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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Dis-locating innovation : amphibious geographies of creative reuse and alternative value production
Barba Lata, Iulian I.V. - \ 2017
University. Promotor(en): Claudio Minca, co-promotor(en): Martijn Duineveld. - Wageningen : Wageningen University - ISBN 9789463430135 - 131
landscape - cultural landscape - innovations - creativity - imagination - urban sites - urban development - waste land - rural areas - topology - landschap - cultuurlandschap - innovaties - creativiteit - verbeelding - stedelijke terreinen - stadsontwikkeling - woeste grond - platteland - topologie

This dissertation dwells on an experimental approach to the emergence of alternative innovations, interrogated through their spatiotemporal and material conditions. Proceeding from the more recent spate of contributions that grant recognition to innovation processes as a common feature of any practice, this research seeks to expand the understanding of innovation beyond canonical interpretations of the subject matter. This opens up a bewildering matrix of potentialities to tackle the emergence of alternatives, often to be recovered from the very dynamics of mainstream innovations that branch out beyond their original purpose. Moreover, the contingent character of mainstream and alternative innovations connotes processes of varying dynamics and rhythmic qualities, which appear to escape the sole grip of linear or cyclical interpretations. Instructed by this preliminary set of assumptions, this investigation belongs to an amphibious domain of enquiry, one that takes shape at the interface between presumably grounded and more fluid readings of innovation processes. Aligned to the amphibious conceptual imaginary, there is also the thematic repertoire and empirical ambit of case studies explored within the dissertation. As such, the evoked conceptual liminality dictated the particular focus on amphibious practices, as the referents of material and affective dispositions, as well as of narratives of belonging scored across land-water interfaces.

The main case studies presented in chapters IV and V were the result of an exploratory phase, with its point of departure in a pilot study conducted on the emergence of floating urbanization solutions in the Netherlands. The surveyed modalities of inhabiting land-water interfaces led me to wonder on the existence of alternative conditions of possibility to what otherwise appeared and were also tagged as very innovative attempts to reimagine urban dwelling. This struck me as a thorny task: where do you start in qualifying something as innovative or not? It took another survey of historical practices and some lengthy reflection sessions to realize that beyond the shifts and turns it has supposedly informed, innovation is much more performative than I initially thought. Thus, I started conducting ethnographic fieldwork by focusing on a pretty unusual case – floating churches, in Volgograd, Russia, more rural than urban, and definitely not the kind of instance you would run across in the mainstream innovation literature. The second case selection followed more or less the same oddly-informed pattern, this time – an on-land harbour, the brainchild of an experimental self-sufficient community recently established in Amsterdam, The Netherlands.

Speaking from the field of Cultural Geography such an endeavour appears to be an opportune exercise, particularly for better understanding the underlying conditions of the current innovation ethos and the ways it (potentially) shapes future trajectories. The investigation draws on three main research questions, which address the meanings (1), workings (2) and expectations (3) connected to various innovation imaginaries, as follows:

In what ways do different amphibious practices acknowledge the spatiotemporal and material conditions of innovation?

How do those conditions enable the emergence of alternative innovations?

To what extent are emergent alternatives influencing incumbent political repertoires as part of the current innovation ethos?

To answer these research questions, the dissertation brings into dialogue multiple disciplinary filiations and, as a secondary and more subtle objective, it reflects upon a new set of spatial (and temporal) imaginaries that would add up to the emergent spatial grammars currently animating geographical thought. Within the broader ambit of unpacking the workings of innovation processes, the theoretical and empirical exploration weaves contributions to the burgeoning strands of work on topological thinking, geographies of religion and secularism, archival practices and knowledge mobilities, urban progressive movements, and particularly, to the ongoing debates on new materialism. Consequently, the methodological sway of this study covers a spectrum ranging from grand theory to ethnographic accounts of micro-societal shifts.

