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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Shaping plant microtubule networks via overlap formation
Keijzer, Jeroen de - \ 2017
University. Promotor(en): Marcel Janson, co-promotor(en): Tijs Ketelaar. - Wageningen : Wageningen University - ISBN 9789463438100 - 151
microtubules - microtubuli

Microtubules are long filaments made up from protein building blocks and ubiquitously employed by eukaryotic cells for a wide range of often essential cellular processes. To perform these functions, microtubules are virtually always organized into higher order networks. Microtubule networks in cells of land plants are fundamental for guiding growth processes and for bringing about their unique mode of cell division. The latter is facilitated by the so‑called phragmoplast network, consisting of two opposing sets of microtubules that foster in their centre the formation and radial outgrowth of a disc-shaped membrane compartment (termed the cell plate) that ultimately divides the two daughter cells. The mechanisms driving the spatial organisation of such networks are of outstanding interest because plant cells do not rely on major microtubule organizers as in most other organisms. Instead, plant cells use a wide range of dispersed interactions among individual microtubules to shape functional microtubule networks. Chapter 1 introduces encounters between microtubules of opposite polarity and consequent bundling as potentially powerful handles to organize microtubules into networks. These encounters generate an area of antiparallel microtubule overlap and such overlaps are a striking feature of the phragmoplast microtubule network.

For long it is recognized that the short overlaps formed among the two opposing sets of phragmoplast microtubules and the membranous structures of the cell plate fall within the same plane. In chapter 2 we hypothesize that the limited length of these overlaps is required for the confined accumulation of cell plate membranes. To investigate this, we start out by co-visualizing overlaps and cell-plate membrane material in living cells of the moss Physcomitrella patens, an emerging model plant system with a convenient genetic toolset and tissues readily observable through microscopy. We reaffirm an early association between overlaps and membranes and further explored this association by experimentally altering overlap length. Incited by length control mechanisms of overlaps in animal cells, we identify two kinesin-4 motor proteins that jointly limit the length of phragmoplast microtubule overlaps in moss. Using cells lacking these kinesin-4s we then show that over-elongation of microtubule overlaps leads to a broadening of initial cell plate membrane depositions and a delayed progression of radial cell plate outgrowth. The cross walls ultimately formed by the wider membrane depositions were found to be thick and irregularly shaped. We thus demonstrate that kinesin-4-dependent overlap shortening in the phragmoplast defines the site of cell plate synthesis for the proper scaffolding of a new cell wall segment separating two daughter cells.

In chapter 3 we further investigate molecular mechanisms that could explain how linkage between a microtubule overlap and membrane assembly activity is realized. We focus on the exocyst tethering complex, one of the membrane tethering complexes involved in cell plate formation in flowering plants. We survey the localization of several moss exocyst subunits during cell division and find that one (Sec6) localizes to microtubule overlaps already before the onset of cell plate biogenesis. Experiments in which overlap length is altered and overlap formation is suppressed reveal that these structures play an important role in positioning Sec6 during cell division. The ability of moss Sec6 to interact with an evolutionary conserved factor in cell plate membrane fusion called KEULE is demonstrated, signifying a potential functional link between membrane tethering and fusion activities during cell plate formation. The precise role of Sec6 positioning by overlaps is as yet unclear, but in the light of the importance of overlaps for spatial control of cytokinesis will prove to be an intriguing direction for future research efforts.

In chapter 4 we gain further mechanistic insight in kinesin-4 mediated overlap length control and governance of division apparatus length as a whole. We focus on microtubule growth in overlaps regulated by kinesin-4, the poleward transport of microtubule polymers (termed flux), and the interplay between these processes. First, a method based on localized photo-activation is established for the quantitative assessment of microtubule flux. We demonstrate that initially flux in the metaphase spindle occurs synchronized and at high rates, to be replaced by a heterogeneous and on average much slower microtubule flux in the phragmoplast. Since polymerisation of microtubules could provide direct fuel for flux, we postulate that the rate of microtubule growth at sites of overlap could determine flux rates. To test this, we experimentally enhance polymerisation rates through knock-out of kinesin-4 proteins. This approach is validated by experiments demonstrating that they can supress microtubule outgrowth at overlaps in an in vivo setting. Upon kinesin-4 removal, flux rates are enhanced signifying coupling to rates of polymerization. We also find that lack of kinesin-4s leads elongation of the entire division apparatus and that this length change is proportional to the temporal activity patterns of the two kinesin-4s. Based on these findings we propose a mechanism for length regulation through a balance of microtubule growth in the overlap zone, retrograde microtubule translocation and putatively microtubule breakdown at the poles. Microtubule turnover in this system is high in the metaphase spindle (~1.5 μm/min), which, partly through kinesin-4 action, is succeeded by a more slowly turning over system in the form of the phragmoplast.

While in general the involvement of antiparallel microtubule overlaps in spatial organization of bipolar microtubule configurations is evident, how they could help shape other geometries is largely unknown. Chapter 5 starts out with the observation that within the unipolarized microtubule array of tip growing moss cells during interphase, there is occasional formation of overlaps at dispersed sites in the network. Tip growth is a mode of growth allowing rapid colonization of the environment and is achieved through highly polarized secretion, whereby the microtubule network reportedly steers the grows axis. We identify one kinesin-4 motor (Kin4-Ia) recruited to the observed overlaps within this network and use knock-out of Kin4-Ia to assess its role in tip growth. This reveals that absence of Kin4-Ia leads to a less adaptable axis of tip growth, prompting further investigation of Kin4-Ia behaviour at interphase overlaps. We find that this kinesin-4 is recruited with a slight delay to overlaps after their formation and inhibits plus end polymerization of overlap microtubules, thereby limiting overlap length. We then uncover that this activity helps to keep the network polarized towards the tip and prevent the overall organization from becoming hyperaligned with the cell axis. We propose that the latter observation might explain the decrease in growth axis adaptability. Overall, this thesis demonstrates that in plant microtubule networks of varying architecture, the formation of antiparallel overlaps provides a defined network feature for the recruitment of other microtubule-based process. Together, overlaps and activities coordinated from there, are potent organizers of functional plant microtubule arrays. The potential wider implications of these findings, their relationship to membrane-bound cytokinetic processes, and their evolutionary context are briefly discussed in Chapter 6.

