Participatory crop improvement: the challenges of and opportunities for institutionalisation in the Indian public research sector

This thesis considers Participatory Crop Improvement (PCI) methodologies and examines the reasons behind their continued contestation and limited mainstreaming in conventional modes of crop improvement research within National Agricultural Research Systems (NARS). In particular, it traces the experiences of a long-established research network with over 20 years of experience in developing and implementing PCI methods across South Asia, and specifically considers its engagement with the Indian NARS and associated state-level agricultural research systems. In order to address the issues surrounding PCI institutionalisation processes, a novel conceptual framework was derived from a synthesis of the literatures on Strategic Niche Management (SNM) and Learning-based Development Approaches (LBDA) to analyse the socio-technical processes and structures which constitute the PCI ‘niche’ and NARS ‘regime’. In examining the niche and regime according to their socio-technical characteristics, the framework provides explanatory power for understanding the nature of their interactions and the opportunities and barriers that exist with respect to the translation of lessons and ideas between niche and regime organisations. The research shows that in trying to institutionalise PCI methods and principles within NARS in the Indian context, PCI proponents have encountered a number of constraints related to the rigid and hierarchical structure of the regime organisations; the contractual mode of most conventional research, which inhibits collaboration with a wider group of stakeholders; and the time-limited nature of PCI projects themselves, which limits investment and hinders scaling up of the innovations. It also reveals that while the niche projects may be able to induce a ‘weak’ form of PCI institutionalisation within the Indian NARS by helping to alter their institutional culture to be more supportive of participatory plant breeding approaches and future collaboration with PCI researchers, a ‘strong’ form of PCI institutionalisation, in which NARS organisations adopt participatory methodologies to address all their crop improvement agenda, is likely to remain outside of the capacity of PCI development projects to deliver

Developing a Functional Food Systems Literacy for Interdisciplinary Dynamic Learning Networks

The impact of human activity on the planet cannot be overstated. Food systems are at the centre of a tangled web of interactions affecting all life. They are a complex nexus that directly and indirectly affects, and is affected by, a diverse set of social, environmental and technological phenomena. The complexity and often intractability of these interactions have created a variety of food-related problems that people seek to address in a collaborative and interdisciplinary manner through the adoption of a holistic food systems perspective. However, operationalising a systemic approach to address food system challenges is not a guarantee of success or positive outcomes. This is largely due to the partiality inherent in taking a systems perspective, and the difficulty in communicating these different perspectives among stakeholders. A functional food systems literacy is therefore required to aid people in communicating and collaborating on food system problems within dynamic learning networks. The Interdisciplinary Food Systems Teaching and Learning (IFSTAL) programme has been operating since 2015 as a social learning system to develop a food systems pedagogy with a range of multi-sectoral partners. The findings in this paper arise out of iterative reflexive practice into our teaching approach and delivery methods by former and current staff. In order to foster integrative engagement on food system challenges, we propose and define a functional food systems literacy—a theoretical minimum that can aid diverse stakeholders to explore and intervene in food systems through more effective communication and collaboration. Derived from a reflective analysis of instruments and methods in delivering the IFSTAL programme, we provide a framework that disaggregates functional food systems literacy according to four knowledge types, and includes examples of skills and activities utilised in the IFSTAL programme to support learning in these different domains. We argue that claims to comprehensive food systems knowledge are unrealistic and therefore propose that a functional food systems literacy should focus on providing a means of navigating partial claims to knowledge and uncertainty as well as fostering effective collaboration. We believe that this will enhance the capabilities of stakeholders to work effectively within dynamic learning networks

Designed artificial protein heterodimers with coupled functions constructed using bio-orthogonal chemistry

