Mapping, isolation and characterization of genes responsible for late blight resistance in potato

Late blight (LB), caused by the oomycete Phytophthora infestans, is one of the most devastating diseases on potato. Resistance (R) genes from the wild species Solanum demissum have been used by breeders to generate late blight resistant cultivars, but resistance was soon overcome by the pathogen. A more recent screening of a large number of wild species has led to the identification of novel sources of resistance, many of which are currently being characterized. R-gene based resistance to any plant pathogen has been conceptualized according to a model known as gene-for-gene interaction. When matching avirulence (Avr) and resistance (R) proteins are produced by the pathogen and the plant respectively, a resistance response is triggered resulting in a hyper-sensitive response (HR) causing necrosis and cell death at the infection site. If one of these components is missing the plant-pathogen interaction is compatible and will result in completion of the life cycle of the pathogen. This thesis describes the cloning and the characterization of the resistant alleles Rpi-vnt1.1, Rpivnt1.2 and Rpi-vnt1.3 from Solanum venturii and their counterpart Avr-vnt1 from Phytophthora infestans. The Rpi-/Avr- genes pair Rpi-vnt1/Avr-vnt1 along with R3a/Avr3a and Rpi-blb3/Avr2 have been used to study the genetic and molecular mechanisms behind tuber blight resistance. The cloning of Rpi-vnt1 alleles (Rpi-vnt1.1, Rpi-vnt1.2 and Rpi-vnt1.3) was achieved by the combination of long range PCR (Chapter 2) and a classical map based cloning strategy (Chapter 3). The long range PCR made use of Tm2 homologous PCR primers, upon identification of Tm2 sequence homology in associated markers generated with an NBStargeted fingerprinting technique. Rpi-vnt1 alleles belong to the CC-NBS-LRR class of plant R genes and encode predicted peptides of 891 and 905 amino acids, respectively, which share 75% amino acid (a.a.) identity with the ToMV resistance protein Tm-22 from tomato. Compared to Rpi-vnt1.1, the allele Rpi-vnt1.3 harbors a 14 amino acid insertion in the Nterminal region of the protein and two different amino acids in the LRR domain. Despite these differences, Rpi-vnt1.1 and Rpi-vnt1.3 genes have the same resistance spectrum. An allele mining study of Rpi-vnt1 alleles across Solanum section Petota showed that the three functional alleles were confined within S. venturii as only two accessions from the closely related species S. weberbaueri and S. mochiquense carried Rpi-vnt1.1 (Chapter 4). Subsequent alignment of Rpi-vnt1-like homologs with Rpi-vnt1 alleles revealed the presence of illegitimate recombination (IR) signatures suggesting that two successive deletion events might have occurred in the CC domain. Meanwhile, the construction of a Neighbor Joining tree, based on AFLP data from all the accessions carrying Rpi-vnt1 alleles or Rpi-vnt1-like homologs showed that Rpi-vnt1.1, Rpi-vnt1.2 and Rpi-vnt1.3 alleles belong to a monophyletic clade. Signatures of illegitimate recombination and the monophyletic grouping of Rpi-vnt1 alleles suggested how Rpi-vnt1.1, Rpi-vnt1.2 and Rpi-vnt1.3 could have evolved. Extensive phenotyping with various Phytophthora isolates identified another Rpi gene in S. venturii named Rpi-vnt2, complementing the Rpi-vnt1 allelic resistance spectrum. The genetic position of this second independent locus is not yet identified. The identification of the matching avirulence factor from the pathogen, Avr-vnt1, was achieved by using an efficient and high throughput effector screen of resistant wild potato species (Chapter 5). Avr-vnt1 encodes a typical RXLR-EER effector which expression is induced 2 days post inoculation. Avr-vnt1 is located on a single locus in the reference strain T30-4. Among nine isolates, four alleles were identified. The virulent strain EC1 carries a functional coding sequence of Avr-vnt1 but fails to express the gene. In Chapter 6, the genetic and molecular mechanisms of tuber late blight have been investigated. Using transgenic cv. Desiree plants transformed with Rpi-vnt1.1, R3a or Rpiblb3 tuber blight resistance could be studied in an identical genetic background. First, we demonstrated that transient co-expression of the matching Avr- genes in these transgenic tuber slices trigger a hypersensitive responses (HR), showing that the presence and interaction of both proteins is sufficient to establish tuber blight resistance. Second, phenotypic and molecular analysis of a panel of transformants for Rpi-vnt1.1, R3a and Rpi-blb3, and transcriptional analysis of the corresponding effectors (Avr-vnt1, Avr3a and Avr2 respectively) during leaf and tuber infection showed that the expression level of a given Rgene should equal or exceed the expression level of the matching effector in order to trigger an efficient resistance response in the tuber. Therefore, foliar and tuber late blight resistance are controlled by similar genetic mechanisms. The perceived lack of phenotypic correlation between foliage and tuber blight resistance is thus solely due to the tissue specific expression level of the Rpi-gene. In the general discussion (Chapter 7), results from the experimental chapters are discussed in a broader perspective. <br/