Leveraging social networks for agricultural development in Africa
Ross, Martha - \ 2017
University. Promotor(en): Erwin Bulte, co-promotor(en): Maarten Voors. - Wageningen : Wageningen University - ISBN 9789463431910 - 174
social networks - agricultural development - economic development - agricultural production - networks - technology transfer - innovations - innovation adoption - diffusion - interpersonal relations - communication - observation - social learning - social interaction - sociale netwerken - landbouwontwikkeling - economische ontwikkeling - landbouwproductie - netwerken - technologieoverdracht - innovaties - innovatie adoptie - diffusie - intermenselijke relaties - communicatie - observatie - sociaal leren - sociale interactie

This thesis contributes to a growing literature that explores relationships between social networks and innovation diffusion within a developing country context. Given this context, the networks of interest within this thesis are the offline interpersonal relationships between community members. Diffusion channels for new innovation are therefore limited to word-of-mouth communication, observation, and personal experience.

Chapter 2 of this thesis analyses two policy tools in targeting these information gaps. The first is through social learning as part of a farmer extension program. The second combines social learning with experiential learning, reducing the cost to personal experimentation with subsidized improved input packages. Our results indicate that farmers who are exposed to both social learning and learning-by-doing more significantly impacts farmer productivity relative to those receiving no intervention and those exposed only to social learning. I interpret this result as an indication of learning-by-doing combined with social learning being a more effective strategy for facilitating adoption of technologies that have more heterogeneous returns to adoption.

Chapter 3 of this thesis tests the difference in diffusion patterns that result by varying the network contact- point. Specifically, network contact-points are selected as being either the most central or least central individuals within the network. I find evidence that centrality affects the speed of distribution but does not affect the width of diffusion nor which individuals are participating within the diffusion process. Furthermore, large attenuation is observed throughout the diffusion process, which suggests the importance of selecting a sufficiently large set of lead community members for the spread of new technology.

Chapter 4 combines a community-wide polling of network entry-points combined with detailed community network and socio-economic data. First we explore what attributes are prioritized by community members in nominating a resident farmer as an extension contact-point. Second, we use simulations to compare the diffusion spread of top-nominated individuals as network entry-points compared to entry-points that achieve maximal spread within diffusion simulations. We find that community members prioritize network connectedness, pro-social preferences, and socioeconomic indicators of gender, age, formal leadership, and education levels within their nomination decisions. Furthermore, receiving the top three most amount of nominations is found to be significantly correlated with selection as an optimal entry-point within the diffusion simulation. These results suggest that community-wide polling offers a less data-intensive opportunity to realize gains in diffusion warranted through network-based seeding.

Chapter 5 explore whether an individual’s observed social preferences is correlated with an individual’s centrality within the network structure. Our results indicate that individuals with high centrality are more trusting and more trustworthy than individuals with lower centrality. Moreover, individuals with low centrality are treated worse in these interactions—people trust them less initially, and return less money to them. Within a group context, little evidence is found of more central individuals displaying more cooperative behavior. Instead, for group cooperation, when a single monitor can observe contribution decisions, the presence of a direct link and more mutual network connections with a monitor correlates to more cooperative behavior by that individual. Our results suggest that network centrality and pro-social preferences are related but more localized network ties are more strongly correlated with pro-sociality than overall network connectedness.

Using probabilistic graphical models to reconstruct biological networks and linkage maps
Wang, Huange - \ 2017
University. Promotor(en): Fred van Eeuwijk, co-promotor(en): Hans Jansen. - Wageningen : Wageningen University - ISBN 9789463431538 - 150
probabilistic models - models - networks - linkage - mathematics - statistics - quantitative trait loci - phenotypes - simulation - waarschijnlijkheidsmodellen - modellen - netwerken - koppeling - wiskunde - statistiek - loci voor kwantitatief kenmerk - fenotypen - simulatie

Probabilistic graphical models (PGMs) offer a conceptual architecture where biological and mathematical objects can be expressed with a common, intuitive formalism. This facilitates the joint development of statistical and computational tools for quantitative analysis of biological data. Over the last few decades, procedures based on well-understood principles for constructing PGMs from observational and experimental data have been studied extensively, and they thus form a model-based methodology for analysis and discovery. In this thesis, we further explore the potential of this methodology in systems biology and quantitative genetics, and illustrate the capabilities of our proposed approaches by several applications to both real and simulated omics data.

In quantitative genetics, we partition phenotypic variation into heritable, genetic, and non-heritable, environmental, parts. In molecular genetics, we identify chromosomal regions that drive genetic variation: quantitative trait loci (QTLs). In systems genetics, we would like to answer the question of whether relations between multiple phenotypic traits can be organized within wholly or partially directed network structures. Directed edges in those networks can be interpreted as causal relationships, causality meaning that the consequences of interventions are predictable: phenotypic interventions in upstream traits, i.e. traits occurring early in causal chains, will produce changes in downstream traits. The effect of a QTL allele can be considered to represent a genetic intervention on the phenotypic network. Various methods have been proposed for statistical reconstruction of causal phenotypic networks exploiting previously identified QTLs. In chapter 2, we present a novel heuristic search algorithm, namely the QTL+phenotype supervised orientation (QPSO) algorithm, to infer causal relationships between phenotypic traits. Our algorithm shows good performance in the common, but so far uncovered case, where some traits come without QTLs. Therefore, our algorithm is especially attractive for applications involving expensive phenotypes, like metabolites, where relatively few genotypes can be measured and population size is limited.