The dissertation is structured into seven chapters and its red thread could be envisioned as describing a loop between chapters II and VI, accordingly entitled The Magic Mirror I and The Magic Mirror II. The second chapter provides a critical overview of grand innovation narratives and their diverse filiations across Western thought, to outline the conceptual imaginary that drives this investigation. The thematic focus of The Magic Mirror I concerns the normative distinction between innovation and imitation, which arguably deters an ampler understanding of innovation processes. Chapter III, The surface and the abyss, expands on this preliminary vision by resorting to an extensive genealogical exercise. Through a critical deployment of the surface/depth metaphor, it explores the catalytic potential of topological thinking to establish points of articulation between apparently opposed notions and canons of thought. Starting from a genealogy of mathematical developments and philosophical mediations toward the end point of geography, it addresses the interplay between the formal (axiomatic) and conceptual (problematic) dimensions of topology in suggesting some potentially alternative ways of re-imagining the role of topological thinking for spatial theory and human geography, and connecting these to the empirical exploration presented in chapter IV.

Chapter IV explores the concept of creative reuse as an alternative modality to interrogate the materiality of things and their documentary sway beyond the immediate affordances dictated by circumstances of disposal or dissolution. Drawing on an ethnographic study of the Volga and Don riverscapes, it evokes the case of the floating churches built to support the revival of faith practices in the Volgograd oblast after the collapse of the Soviet Union. In attending to their impact in warping various temporal and geographical proximities, it suggests that their workings rely on topologies of fixed points and shifting spatialities, animated by forms of religious ritual and related creative manifestations. Through recourse to questions of materiality, mobility and affect it argues that creative reuse interventions provide productive ways of exposing and altering the residual surplus on which both things and processes of place-making rest upon.

Chapter V examines the role of creative reuse as an alternative imaginary specifically concerned with the residual surplus that results along dominant processes of accumulation and value production. In moving beyond circumstances of disposal or dissolution, it argues that creative reuse interventions provide inventive ways to exploit the productive latencies scored across incumbent sociotechnical arrangements. Building upon an ethnographic study of De Ceuvel’s on-land harbour, an experimental self-sufficient community recently established in Amsterdam, it shows how things that were otherwise redundant/disposed/forgotten can stimulate new material and affective dispositions that call into question established practices around sustainable, creative and inclusive city-making. Based on the findings, it goes on to suggest that creative reuse interventions enable new conditions of possibility for the enactment of alternative urban futures.

Chapter VI, The Magic Mirror II, closes the loop by connecting the findings to the introductory discussion from The Magic Mirror I, and elaborating further upon a more generous imaginary to tackle the workings of innovations, as well as the emergence of related alternatives. Thus, from the genealogical interrogation of topology to the unconventional interventions discussed in the empirical sections, creative reuse emerges as the vehicle of surprising returns. These enable a more generous reading that transcends the immediate affordances of mere imitation or circumstances of disposal – one that pivots on the key role of variation through mimesis or the potent afterlives of things and affects in animating alternative forms of innovation. The reference to alternatives should be understood both in relation to the dominant narrative of creative destruction, as well as to how various imaginaries – whether digested as secular, religious or otherwise – become entangled and mirror each other in intriguing ways. Consequently, even when proceeding from the fairly basic distinction that things envisioned as fixed end up afloat and travelling around, as much as things expected to float and travel around become stranded, the idea of surprising returns opens a broad spectrum of meanings and potentialities. As such, the resulting instances expose realities that are much more turbulent than commonly asserted.

Chapter VII answers the main research questions and also grants recognition to creative reuse imaginaries as the inescapable complement to dominant processes of accumulation and value production. As such, the material and affective dispositions cultivated through the emergence of alternatives, within and between various practices, signal the dislocation work occasioned by processes of variation through mimesis. These emergent imaginaries rely on a logic of aspiration and differentiation, which allows them to interfere with, and shape each other, or even morph into new narratives of belonging and creative action. And this is usually achieved through a rather twisted symbiosis, one of peculiar association. The latter pertains to the loose/labile character of creative reuse imaginaries explored in the empirical chapters, which enables them to contract and expand under various readings. Somewhat paradoxically, their dynamics seems to mirror that of mainstream innovations through the performative re-enactment of conditions for success. However, they excel through the disposition for multiple entanglements that often defy the normative distinctions between formal and informal domains. This gives rise to broad fields of resonance in recasting all sorts of anamorphic reflections across the resulting amphibious domains of contingency. In other words, the more imaginaries they interfere with or even subsume, the higher chances become for innovative spin-offs. For a more synthetic overview of the findings, the last section of the chapter packs a final reflection in the form of some tentative corollaries inspired by this exploratory journey.