Non-perturbative renormalisation for overlap fermions

Using non-perturbative techniques we have found the renormalisation factor, Z, in the RI-MOM scheme for quark bilinear operators in quenched QCD. We worked with overlap fermions using the Luescher-Weisz gauge action. Our calculation was performed at beta=8.45 at a lattice spacing of 1/a=2.1 GeV using a value of rho=1.4. Our results show good agreement between the vector and the axial vector in the zero mass limit. This shows that overlap fermions have good chiral properties. To attempt to improve the discretisation errors in our results we subtracted the O(a^2) terms in one-loop lattice perturbation theory from the Monte Carlo Green functions. In particular we paid attention to the operators for the observable . We found a value for the renormalisation constants Z^msbar_(v_2b) and Z^msbar_(v_2a) just less than 1.9 at mu=1/a=2.1 GeV.Comment: 6 pages, 3 figures, uses PoS style, poster presented at Lattice 2005 (Chiral Fermions), to be published in Proceedings of Scienc

How ions distribute in a drying porous medium: A simple model

Salt crystallization at surfaces is an important problem for buildings and monuments. We do not consider the formation of salt crystals as such, but focus on transport properties of ions in a drying porous medium. We deal with the first phase of the drying process, where the water is still uniformly distributed throughout the medium. An approximate model is presented, which accounts for both convection and diffusion. It is shown that the key parameter is the Peclet number at the evaporating surface, PehL/D, where h, L, , and D are the drying rate, sample size, porosity, and diffusion constant, respectively. When Pe1 (diffusion dominates over convection) the ions remain uniformly distributed throughout the system. Strong accumulation at the evaporating surface occurs for Pe1 (convection dominates over diffusion). Crossover behavior is found for Pe1. Therefore, it is likely that the first crystals will be formed both in the bulk and at the interfaces of the material when Pe1. For high values of Pe the density peak at the evaporating surface will reach the saturation concentration long before it is reached in the bulk of the material. As a consequence, the salt starts to crystallize at the interfaces