Standard QTL mapping typically models phenotypic variations observable in nature in relation to genetic variation in gene expression, regardless of multiple intermediate-level biological variations. In chapter 3, we present an approach integrating Gaussian graphical modeling (GGM) and causal inference for simultaneous modeling of multilevel biological responses to DNA variations. More specifically, for ripe tomato fruits, the dependencies of 24 sensory traits on 29 metabolites and the dependencies of all the sensory and metabolic traits further on 21 QTLs were investigated by three GGM approaches including: (i) lasso-based neighborhood selection in combination with a stability approach to regularization selection, (ii) the PC-skeleton algorithm and (iii) the Lasso in combination with stability selection, and then followed by the QPSO algorithm. The inferred dependency network which, though not essentially representing biological pathways, suggests how the effects of allele substitutions propagate through multilevel phenotypes. Such simultaneous study of the underlying genetic architecture and multifactorial interactions is expected to enhance the prediction and manipulation of complex traits. And it is applicable to a range of population structures, including offspring populations from crosses between inbred parents and outbred parents, association panels and natural populations.

In chapter 4, we report a novel method for linkage map construction using probabilistic graphical models. It has been shown that linkage map construction can be hampered by the presence of genotyping errors and chromosomal rearrangements such as inversions and translocations. Our proposed method is proven, both theoretically and practically, to be effective in filtering out markers that contain genotyping errors. In particular, it carries out marker filtering and ordering simultaneously, and is therefore superior to the standard post-hoc filtering using nearest-neighbour stress. Furthermore, we demonstrate empirically that the proposed method offers a promising solution to genetic map construction in the case of a reciprocal translocation.

In the domain of PGMs, Bayesian networks (BNs) have proven, both theoretically and practically, to be a promising tool for the reconstruction of causal networks. In particular, the PC algorithm and the Metropolis-Hastings algorithm, which are representatives of mainstream methods to BN structure learning, are reported to have been successfully applied to the field of biology. In view of the fact that most biological systems exist in the form of random network or scale-free network, in chapter 5 we compare the performance of the two algorithms in constructing both random and scale-free BNs. Our simulation study shows that for either type of BN, the PC algorithm is superior to the M-H algorithm in terms of timeliness; the M-H algorithm is preferable to the PC algorithm when the completeness of reconstruction is emphasized; but when the fidelity of reconstruction is taken into account, the better one of the two algorithms varies from case to case. Moreover, whichever algorithm is adopted, larger sample sizes generally permit more accurate reconstructions, especially in regard to the completeness of the resulting networks.

Finally, chapter 6 presents a further elaboration and discussion of the key concepts and results involved in this thesis.

Governing cruise tourism at Bonaire: a networks and flows approach
Bets, L.K.J. van; Lamers, M.A.J. ; Tatenhove, J.P.M. van - \ 2017
Mobilities 12 (2017)5. - ISSN 1745-0101 - p. 778 - 793.
cruise tourism - marine community - networks - flows - environmental governance - Bonaire - small island developing state
Conceptual approaches to thoroughly study governance of cruise tourism are lacking in the literature. Relying on Castells’ network society, we analyze how two interconnected flows of cruise ships and passengers are governed by a marine community of users and policy makers. Bonaire is used as a case study. Research shows that the transnational cruise ship flow increasingly determines the local passenger flow at Bonaire. Therefore, the marine community increasingly connects with and adapts to the requirements of the transnational cruise network. Moreover, unequal power relations between cruise networks and flows prioritize the economy over the environment at Bonaire.
Networks, flows and actors : promoting sustainability in globalising food provision
Oosterveer, Peter J.M. - \ 2016
Wageningen : Wageningen University - ISBN 9789462579750 - 24
networks - sustainability - globalization - food - health - social sciences - food chains - governance - netwerken - duurzaamheid (sustainability) - globalisering - voedsel - gezondheid - sociale wetenschappen - voedselketens
Answering the "Call of the Mountain" : co-creating sustainability through networks of change in Colombia
Chaves Villegas, Martha - \ 2016
University. Promotor(en): Arjen Wals, co-promotor(en): Gerard Verschoor. - Wageningen : Wageningen University - ISBN 9789462577251 - 152
sustainable development - sustainability - social networks - networks - communities - rural communities - change - social change - learning - colombia - south america - duurzame ontwikkeling - duurzaamheid (sustainability) - sociale netwerken - netwerken - gemeenschappen - plattelandsgemeenschappen - verandering - sociale verandering - leren - zuid-amerika

In response to the age of the ‘anthropocene,’ as some authors are calling this epoch in which one single species is disrupting major natural systems (Steffen et al 2011), there are calls for more radical, learning-based sustainability that generates deep transformations in individuals and communities so as to transition towards a more reflexive and process-oriented society (Wals 2009, Sterling 2009). The principal contention of this thesis is that new social movements (NSM) of the network society (Castells 2012, Buechler 2016), based on integrated visions of sustainability, can provide platforms for bringing about transformative learning. This thesis is based on empirical research (2012-2016) into a fraction of such NSM named the Council of Sustainable Settlements of Latin America (C.A.S.A.). Comprising a diversity of members from Indigenous pueblos, afro-colombian communities, neo-rural settlements (ecovillages), Hare Krishna communities, campesino farmers, NGOs and urban peoples and initiatives, the C.A.S.A. network organizes intercultural exchanges where transformative learning can be traced. Through new forms of collective action centered on a plurality of ideas and practices, and with a strong focus on reflection and personal development, in such encounters through ‘ontological politics’, ‘optimal dissonance’ and ‘deep reflexivity and flexibility’ members are articulating new paradigms of alternative development and creating spaces for transformation. Yet, such learning processes are incredibly complex, and the value-action gap remains substantial in many cases. What this thesis has shown, however, is that by putting into practice principles of buen vivir and the pluriverse such as reconnecting to ancestral wisdom, acknowledging the other, questioning values of competition and consumerism, and forming new relations to place and territory, one begins to question one's own set of norms, and those of society. Ultimately, the C.A.S.A. network’s struggles, negotiations and learning processes remind us that global sustainability entails more than 'menus' of good practices but a plurality of solutions which include humans and non-humans, different ontologies, and even a multiplicity of worlds, in what is a tough but rewarding aula.