The formation of protein complexes is central to biology, with oligomeric proteins more prevalent than monomers. The coupling of functionally and even structurally distinct protein units can lead to new functional properties not accessible by monomeric proteins alone. While such complexes are driven by evolutionally needs in biology, the ability to link normally functionally and structurally disparate proteins can lead to new emergent properties for use in synthetic biology and the nanosciences. Here we demonstrate how two disparate proteins, the haem binding helical bundle protein cytochrome b562 and the β-barrel green fluorescent protein can be combined to form a heterodimer linked together by an unnatural triazole linkage. The complex was designed using computational docking approaches to predict compatible interfaces between the two proteins. Models of the complexes where then used to engineer residue coupling sites in each protein to link them together. Genetic code expansion was used to incorporate azide chemistry in cytochrome b562 and alkyne chemistry in GFP so that a permanent triazole covalent linkage can be made between the two proteins. Two linkage sites with respect to GFP were sampled. Spectral analysis of the new heterodimer revealed that haem binding and fluorescent protein chromophore properties were retained. Functional coupling was confirmed through changes in GFP absorbance and fluorescence, with linkage site determining the extent of communication between the two proteins. We have thus shown here that is possible to design and build heterodimeric proteins that couple structurally and functionally disparate proteins to form a new complex with new functional properties

A future workforce of food-system analysts

A programme developed across five UK universities aims to equip graduate professionals with the skills, tools and capabilities to better understand and manage food-system complexity for food security, for the environment and for enterprise.<br/

Engagement of Fusiform Cortex and Disengagement of Lateral Occipital Cortex in the Acquisition of Radiological Expertise

The human visual pathways that are specialized for object recognition stretch from lateral occipital cortex (LO) to the ventral surface of the temporal lobe, including the fusiform gyrus. Plasticity in these pathways supports the acquisition of visual expertise, but precisely how training affects the different regions remains unclear. We used functional magnetic resonance imaging to measure neural activity in both LO and the fusiform gyrus in radiologists as they detected abnormalities in chest radiographs. Activity in the right fusiform face area (FFA) correlated with visual expertise, measured as behavioral performance during scanning. In contrast, activity in left LO correlated negatively with expertise, and the amount of LO that responded to radiographs was smaller in experts than in novices. Activity in the FFA and LO correlated negatively in experts, whereas in novices, the 2 regions showed no stable relationship. Together, these results suggest that the FFA becomes more engaged and left LO less engaged in interpreting radiographic images over the course of training. Achieving expert visual performance may involve suppressing existing neural representations while simultaneously developing others

Positive functional synergy of structurally integrated artificial protein dimers assembled by Click chemistry

Construction of artificial higher order protein complexes allows sampling of structural architectures and functional features not accessible by classical monomeric proteins. Here, we combine in silico modelling with expanded genetic code facilitated strain promoted azide-alkyne cycloaddition to construct artificial complexes that are structurally integrated protein dimers and demonstrate functional synergy. Using fluorescent proteins sfGFP and Venus as models, homodimers and heterodimers are constructed that switched ON once assembled and display enhanced spectral properties. Symmetrical crosslinks are found to be important for functional enhancement. The determined molecular structure of one artificial dimer shows that a new long-range polar network comprised mostly of organised water molecules links the two chromophores leading to activation and functional enhancement. Single molecule analysis reveals the dimer is more resistant to photobleaching spending longer times in the ON state. Thus, genetically encoded bioorthogonal chemistry can be used to generate truly integrated artificial protein complexes that enhance function

Association of fluorescent protein pairs and it's significant impact on fluorescence and energy transfer

Fluorescent proteins (FPs) are commonly used in pairs to monitor dynamic biomolecular events through changes in proximity via distance dependent processes such as Förster resonance energy transfer (FRET). The impact of FP association is assessed by predicting dimerization sites in silico and stabilizing the dimers by bio‐orthogonal covalent linkages. In each tested case dimerization changes inherent fluorescence, including FRET. GFP homodimers demonstrate synergistic behavior with the dimer being brighter than the sum of the monomers. The homodimer structure reveals the chromophores are close with favorable transition dipole alignments and a highly solvated interface. Heterodimerization (GFP with Venus) results in a complex with ≈87% FRET efficiency, significantly below the 99.7% efficiency predicted. A similar efficiency is observed when the wild‐type FPs are fused to a naturally occurring protein–protein interface system. GFP complexation with mCherry results in loss of mCherry fluorescence. Thus, simple assumptions used when monitoring interactions between proteins via FP FRET may not always hold true, especially under conditions whereby the protein–protein interactions promote FP interaction