On the metallicity gradient of the Galactic disk

Aims: The iron abundance gradient in the Galactic stellar disk provides fundamental constraints on the chemical evolution of this important Galaxy component. However the spread around the mean slope is, at fixed Galactocentric distance, larger than estimated uncertainties. Methods: To provide quantitative constraints on these trends we adopted iron abundances for 265 classical Cepheids (more than 50% of the currently known sample) based either on high-resolution spectra or on photometric metallicity indices. Homogeneous distances were estimated using near-infrared Period-Luminosity relations. The sample covers the four disk quadrants and their Galactocentric distances range from ~5 to ~17 kpc. Results: A linear regression over the entire sample provides an iron gradient of -0.051+/-0.004 dex/kpc. The above slope agrees quite well, within the errors, with previous estimates based either on Cepheids or on open clusters covering similar Galactocentric distances. However, once we split the sample in inner (Rg < 8 kpc) and outer disk Cepheids we found that the slope (-0.130+/-0.015 dex/kpc) in the former region is ~3 times steeper than the slope in the latter one (-0.042+/-0.004 dex/kpc). We found that in the outer disk the radial distribution of metal-poor (MP, [Fe/H]<-0.02 dex) and metal-rich (MR) Cepheids across the four disk quadrants does not show a clear trend when moving from the innermost to the external disk regions. We also found that the relative fractions of MP and MR Cepheids in the 1st and in the 3rd quadrant differ at 8 sigma (MP) and 15 sigma (MR) level.Comment: 6 pages, 6 figures, A&A accepte

Accelerating Hasenbusch's acceleration of Hybrid Monte Carlo

Hasenbusch has proposed splitting the pseudo-fermionic action into two parts, in order to speed-up Hybrid Monte Carlo simulations of QCD. We have tested a different splitting, also using clover-improved Wilson fermions. An additional speed-up between 5 and 20% over the original proposal was achieved in production runs.Comment: Poster presented by H. Stueben at Lattice2003, meta-data correcte

Contributing to sustainable and just energy systems? The mainstreaming of renewable energy prosumerism within and across institutional logics

Renewable energy (RE) prosumerism comes with promises and expectations of contributing to sustainable and just energy systems. In its current process of becoming mainstream, numerous challenges and doubts have arisen whether it will live up to these. Building on insights from sustainability transitions research and institutional theory, this article unpacks the mainstreaming by considering the range of institutional arrangements and logics through which these contributions might be secured. Taking a Multi-actor Perspective, it analyses the differences, combinations, and tensions between institutional logics, associated actor roles and power relations. Firstly, it unpacks how mainstreaming occurs through mechanisms of bureaucratisation and standardisation (state logic), marketisation and commodification (market logic), as well as socialisation and communalisation (community logic). Secondly, it highlights the concomitant hybridisation of institutional logics and actor roles. Such hybrid institutional arrangements try to reconcile not only the more known trade-offs and tensions between for-profit/non-profit logics (regarding the distribution of benefits for energy activities and resources), but also between formal/informal logics (gaining recognition) and public/private logics (delineating access). This institutional concreteness moves the scholarly discussion and policy debate beyond idealistic discussions of ethical principles and abstract discussions about power: Simplistic framings of ‘prosumerism vs incumbents’ are dropped in favour of a critical discussion of hybrid institutional arrangements and their capacity to safeguard particular transformative ideals and normative commitments.info:eu-repo/semantics/publishedVersio

Paradoxes of Transformative Social Innovation: From Critical Awareness towards Strategies of Inquiry