Rice postharvest learning alliance in Cambodia : comparison of assumptions and implementation of a network approach
Flor, Rica Joy ; Leeuwis, Cees ; Maat, Harro ; Gummert, Martin - \ 2016
Journal of Development Effectiveness 8 (2016)4. - ISSN 1943-9342 - p. 489 - 507.
action theories - innovation - Learning alliance - networks - rice postharvest - theories of change

Research projects employ the learning alliance (LA) approach but there is scepticism that its rhetoric is not evident in practice. The authors examined a case of an implemented LA, comparing its outcomes with assumptions from the project and its conceptual design to evaluate the implementation of an LA. Data were from interviews and network maps of actors involved, as well as farmers and town-level actors in Battambang and Pursat, Cambodia. An LA approach can promote actor–network processes that target social, technical, and institutional reordering. Assumptions about the approach, however, may lead projects to emphasize scaling out and direct efforts away from processes that enable innovation.

Supramolecular networks of telechelic polymers
Bohdan, M.A. - \ 2016
University. Promotor(en): Jasper van der Gucht, co-promotor(en): Joris Sprakel. - Wageningen : Wageningen University - ISBN 9789462578678 - 117 p.
supramolecular chemistry - networks - polymerization - gels - mechanical properties - separation technology - rheology - supramoleculaire chemie - netwerken - polymerisatie - mechanische eigenschappen - scheidingstechnologie - reologie

This thesis focuses on the fundamental understanding of phenomena associated with the gelation of end-functionalized polymers and the dynamic processes occurring inside of the gel network. To address particular questions we use two types of telechelic polymers, in which the assembly occurs due to the solvophobic interactions and due to the metal-ligand coordination, respectively. In this research we employ a number of methods, mostly rheology and light scattering.

In Chapter 2 we revealed new insights into the complex microscopic dynamics of transient networks, assembled by hydrophobic forces. Using light scattering experiments we show how these materials exhibit complex multimodal relaxation spectra. To shed light on the nature of such relaxation processes we systematically changed the network architecture by gradually reducing the network connectivity while keeping the polymer concentration constant. This strategy allows us to disentangle the roles of concentration and connectivity on the dynamic modes of these systems.

In Chapters 3 and Chapter 4 we experimentally explored the pathways of network formation from telechelic polymers association by means of metal-ligand complexation. Interestingly, while some networks exhibit near-ideal Maxwellian behavior, as expected for transient networks, we find certain cases where we observe scale-free critical mechanics. To date this latter behavior was only identified close to a covalent percolation transition. The critical behavior observed for these end-functional self-assembled polymer networks, however, is robust to changes in concentration, temperature and crosslinking degree. Our studies show that such a self-organized and robust critical state is the results of arrested phase separation that kinetically traps the network-forming system at its percolation point. The system thus remains trapped in a critical state resulting in robust power-law scaling of shear and relaxation moduli. We also show how this state depends sensitively on the relaxation kinetics of the nodes by demonstrating an intermediate case where initial critical behavior slowly relaxes over the course of several days to the ideal linear Maxwell case. With our research we highlight the complex pathway where self-assembling systems reach their equilibrium ground state, involving persistent and long-lived kinetically arrested states which give rise to unusual mechanics and highly heterogeneous spinodal structures.

Chapter 5 brought us towards more applicable materials where we develop a highly tunable composite network based on orthogonal supramolecular interactions. For such a design we generate multivalent nanoparticle tectons, which are subsequently linked together into network structures, using metal-coordination interactions. Materials built this way are highly tunable with moduli and viscosities spanning many orders of magnitude.

In the remainder of this chapter, we focus on some unresolved and outstanding questions regarding the physical chemistry and properties of supramolecular networks and we will discuss some preliminary data obtained in our efforts to resolve them.

The Vietnamese State and Administrative Co-Management of Nature Reserves
Nguyen, T.K.D. ; Bush, S.R. ; Mol, A.P.J. - \ 2016
Sustainability 8 (2016)3. - ISSN 2071-1050 - 19 p.
co-management - networks - nature conservation - protected areas - Vietnam
The Vietnamese government has introduced co-management in its national system of special-use forests (SUFs) to improve the effectiveness of nature and biodiversity conservation. One of the major challenges is to allow flexibility and local adaptability of co-management coordinated by SUF management boards within the overall still-rigid structure of vertical state networks. Using a critical institutional perspective, this paper examines the influence of the vertical and horizontal linkages that underline the form and function of SUF co-management. Data is presented from a nation-wide survey of 113 SUFs, 22 random in-depth interviews, and four in-depth case studies of SUFs. The results show that the success of co-management in centralized states like Vietnam depends on the greater devolution of allocative power from central to district governments to facilitate horizontal networked collaboration with local communities. Yet the results also indicate that the central state maintains an important role in setting the conditions that allow for the success of these networked collaborations. Based on these findings the conclusions reflect on the need to further develop a critical institutional approach for understanding the purpose, interests, and resources of co-management in the context of centralized states.
Composite hydrogels of bio-inspired protein polymers : mechanical and structural characterization
Rombouts, W.H. - \ 2015
University. Promotor(en): Jasper van der Gucht. - Wageningen : Wageningen University - ISBN 9789462575721 - 172
gels - formation - proteins - polymers - networks - mechanical properties - formatie - eiwitten - polymeren - netwerken - mechanische eigenschappen