GK4, a G-protein-coupled receptor with a phosphatidylinositol phosphate kinase domain in Phytophthora infestans, is involved in sporangia development and virulence
Hua, C. ; Meijer, H.J.G. ; Keijzer, J. de; Zhao, W. ; Wang, Y. ; Govers, F. - \ 2013
Molecular Microbiology 88 (2013)2. - ISSN 0950-382X - p. 352 - 370.
heterotrimeric g-protein - pollen-tube growth - escherichia-coli - nicotiana-tabacum - genome sequence - alpha-subunit - arabidopsis - gene - topology - fungi
For dispersal and host infection plant pathogens largely depend on asexual spores. Pathogenesis and sporulation are complex processes that are governed by cellular signalling networks including G-protein and phospholipid signalling. Oomycetes possess a family of novel proteins called GPCR-PIPKs (GKs) that are composed of a seven-transmembrane spanning (7-TM) domain fused to a phosphatidylinositol phosphate kinase (PIPK) domain. Based on this domain structure GKs are anticipated to link G-protein and phospholipid signal pathways; however, their functions are currently unknown. Expression analyses of the 12 GK genes in Phytophthora infestans and their orthologues in Phytophthora sojae, revealed differential expression during asexual development. PiGK1 and PiGK4 were fused to monomeric red fluorescent protein (mRFP) and ectopically expressed in P.¿infestans. In growing hyphae different subcellular distribution patterns were observed indicating that these two GKs act independently during development. We focused on the functional analyses of PiGK4. Its localization suggested involvement in cell differentiation and elongation and its 7-TM domain showed a canonical GPCR membrane topology. Silencing of GK4 and overexpression of full-length and truncated constructs in P.¿infestans revealed that PiGK4 is not only involved in spore germination and hyphal elongation but also in sporangia cleavage and infection.
Distant residues mediate picomolar binding affinity of a protein cofactor
Bollen, Y.J.M. ; Westphal, A.H. ; Lindhoud, S. ; Berkel, W.J.H. van; Mierlo, C.P.M. van - \ 2012
Nature Communications 3 (2012). - ISSN 2041-1723
azotobacter-vinelandii apoflavodoxin - hydrogen-exchange - ligand-binding - oxidized flavodoxin - energy landscape - nmr relaxation - dynamics - kinetics - thermodynamics - topology
Numerous proteins require cofactors to be active. Computer simulations suggest that cooperative interaction networks achieve optimal cofactor binding. There is a need for the experimental identification of the residues crucial for stabilizing these networks and thus for cofactor binding. Here we investigate the electron transporter flavodoxin, which contains flavin mononucleotide as non-covalently bound cofactor. We show that after binding flavin mononucleotide with nanomolar affinity, the protein relaxes extremely slowly (time constant ~5 days) to an energetically more favourable state with picomolar-binding affinity. Rare small-scale openings of this state are revealed through H/D exchange of N(3)H of flavin. We find that H/D exchange can pinpoint amino acids that cause tight cofactor binding. These hitherto unknown residues are dispersed throughout the structure, and many are located distantly from the flavin and seem irrelevant to flavodoxin's function. Quantification of the thermodynamics of ligand binding is important for understanding, engineering, designing and evolving ligand-binding proteins
Asymmetric dipping of bacteriophage M13 coat protein with increasing lipid bilayer thickness
Stopar, D. ; Koehorst, R.B.M. ; Spruijt, R.B. ; Hemminga, M.A. - \ 2009
Biochimica et Biophysica Acta. Biomembranes 1788 (2009)10. - ISSN 0005-2736 - p. 2217 - 2221.
membrane-proteins - tryptophan residues - amino-acids - peptides - topology - helix - spectroscopy - orientation
