complex remains soluble, in the latter a non-soluble coacervate is formed. Both kinds of loading processes have been reported in the literature.

    Long-term genetic contributions : prediction of rates of inbreeding and genetic gain in selected populations
    Bijma, P. - \ 2000
    Agricultural University. Promotor(en): E.W. Brascamp; J.A.M. van Arendonk; J.A. Woolliams. - S.l. : s.n. - ISBN 9789058082411 - 225
    vee - dierveredeling - inteelt - genetische winst - genetische diversiteit - selectie - livestock - animal breeding - inbreeding - genetic gain - genetic diversity - selection - cum laude

    This dissertation focuses on the prediction of long-term genetic contributions, rates of inbreeding and rates of gain in artificially selected populations. The long-term genetic contribution ( r i ) of ancestor i born at time t 1 , is defined as the proportion of genes from i that are present in individuals in generation t 2 deriving by descent from i , where ( t 2 - t 1 )→∞.

    The long-term genetic contribution of an individual was predicted by linear regression on the selective advantage of the individual. With overlapping generations, long-term genetic contributions were predicted using a modified gene flow approach. A novel definition of generation interval was introduced, which states that the generation interval is the length of time in which long-term genetic contributions sum to unity. It was shown that the rate of inbreeding is proportional to the sum of squared of expected long-term genetic contributions and that the rate of genetic gain is proportional to the sum of cross products of long-term genetic contributions and Mendelian sampling terms. Accurate predictions of rates of inbreeding were obtained for populations with discrete or overlapping generations undergoing either mass selection or selection on Best Linear Unbiased Prediction of breeding values. The method was applied to crossbreeding systems, which showed that the use of crossbred information may increase the rate of genetic gain, but measures to restrict the rate of inbreeding are required.

    Chinantec shifting cultivation : InTERAcTIVE landuse : a case-study in the Chinantla, Mexico, on secondary vegetation, soils and crop performance under indigenous shifting cultivation
    Wal, H. van der - \ 1999
    Agricultural University. Promotor(en): R.A.A. Oldeman. - S.l. : s.n. - ISBN 9789058081315 - 162
    zwerflandbouw - vegetatietypen - bosbouw - agroforestry - landgebruik - vegetatie - herbegroeiing - vegetatiebeheer - secundaire bossen - mexico - shifting cultivation - vegetation types - forestry - agroforestry - land use - vegetation - revegetation - vegetation management - secondary forests - mexico - cum laude

    The development of secondary vegetation, soils and crop performance was studied in local variants of shifting cultivation in two villages in the Chinantla, Mexico. In Chapter 1, the institutional, social and political context of the research are presented and the reader is advertised that the scope of the study is limited to the interaction between ecological-productive aspects and the landuse pattern as practiced by the farmers.

    In Chapter 2 a conceptual framework is presented. Indigenous shifting cultivation is defined as a general form of landuse, characterized by the continuous recontextualization of a many-sided relation between man and nature, the continuous recreation of knowledge and the making and use of dynamic fields according to a landuse pattern. A great specificity of indigenous shifting cultivation in response to local environmental and socio-economical factors is observed.

    The ecology of secondary vegetation is reviewed, paying attention to mountain areas such as the Chinantla. The development of forest eco-units is not a simple, unilinear process, but, on the contrary, a process that can take one of many possible courses, influenced by environmental factors and the use-history of the land. Soils develop as an integral part of eco-units, as has been observed by comparing the soil in hurricane tracts and eco-units of different ages. The development of secondary vegetation and soils, as related to the landuse pattern for shifting cultivation, leads to variation in the ecological conditions within the mosaic of fields. Consequently, the performance of crops may vary within the mosaic of fields.

    In the Chinantla region a large variation in climate occurs due to a wide altitudinal range (Chapter 3). As a consequence, several vegetation types occur. Soils in the area have developed from limestone or sandstone/metamorphic rocks. Chapter 4 describes the variants of shifting cultivation and the landuse pattern in the Chinantec communities Santa Cruz Tepetotutla and Santiago Tlatepusco. Three variants of shifting cultivation were distinguished: shifting cultivation in the area of 'selva alta perennifolia de montaña' (the most widely practised), shifting cultivation in the limestone area, and shifting cultivation in the Quercus -forests. In all variants maize is the principal crop.