In this thesis we presented various combinations of custom-designed protein polymers that formed composite hydrogels. In chapter 2, composite hydrogels were prepared by mixing silk-like block copolymers (CP2SE48CP2) with collagen-like block copolymers (T9CR4T9). We found that by adding the collagen-like protein polymer the storage modulus, the critical stress and critical strain values of the composite hydrogels were significantly improved in comparison to the single networks. With cryo-transmission electron microscopy (cryo-TEM) we observed that the silk-like fibers were bundled in the presence of the collagen-like protein polymer, probably due to depletion attraction interactions. In follow-up research on these composite hydrogels in chapter 3, we tried to get more insight into the exact toughening mechanism and self-healing capabilities of the composite network by performing cyclic loading/unloading tests. We found that mechanical hysteresis occurred in these composite hydrogels. The energy that was dissipated could be split into two contributions: a part belonging to the permanent rupture of silk-like fibers, and a viscoelastic part belonging to the assembly and disassembly of collagen-like triple helices. Both these contributions increased as the concentration of the collagen-like protein polymer in the composite network was increased, resulting in toughening of the composite network. Furthermore, it was observed that the silk-like fiber network was not able to recover, while the composites could recover up to 70% of the original storage modulus after failure. In chapter 4 we studied composite networks of silk-like block copolymers (CP2SE48CP2) and a FMOC-functionalized dipeptide (FMOC-LG) which could both form fibers. With cryo-TEM and atomic force microscopy (AFM) we found that two different types of fibers were formed, indicating that orthogonal self-assembly occurred in this system. We found with rheology that the storage moduli of the composite fiber networks were significantly higher (75 kPa vs. 400 kPa) than that of the single networks. Strain-hardening present in the FMOC-LG fiber network disappeared when the silk-like protein polymer was present. In chapter 5 hydrogels with both physical and chemical crosslinks were prepared from collagen-like protein polymers (T9CRT9). The chemical crosslinks were introduced by crosslinking lysine residues present in the random-coil middle blocks with glutaraldehyde. We found with rheology that the order in which the physical and chemical networks were formed did not influence the final storage modulus of the hydrogel. Depending on the amount of glutaraldehyde added we found an increase of up to an order of magnitude in the storage modulus for the collagen-like hydrogels. To investigate effects on the nonlinear rheological properties cyclic loading/unloading tests were performed. It was observed that before hydrogel failure occurred no hysteresis was observed between consecutive cycles. Both physical and chemical crosslinks ruptured when the hydrogel was fractured. In chapter 6 we studied hydrogels formed by the co- assembly of an asymmetric silk-collagen-like protein polymer (SH8CR4T9) with a symmetric oppositely charged silk-like protein polymer (CP2SE48CP2). This was done in a step-wise approach: (1) the S blocks were co-assembled into silk-like fibers. (2) the T blocks were assembled into triple helical nodes by reducing the temperature. We confirmed with confocal laser scanning microscopy and NMR that both monomers were present in the same fibers. With rheology we found that these composite hydrogels did respond in a reversible manner to temperature changes, with which the mechanical strength of the hydrogel can be tuned. In chapter 7 hydrogel formation of a modified silk-like protein polymer with a cysteine-residue attached to the C-terminal side (CP2SH48CP2-Cys) was studied. With rheology we showed that hydrogels that were formed in oxidizing conditions, where disulfide-bridges could form, were much stronger than those formed in reducing conditions. Both hydrogels formed in oxidizing and reducing conditions showed a scaling of modulus versus concentration consistent with entangled semi-flexible networks. This result implied that the disulfide-bridges formed between cysteine-residues formed loops in the coronae of the fibers. The increase in mechanical strength of the fibers was related to the increase in persistence length of the fibers in oxidizing conditions observed with AFM. With self-consistent field theory-simulations it was shown that the formation of loops in the corona resulted in a slight reduction of the lateral pressure in the corona of the fibers. However, this effect is by itself not sufficient to cause a significant change in persistence length. Due to the reduction in lateral pressure, the stacking of monomers into fibers is probably influenced: fibers with a more crystalline structure and with less detects are formed, resulting in improved mechanical properties of the hydrogels. In the general discussion in chapter 8, we reflect on our work, discuss about future directions of research, and possible applications of protein polymers.

Nieuwe kansen voor traditionele groenten : Traditional Food Network to improve the transfer of knowledge for innovation (TraFooN)
Kik, Chris - \ 2015
horticulture - vegetables - regional specialty products - old varieties - knowledge transfer - workshops (programs) - eu regulations - marketing - networks
Local institutions and rural development : evidence from Liberia
Beekman, G. - \ 2015
University. Promotor(en): Erwin Bulte, co-promotor(en): Lonneke Nillesen. - Wageningen : Wageningen University - ISBN 9789462575080 - 200
plattelandsontwikkeling - gezinnen - netwerken - lokale netwerken - sociale netwerken - instellingen - micro-economische analyse - micro-economie - economische ontwikkeling - landbouwontwikkeling - liberia - west-afrika - rural development - families - networks - local area networks - social networks - institutions - microeconomic analysis - microeconomics - economic development - agricultural development - west africa

Local institutions and rural development: Evidence from Liberia

This thesis focusses on the role of local (informal) institutions for development, based on data from Liberia. I show that dense family networks can be an obstacle for economic decision making, due to strict income sharing obligations that often belong to them. I also demonstrate the importance of local governance quality: corrupt village leaders negatively affect daily investment decisions by villagers. Finally, I evaluate the impact of a rural development project that aims to strengthen food security and social cohesion between villagers. The results indicate that the impact is marginal at most, and local institutions again do play a role.

Institutions are difficult to change, as they are rooted in an historical context. However, policy makers could support the emergence of alternative institutions. Either way, a deeper understanding of the far-going impact of local institutions is important: this research contributes to that.