Knowledge about the vertical movement of a protein with respect to the lipid bilayer plane is important to understand protein functionality in the biological membrane. In this work, the vertical displacement of bacteriophage M13 major coat protein in a lipid bilayer is used as a model system to study the molecular details of its anchoring mechanism in a homologue series of lipids with the same polar head group but different hydrophobic chain length. The major coat proteins were reconstituted into 14:1PC, 16:1PC, 18:1PC, 20:1PC, and 22:1PC bilayers, and the fluorescence spectra were measured of the intrinsic tryptophan at position 26 and BADAN attached to an introduced cysteine at position 46, located at the opposite ends of the transmembrane helix. The fluorescence maximum of tryptophan shifted for 700 cm-1 on going from 14:1PC to 22:1PC, the corresponding shift of the fluorescence maximum of BADAN at position 46 was approximately 10 times less ( 70 cm-1). Quenching of fluorescence with the spin label CAT 1 indicates that the tryptophan is becoming progressively inaccessible for the quencher with increasing bilayer thickness, whereas quenching of BADAN attached to the T46C mutant remained approximately unchanged. This supports the idea that the BADAN probe at position 46 remains at the same depth in the bilayer irrespective of its thickness and clearly indicates an asymmetrical nature of the protein dipping in the lipid bilayer. The anchoring strength at the C-terminal domain of the protein (provided by two phenylalanine residues together with four lysine residues) was estimated to be roughly 5 times larger than the anchoring strength of the N-terminal domain
Structural properties of a peptide derived from H+-V-ATPase subunit a
Vermeer, L.S. ; Reat, V. ; Hemminga, M.A. ; Milon, A. - \ 2009
Biochimica et Biophysica Acta. Biomembranes 1788 (2009)5. - ISSN 0005-2736 - p. 1204 - 1212.
proton translocation channel - mediated cross-linking - vacuolar (h+)-atpases - transmembrane segments - magnetic-resonance - nmr-spectra - topology - domain - spectroscopy - surfaces
The 3D structure of a peptide derived from the putative transmembrane segment 7 (TM7) of subunit a from H+-V-ATPase from Saccharomyces cerevisiae has been determined by solution state NMR in SDS. A stable helix is formed from L736 up to and including Q745, the lumenal half of the putative TM7. The helical region extends well beyond A738, as was previously suggested based on NMR studies of a similar peptide in DMSO. The pKa of both histidine residues that are important for proton transport was measured in water and in SDS. The differences that are found demonstrate that the histidine residues interact with the SDS polar heads. In detergent, circular dichroism data indicate that the secondary structure of the peptide depends on the pH and the type of detergent used. Using solid-state NMR, it is shown that the peptide is immobile in phospholipid bilayers, which means that it is probably not a single transmembrane helix in these samples. The environment is important for the structure of TM7, so in subunit a it is probably held in place by the other transmembrane helices of this subunit
Extensive formation of off-pathway species during folding of an alpha-beta parallel protein is due to docking of (non)native structure elements in unfolded molecules
Nabuurs, S.M. ; Westphal, A.H. ; Mierlo, C.P.M. van - \ 2008
Journal of the American Chemical Society 130 (2008)50. - ISSN 0002-7863 - p. 16914 - 16920.
azotobacter-vinelandii apoflavodoxin - nmr chemical-shifts - 8 m urea - secondary structure - denatured state - hydrogen-exchange - energy landscape - intermediate - topology - conformations