Society is transforming through a whirlpool of innovations. This includes technological as well as social innovations, i.e. changes in social relations involving new ways of doing, organizing, framing and knowing. Especially the potentials for transformative social innovation (TSI) are gaining the interest of progressive political actors and critical scholars. Occurring in the form of new modes of governance and alternative ways of working and living together, TSI involves the challenging, altering or replacing of dominant institutions. As documented in various strands of critical social inquiry and innovation research, TSI praxis is pervaded with contradictions, anomalies and paradoxes. This methodological contribution addresses the challenge that tends to remain: How to elaborate this general critical awareness into more operational ‘strategies of inquiry’? The paper discusses paradoxes of a) system reproduction, b) temporality, and c) reality construction. Identifying distinct kinds of contradictions and distinct empirical phenomena, this differentiation also calls attention to the associated differences between realist, processual and constructivist research philosophies. Gathering the empirical analyses, theoretical interpretations and methodological advances that have been made on these paradoxes, this contribution opens up the scope for critical and practically relevant innovation research: It is important to bridge the divide between rigorous but sterile methodological know-how, and critical-reflexive theorizing that lacks operational insights.Society is transforming through a whirlpool of innovations. This includes technological as well as social innovations, i.e. changes in social relations involving new ways of doing, organizing, framing and knowing. Especially the potentials for transformative social innovation (TSI) are gaining the interest of progressive political actors and critical scholars. Occurring in the form of new modes of governance and alternative ways of working and living together, TSI involves the challenging, altering or replacing of dominant institutions. As documented in various strands of critical social inquiry and innovation research, TSI praxis is pervaded with contradictions, anomalies and paradoxes. This methodological contribution addresses the challenge that tends to remain: How to elaborate this general critical awareness into more operational ‘strategies of inquiry’? The paper discusses paradoxes of a) system reproduction, b) temporality, and c) reality construction. Identifying distinct kinds of contradictions and distinct empirical phenomena, this differentiation also calls attention to the associated differences between realist, processual and constructivist research philosophies. Gathering the empirical analyses, theoretical interpretations and methodological advances that have been made on these paradoxes, this contribution opens up the scope for critical and practically relevant innovation research: It is important to bridge the divide between rigorous but sterile methodological know-how, and critical-reflexive theorizing that lacks operational insights

The nucleon mass in N_f=2 lattice QCD: finite size effects from chiral perturbation theory

In the framework of relativistic SU(2)_f baryon chiral perturbation theory we calculate the volume dependence of the nucleon mass up to and including O(p^4). Since the parameters in the resulting finite size formulae are fixed from the pion mass dependence of the large volume nucleon masses and from phenomenology, we obtain a parameter-free prediction of the finite size effects. We present mass data from the recent N_f=2 simulations of the UKQCD and QCDSF collaborations and compare these data as well as published mass values from the dynamical simulations of the CP-PACS and JLQCD collaborations with the theoretical expectations. Remarkable agreement between the lattice data and the predictions of chiral perturbation theory in a finite volume is found.Comment: 23 pages, 5 figures; references added + minor corrections; one more reference added, typo in eq.(25) corrected, additional clarifying remark

Constructing delta realities; Joint Fact Finding challenges in Serious Game Design

__Abstract__ This paper addresses the challenges of Joint Fact Finding (JFF) in spatial planning and design. JFF is an important component of a deliberative planning practice: The construction of (problematic) realities is fundamental for the formulation of challenges and solutions. Information is often contested in complex planning processes due to different interests, values and perspectives. Carefully designed interaction procedures are needed to negotiate the relevance and validity of information sources. Particularly promising procedures for this are Serious Games: Facilitating joint reality construction through immersive simulations, they are appealing ways to engage not only knowledge-oriented researchers, but also practice-oriented stakeholders and professionals. Their concreteness speaks to spatial planning and design as crafts. Still, the development of such games is not without its challenges and trade-offs. As procedures for reality construction, they cannot escape the power-laden nature of knowledge. We present a case study on developing a spatial design-oriented game, and analyze it in the tradition of the sociology of translations, aided by literature on serious game development. As indicated, Serious Games could function as JFF procedures in spatial planning and design. Moreover, their architecture can be considered a ‘boundary object’ providing actors an environment that accommodates information sharing, learning and joint reality construction. In this way the game facilitates the building of capacity to generate and integrate knowledge for spatial planning and design. In our project on integrative planning in delta areas, the game architecture accommodated researchers and practitioners in governance, spatial design and geo-information. Striving for interdisciplinary synergies, the game architecture was to be accordingly polyvalent. Its main innovative features would be its generative and integrative capacity, i.e. its capacity to both co-produce and integrate a diversity of information sources and to co-develop/generate spatial designs on this basis. How can joint fact finding in spatial planning and design be organized through a serious game in such a way that it develops integrative and generative capacity, and which challenges and trade-offs are faced in realizing this goal? In this paper we describe and discuss the practical sh