Self-assembly in a near-frictionless granular material: Conformational structures and transitions in uniaxial cyclic compression of hydrogel spheres
Walker, D.M. ; Tordesillas, A. ; Brodu, N. ; Dijksman, J.A. ; Behringer, R.P. ; Froyland, G. - \ 2015
Soft Matter 11 (2015). - ISSN 1744-683X - p. 2157 - 2173.
force chains - packing - systems - shear - continuum - networks - matter
We use a Markov transition matrix-based analysis to explore the structures and structural transitions in a three-dimensional assembly of hydrogel spheres under cyclic uniaxial compression. We apply these methods on experimental data obtained from a packing of nearly frictionless hydrogel balls. This allows an exploration of the emergence and evolution of mesoscale internal structures — a key micromechanical property that governs self-assembly and self-organization in dense granular media. To probe the mesoscopic force network structure, we consider two structural state spaces: (i) a particle and its contacting neighbours, and (ii) a particle's local minimal cycle topology summarized by a cycle vector. In both spaces, our analysis of the transition dynamics reveals which structures and which sets of structures are most prevalent and most likely to transform into each other during the compression/decompression of the material. In compressed states, structures rich in 3-cycle or triangle topologies form in abundance. In contrast, in uncompressed states, transitions comprising poorly connected structures are dominant. An almost-invariant transition set within the cycle vector space is discovered that identifies an intermediate set of structures crucial to the material's transition from weakly jammed to strongly jammed, and vice versa. Preferred transition pathways are also highlighted and discussed with respect to thermo-micro-mechanical constitutive formulations.
Towards food autonomy: connectivity and self-help groups in Hisar, India
Singh, S. - \ 2015
University. Promotor(en): Guido Ruivenkamp; Han Wiskerke, co-promotor(en): Joost Jongerden. - Wageningen : Wageningen University - ISBN 9789462574922 - 228
landbouw bedrijven in het klein - voedsel - autonomie - voedselproductie - voedselconsumptie - zelfhulp - samenwerking - boerenstand - plattelandsgemeenschappen - netwerken - ondernemerschap - mungbonen - landbouwontwikkeling - rurale sociologie - india - peasant farming - food - autonomy - food production - food consumption - self help - cooperation - peasantry - rural communities - networks - entrepreneurship - mung beans - agricultural development - rural sociology

Keywords: self-help groups, connectivity, food autonomy, peasants, micro-enterprise

Towards Food Autonomy: Connectivity and Self-help Groups in Hisar, India

PhD Thesis

Shweta Singh

Rural Sociology Group, Wageningen University, Netherlands

Abstract Food autonomy requires consideration of the various connectivity and self-help action organizing by the peasants’ communities. The socio-spatial organization of mung-bean production, household processing and consumption practices in Hisar district of Haryana-India are studied. The socio-spatial organization of food connects agriculture to its local environment, the regionally tied agriculture produce to local consumption patterns, and food production and consumption to livelihood and health, which are enabled by the abilities and practices of peasants and stimulate food autonomy. The connections are related to mung-bean food qualities at various levels of production, processing and consumption. Local mung-bean preferences of producers, processors, consumers and the market conditions are studied. It showed that local mung-bean food qualities related to suitability in the local cropping system, processing requirement (short cooking-time, better consistency and appearance) and consumption choice (easy to cook, healthy food). Mung-bean market conditions indicated that the market works against peasants (traders and urban processors are winners). However, the producers’ viewpoint on mung-bean processing at the community level is linked to the creation of new social relations in the mung-bean food network to strengthen the territorial connectivity of mung-bean for reinforcing mung-bean food autonomy. The possibilities of Self-Help Group (SHG) and SHG-based (food) Micro-Enterprise (ME) developments were discussed. In reviewing the literature on SHGs and previous empirical studies, various factors were identified that contribute to a success or failure of a functioning of SHG. These include full participation from and homogeneity among members, and clear group goals and transparency in group operations and functioning. The SHG mung-bean food-based ME initiated in Mangali village of Hisar was studied, to investigate ways in which this group functions. Results revealed three identifiable roles of the self-help peasants’ group: i) it consolidates local mung-bean food production, local resources and motivations of the peasants; ii) it develops another perspective of development based upon a more localized choice for processing, distributing, marketing and accessing local mung-bean food; and iii) it empowers local people (especially peasants and the poor rural community) and strengthens the connectivity between local mung-bean production and consumption. The need remains for technological efforts to address the specific location of peasant resources while in the SHG there is clearly a need to restore or redefine collective responsibility.

Seeds, food networks and politics: different ontologies in relation to food sovereignty in Ecuador
Martinez Flores, L.A. - \ 2015
University. Promotor(en): Guido Ruivenkamp; Han Wiskerke, co-promotor(en): Joost Jongerden. - Wageningen : Wageningen University - ISBN 9789462574908 - 194
voedselsoevereiniteit - landbouw bedrijven in het klein - gemeenschappen - voedsel - netwerken - ontologieën - zaden - politiek - lupinus - voedselketens - landbouwbeleid - overheidsbeleid - etnografie - andes - ecuador - food sovereignty - peasant farming - communities - food - networks - ontologies - seeds - politics - food chains - agricultural policy - government policy - ethnography

Abstract

In this thesis I explore the ontological proposal of food sovereignty and I discuss the possibilities offered by studies like this one to the attempts of the social sciences to explain – in a symmetrical fashion - that develop between humans and other entities at the time of production, processing and consumption of food. In this effort I combine ethnography and history.

I argue that in countries like Ecuador, food networks such as that of the lupine, Lupino mutabilis Sweet, since they do not establish ontological differences between nature and culture, promote the implementation of food sovereignty in practice, as long as agricultural and science and technology (S&T) policies enable the autonomous development of such networks. More specifically, food networks in the Andean highlands have functioned in a rhizomatic way, without establishing hierarchies between entities of different ontology: foods as goods or foods as gifts, society and nature, and have spread without discontinuities between town and country. This analysis enables me to show that these networks can promote food sovereignty, because in them is condensed an ontology distinct from that of modernity with regard to the cultivation, processing and consumption of food. Considering these findings I analyse the rationality of S&T policies and the current policies of the Ecuadorian State. I argue that such policies go against the logic of food networks. Food sovereignty is an achievable goal if Ecuadorian government policies contribute to the strengthening of food networks, creating new links so that they can sidestep the agribusiness model.