Detailed information about unfolded states is required to understand how proteins fold. Knowledge about folding intermediates formed subsequently is essential to get a grip on pathological aggregation phenomena. During folding of apoflavodoxin, which adopts the widely prevalent ¿¿ß parallel topology, most molecules fold via an off-pathway folding intermediate with helical properties. To better understand why this species is formed, guanidine hydrochloride-unfolded apoflavodoxin is characterized at the residue level using heteronuclear NMR spectroscopy. In 6.0 M denaturant, the protein behaves as a random coil. In contrast, at 3.4 M denaturant, secondary shifts and 1H¿15N relaxation rates report four transiently ordered regions in unfolded apoflavodoxin. These regions have restricted flexibility on the (sub)nanosecond time scale. Secondary shifts show that three of these regions form ¿-helices, which are populated about 10% of the time, as confirmed by far-UV CD data. One region of unfolded apoflavodoxin adopts non-native structure. Of the ¿-helices observed, two are present in native apoflavodoxin as well. A substantial part of the third helix becomes ß-strand while forming native protein. Chemical shift changes due to amino acid residue replacement show that the latter ¿-helix has hydrophobic interactions with all other ordered regions in unfolded apoflavodoxin. Remarkably, these ordered segments dock non-natively, which causes strong competition with on-pathway folding. Thus, rather than directing productive folding, conformational preorganization in the unfolded state of an ¿¿ß parallel-type protein promotes off-pathway species formation.
The folding energy landscape of apoflavodoxin is rugged. hydrogen exchange reveals non-productive misfolded intermediates.
Bollen, Y.J.M. ; Kamphuis, M.B. ; Mierlo, C.P.M. van - \ 2006
Proceedings of the National Academy of Sciences of the United States of America 103 (2006)11. - ISSN 0027-8424 - p. 4095 - 4100.
azotobacter-vinelandii apoflavodoxin - protein - pathways - equilibrium - cooperativity - spectroscopy - sensitivity - topology - ensemble - dynamics
Many native proteins occasionally form partially unfolded forms (PUFs), which can be detected by hydrogen/deuterium exchange and NMR spectroscopy. Knowledge about these metastable states is required to better understand the onset of folding-related diseases. So far, not much is known about where PUFs reside within the energy landscape for protein folding. Here, four PUFs of the relatively large apoflavodoxin (179 aa) are identified. Remarkably, at least three of them are partially misfolded conformations. The misfolding involves side-chain contacts as well as the protein backbone. The rates at which the PUFs interconvert with native protein have been determined. Comparison of these rates with stopped-flow data positions the PUFs in apoflavodoxin's complex folding energy landscape. PUF1 and PUF2 are unfolding excursions that start from native apoflavodoxin but do not continue to the unfolded state. PUF3 and PUF4 could be similar excursions, but their rates of formation suggest that they are on a dead-end folding route that starts from unfolded apoflavodoxin and does not continue all of the way to native protein. All PUFs detected thus are off the protein's productive folding route
Gaafheid van bodem en reliëf gemeente Lingewaal en gemeente Geldermalsen; kennisinstrument bij de relatie cultuurhistorie en ruimtelijke ontwikkelingen
Weijschedé, T.J. ; Exaltus, R.P. ; Koomen, A.J.M. ; Bemmel, B. van - \ 2006
Wageningen : Alterra (Alterra-rapport 1249) - 82
geomorfologie - fysiografische elementen - verstoord land - bodemstructuur (soil fabric) - bodemmorfologische kenmerken - cultureel erfgoed - landinrichting - instrumentatie - nederland - informatiesystemen - topologie - betuwe - geomorphology - physiographic features - disturbed land - soil fabric - soil morphological features - cultural heritage - land development - instrumentation - netherlands - information systems - topology
Dit project betreft een kennisproject dat als doelstelling heeft om nieuwe, breed toepasbare kennis te ontwikkelen over cultuurhistorische waarden in samenhang met de gaafheid van bodem en reliëf. Dit heeft voor de gemeenten Lingewaal en Geldermalsen een reëel (kaart)beeld opgeleverd van de gaafheid van bodem en reliëf en de aanwezigheid hierin en samenhang hiermee met archeologische, cultuurhistorische en aardkundige waarden. Deze informatie is gebundeld in een webportaal
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