    In Chapter 5 the development of secondary vegetation as related to the use-history of fields is studied, concentrating on secondary vegetation in the area of 'selva alta perennifolia de montaña'. Secondary regrowths were sampled in 28 fields. Ages of regrowths varied from 5 to 50 years, and orders of regrowths (first-order regrowths develop after cutting primary or old secondary vegetation; second-order regrowths after cutting a first-order regrowth) varied from 1 to 4. On each field, data on the trees and shrubs with a diameter at breast-height of more than 2 cm were recorded in four transects, each of 100 m 2surface area, which were all laid out on steep slopes.

    A total of 5691 trees and shrubs, belonging to 229 species, were found on the sampled area. Thirty-seven species comprised 90% of all sampled individuals. Cluster and ordination analysis showed variation of the species composition of secondary vegetation with age, altitude, geographic location, lithology and order of regrowth. Analysis of farmers' information on the relation between order of regrowth and species composition confirmed the results of sampling.

    Structural parameters, species composition, tree development and eco-unit development varied between orders of regrowth. Basal area, number of trees and crown area index were high in first- and second-order regrowths, but fell sharply in subsequent regrowths. First-order regrowths were dominated by one or two species. In several second-order regrowths, Hedyosmum mexicanum was the single dominant. In other second-order and in later-order regrowths polydominance was observed. Analysis of height-diameter relations in frequent species also indicated a relation between the order of regrowth and the development of the trees of a certain species, demonstrating the flexibility of trees in responding to a changing environment. Whereas first- and second-order regrowths were composed of few eco-units, third- and fourth-order regrowths showed fragmentation of eco-units from early phases of development onwards. The results indicate that the number of consecutive eco-units per time unit diminishes with increasing order of regrowth.

    Changes in soils during one cropping season were studied by comparing soil parameters in samples obtained after slashing the vegetation (May), after burning (June) and at harvest (October-November). No significant differences in bases, pH, nitrogen and carbon were found between May- and June-samples on limestone-derived soils. Between burning and harvest, pH and the sum of exchangeable bases increased slightly. In the area of 'selva alta perennifolia de montaña' pH and exchangeable bases increased significantly between May and June. During the cropping season (June to October-November), the sum of exchangeable bases declined slightly. No relation of these changes with the use-history of fields was found, possibly due to the small number of sampled fields and burns being partial and heterogenous in the year of sampling (1993).

    Sampling of soils in a chronosequence of fields in the area of 'selva alta perennifolia de montaña' gave strong indications of an increase of pH and exchangeable bases in the course of several decades, from the cutting of primary or old secondary vegetation onwards. The strongest increase was observed in the quantity of exchangeable calcium. Correlations between use-history parameters and carbon, nitrogen and phosphorus were not significant. A mechanism of soil change based on a combination of physical and biological processes is proposed, wherein an initial increase in pH through the addition of bases triggers of an increased biological activity resulting in a more hospitable soil.

    The performance of maize crops in a chronosequence of fields was studied in 1994 by determining several parameters referring to the crops (Chapter 7). Crop performance varied strongly between fields, both in the limestone area and in the area of 'selva alta perennifolia de montaña'. In the limestone area, yield per square meter sloping surface diminished with increasing number of burns; there was no relation between yield and any of the measured soil parameters. In the area of 'selva alta perennifolia de montaña', yields were not significantly correlated with any of the parameters applied to characterize the use-history of fields. However, yields per square meter sloping surface were correlated with several soil parameters: CEC-BaCl 2 , exchangeable calcium, total phosphorus and the C/N-ratio. At values smaller than 3.9 also pH-KCl was positively correlated with yields. In fertilization experiments, the combined application of nitrogen and phosphorus improved yield on a field where without fertilization a low yield was obtained; fertilization had no effect where high yields were obtained without fertilization.

    The development of secondary vegetation, soils and crop performance in indigenous shifting cultivation in two villages in the Chinantla, Mexico, illustrates the interactive and iterative character of this form of agriculture. This character should be taken as the point of departure for its redesign in such a way that the production of a variety of goods is combined with the production of a variety of services in a complex mosaic of eco-units.

    Treemail Publishers
    all rights reserved - ISBN 90-804443-4-0
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