The organisation of this thesis is unusual, as the object of study is a food network. This forced me to research and structure this dissertation in a particular way. So, I start with the ethnographic explanation of a food network. Here I analyse its operation, relationships and the paths it establishes. From this analysis it is possible to understand why S&T policies, specifically those related to plant breeding, created new social relations that affected the food networks of the highlands. I show here how the modern rationality on which agricultural policies are based inhibits the growth of food networks and works against food sovereignty. Then, from the analysis of the formation of the food sovereignty network, I examine the introduction of the food sovereignty proposal into the Ecuadorian Constitution and the changes made to the original proposal. I show how the translation of the Via Campesina proposal present in the constitution and the subsequent law is possible due to the intervention of actors linked with the big businesses of the food trade. All this enables me, finally, to discuss my contribution: the analysis of the ontological promise present in the food sovereignty proposal.

Dierenwelzijn in groen onderwijs
Ruis, M.A.W. ; Man, A. de - \ 2015
Tijdschrift voor Diergeneeskunde 140 (2015)7. - ISSN 0040-7453 - p. 16 - 16.
dierenwelzijn - agrarisch onderwijs - middelbaar beroepsonderwijs - kennisoverdracht - lesmaterialen - informatieverspreiding - netwerken - samenwerking - animal welfare - agricultural education - intermediate vocational training - knowledge transfer - teaching materials - diffusion of information - networks - cooperation
Composition properties in the river claims problem
Ansink, E.J.H. ; Weikard, H.P. - \ 2015
Social Choice and Welfare 44 (2015)4. - ISSN 0176-1714 - p. 807 - 831.
international water law - climate-change - game-theory - rights - rules - allocation - resources - networks - stability
In a river claims problem, agents are ordered linearly, and they hve both an initial water endowment as well as a claim to the total water resou8rce. We provide characterizations of two solutions to this problem, using Composition properties which have particularly relevant interpretations for the river claims problem. Specifically, these properties relate to situations where river flow is uncertain or highly variable, possibly due to climate change impacts. The only solution that satisfies all says that agents are free to use any water available on their teerritory, without concern for downstream impacts. The other solution that we assess is the "No-harm rule", an extreme interpretation of the "no-harm" principle from international water law, which implies that water is allocated with priority to downstream needs. In addition to characerizing both solutions, we show their relation to priority rules and to sequential sharing rules, and we extend our analysis to general river systems.
Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain
Gavai, A.K. ; Supandi, F. ; Hettling, H. ; Murrell, P. ; Leunissen, J.A.M. ; Beek, J.H.G.M. van - \ 2015
PLoS One 10 (2015)3. - ISSN 1932-6203 - 21 p.
alzheimers-disease - energy-metabolism - balance analysis - in-silico - models - glucose - biology - networks - neurons - oxygen
Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment. Given the large user community for the R computing environment, a simple implementation of flux analysis in R appears desirable and will facilitate easy interaction with computational tools to handle gene expression data. We extended the R software package BiGGR, an implementation of metabolic flux analysis in R. BiGGR makes use of public metabolic reconstruction databases, and contains the BiGG database and the reconstruction of human metabolism Recon2 as Systems Biology Markup Language (SBML) objects. Models can be assembled by querying the databases for pathways, genes or reactions of interest. Fluxes can then be estimated by maximization or minimization of an objective function using linear inverse modeling algorithms. Furthermore, BiGGR provides functionality to quantify the uncertainty in flux estimates by sampling the constrained multidimensional flux space. As a result, ensembles of possible flux configurations are constructed that agree with measured data within precision limits. BiGGR also features automatic visualization of selected parts of metabolic networks using hypergraphs, with hyperedge widths proportional to estimated flux values. BiGGR supports import and export of models encoded in SBML and is therefore interoperable with different modeling and analysis tools. As an application example, we calculated the flux distribution in healthy human brain using a model of central carbon metabolism. We introduce a new algorithm termed Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA) to predict flux changes from gene expression changes, for instance during disease. Our estimates of brain metabolic flux pattern with Lsei-FBA for Alzheimer’s disease agree with independent measurements of cerebral metabolism in patients. This second version of BiGGR is available from Bioconductor
Dutch City Network feeds the Innovation of Urban Agriculture
Jansma, J.E. ; Veen, E.J. ; Kop, P.J. van de; Eijk, O.N.M. van - \ 2015
Urban Agriculture Magazine 28 (2015). - ISSN 1571-6244 - p. 38 - 41.
urban areas - urban society - urban agriculture - networks - innovations - cooperation - knowledge transfer - stedelijke gebieden - stedelijke samenleving - stadslandbouw - netwerken - innovaties - samenwerking - kennisoverdracht
Since 2010, the Dutch City Network on Urban Agriculture (Stedennetwerk in Dutch), has linked up civil servants of fourteen cities in order to see opportunities, share knowledge and solve issues on urban agriculture in their cities. Though it started as an internally focused network for civil servants to learn and share experiences, the network gradually evolved into a more outward-oriented Community of Practice that seeks to incorporate a broader range of participants. Participants developed an urban agriculture charter to influence local and national policies in support of urban agriculture.
Systems biology of plant molecular networks: from networks to models
Valentim, F.L. - \ 2015
University. Promotor(en): Gerco Angenent, co-promotor(en): Aalt-Jan van Dijk. - Wageningen : Wageningen University - ISBN 9789462572171 - 139
systeembiologie - netwerken - modellen - genetische regulatie - genexpressie - planten - moleculaire biologie - systems biology - networks - models - genetic regulation - gene expression - plants - molecular biology

Developmental processes are controlled by regulatory networks (GRNs), which are tightly

coordinated networks of transcription factors (TFs) that activate and repress gene expression

within a spatial and temporal context. In Arabidopsis thaliana, the key components and network

structures of the GRNs controlling major plant reproduction processes, such as floral transition

and floral organ identity specification, have been comprehensively unveiled. This thanks to

advances in ‘omics’ technologies combined with genetic approaches. Yet, because of the

multidimensional nature of the data and because of the complexity of the regulatory

mechanisms, there is a clear need to analyse these data in such a way that we can understand

how TFs control complex traits. The use of mathematical modelling facilitates the

representation of the dynamics of a GRN and enables better insight into GRN complexity; while

multidimensional data analysis enables the identification of properties that connect different

layers from genotype-to-phenotype. Mathematical modelling and multidimensional data

analysis are both parts of a systems biology approach, and this thesis presents the application of

both types of systems biology approaches to flowering GRNs.

Chapter 1 comprehensively reviews advances in understanding of GRNs underlying plant

reproduction processes, as well as mathematical models and multidimensional data analysis

approaches to study plant systems biology. As discussed in Chapter 1, an important aspect of

understanding these GRNs is how perturbations in one part of the network are transmitted to

other parts, and ultimately how this results in changes in phenotype. Given the complexity of

recent versions of Arabidopsis GRNs - which involves highly-connected, non-linear networks

of TFs, microRNAs, movable factors, hormones and chromatin modifying proteins - it is not

possible to predict the effect of gene perturbations on e.g. flowering time in an intuitive way by

just looking at the network structure. Therefore, mathematical modelling plays an important role

in providing a quantitative understanding of GRNs. In addition, aspects of multidimensional

data analysis for understanding GRNs underlying plant reproduction are also discussed in the

first Chapter. This includes not only the integration of experimental data, e.g. transcriptomics

with protein-DNA binding profiling, but also the integration of different types of networks

identified by ‘omics’ approaches, e.g. protein-protein interaction networks and gene regulatory

networks.

Chapter 2 describes a mathematical model for representing the dynamics of key genes in the

GRN of flowering time control. We modelled with ordinary differential equations (ODEs) the

physical interactions and regulatory relationships of a set of core genes controlling Arabidopsis

flowering time in order to quantitatively analyse the relationship between their expression levels

and the flowering time response. We considered a core GRN composed of eight TFs: SHORT

VEGETATIVE PHASE (SVP), FLOWERING LOCUS C (FLC), AGAMOUS-LIKE 24 (AGL24),

SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), APETALA1 (AP1),

FLOWERING LOCUS T (FT), LEAFY (LFY) and FD. The connections and interactions

amongst these components are justified based on experimental data, and the model is

parameterised by fitting the equations to quantitative data on gene expression and flowering

time. Then the model is validated with transcript data from a range of mutants. We verify that

the model is able to describe some quantitative patterns seen in expression data under genetic

perturbations, which supported the credibility of the model and its dynamic properties. The

proposed model is able to predict the flowering time by assessing changes in the expression of

the orchestrator of floral transition AP1. Overall, the work presents a framework, which allows

addressing how different quantitative inputs are combined into a single quantitative output, i.e.

the timing of flowering. The model allowed studying the established genetic regulations, and we

discuss in Chapter 5 the steps towards using the proposed framework to zoom in and obtain new

insides about the molecular mechanisms underlying the regulations.

Systems biology does not only involve the use of dynamic modelling but also the development

of approaches for multidimensional data analysis that are able to integrate multiple levels of

systems organization. In Chapter 3, we aimed at comprehensively identifying and characterizing

cis-regulatory mutations that have an effect on the GRN of flowering time control. By using

ChIP-seq data and information about known DNA binding motifs of TFs involved in plant

reproduction, we identified single-nucleotide polymorphisms (SNPs) that are highly

discriminative in the classification of the flowering time phenotypes. Often, SNPs that overlap

the position of experimentally determined binding sites (e.g. by ChIP-seq), are considered

putative regulatory SNPs. We showed that regulatory SNPs are difficult to pinpoint among the

sea of polymorphisms localized within binding sites determined by ChIP-seq studies. To

overcome this, we narrowed the resolution by focusing on the subset of SNPs that are located

within ChIP-seq peaks but that are also part of known regulatory motifs. These SNPs were used

as input in a classification algorithm that could predict flowering time of Arabidopsis accessions

relative to Col-0. Our strategy is able to identify SNPs that have a biological link with changes

in flowering time. We then surveyed the literature to formulate hypothesis that explain the

regulatory mechanism underlying the difference in phenotype conferred by a SNP. Examples

include SNPs that disrupt the flowering time gene FT; in which the mutation presumably disrupts the binding region of SVP. In Chapter 5 we discuss the steps towards extending our approach to obtain a more comprehensive survey of variants that have an effect on the flowering time control.

In Chapter 4, we propose a method for genome-wide prediction of protein-protein interaction

(PPI) sites form the Arabidopsis interactome. Our method, named SLIDERbio, uses features

encoded in the sequence of proteins and their interactions to predict PPI sites. More specifically,

our method mines PPI networks to find over-represented sequence motifs in pairs of interacting

proteins. In addition, the inter-species conservation of these over-represented motifs, as well as

their predicted surface accessibility, are take into account to compute the likelihood of these

motifs being located in a PPI site. Our results suggested that motifs overrepresented in pairs of

interacting proteins that are conserved across orthologs and that have high predicted surface

accessibility, are in general good putative interaction sites. We applied our method to obtain

interactome-wide predictions for Arabidopsis proteins. The results were explored to formulate

testable hypothesis for the molecular mechanisms underlying effects of spontaneous or induced

mutagenesis on e.g. ZEITLUPE, CXIP1 and SHY2 (proteins relevant for flowering time). In

addition, we showed that the binding sites are under stronger selective pressure than the overall

protein sequence, and that this may be used to link sequence variability to functional

divergence.

Finally, Chapter 5 concludes this thesis and describes future perspectives in systems biology

applied to the study of GRNs underlying plant reproduction processes. Two key directions are

often followed in systems biology: 1) compiling systems-wide snapshots in which the

relationships and interactions between the molecules of a system are comprehensively

represented; and 2) generating accurate experimental data that can be used as input for the

modelling concepts and techniques or multi-dimensional data analysis. Highlighted in Chapter 5

are the limitations in key steps within the systems biology framework applied to GRN studies.

In addition, I discussed improvements and extensions that we envision for our model related to

the GRN underlying the control of flowering time. Future steps for multi-dimensional data

analysis are also discussed. To sum up, I discussed how to connect the different technologies

developed in this thesis towards understanding the interplay between the roles of the genes,

developmental stages and environmental conditions.

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