The Arabidopsis thaliana SERK1 kinase domain spontaneously refolds to an active state in vitro

Auto-phosphorylating kinase activity of plant leucine-rich-repeat receptor-like kinases (LRR-RLK's) needs to be under tight negative control to avoid unscheduled activation. One way to achieve this would be to keep these kinase domains as intrinsically disordered protein (IDP) during synthesis and transport to its final location. Subsequent folding, which may depend on chaperone activity or presence of interaction partners, is then required for full activation of the kinase domain. Bacterially produced SERK1 kinase domain was previously shown to be an active Ser/Thr kinase. SERK1 is predicted to contain a disordered region in kinase domains X and XI. Here, we show that loss of structure of the SERK1 kinase domain during unfolding is intimately linked to loss of activity. Phosphorylation of the SERK1 kinase domain neither changes its structure nor its stability. Unfolded SERK1 kinase has no autophosphorylation activity and upon removal of denaturant about one half of the protein population spontaneously refolds to an active protein in vitro. Thus, neither chaperones nor interaction partners are required during folding of this protein to its catalytically active state

Molecular control of stomatal development

Plants have evolved developmental plasticity which allows the up- or down-regulation of photosynthetic and water loss capacities as new leaves emerge. This developmental plasticity enables plants to maximise fitness and to survive under differing environments. Stomata play a pivotal role in this adaptive process. These microscopic pores in the epidermis of leaves control gas exchange between the plant and its surrounding environment. Stomatal development involves regulated cell fate decisions that ensure optimal stomatal density and spacing, enabling efficient gas exchange. The cellular patterning process is regulated by a complex signalling pathway involving extracellular ligand-receptor interactions, which, in turn, modulate the activity of three master transcription factors essential for the formation of stomata. Here, we review the current understanding of the biochemical interactions between the epidermal patterning factor ligands and the ERECTA family of leucine-rich repeat receptor kinases. We discuss how this leads to activation of a kinase cascade, regulation of the bHLH transcription factor SPEECHLESS and its relatives, and ultimately alters stomatal production

Design-space exploration of an integrated automotive architecture

A real-time model is presented for an innovative automotive distributed control system with resource sharing. The model is developed to perform design-space exploration of a racecar (IM01) control system early in the design loop. Performance of this control system will be simulated with SHESim after the application, platform and mapping are defined. The model is calibrated on a low-cost development platform and used to explore suitable hardware configurations for the IM01 control system to demonstrate relevance of performance modeling at early design stages. A real-time model is presented for an innovative automotive distributed control system with resource sharing. The model is developed to perform design-space exploration of a racecar (IM01) control system early in the design loop. Performance of this control system will be simulated with SHESim after the application, platform and mapping are defined. The model is calibrated on a low-cost development platform and used to explore suitable hardware configurations for the IM01 control system to demonstrate relevance of performance modeling at early design stages

The integration of environmental and social sustainability impacts of the biojet fuel product system within the life cycle assessment framework

The Master's programme Industrial Ecology is jointly organised by Leiden University and Delft University of Technology - Biojet fuel is developed as a potentially more sustainable alternative to existing petroleum based jet fuels. To establish the environmental and social sustainability of the biojet fuel product system, the full life cycle of the production should be analyzed. The environmental LCA (ELCA)and social LCA (SLCA) have been developed as two independent tools, but they cannot be used to analyze the same product system as their system boundaries differ. This research studies the possibility of harmonizing the two tools into a single social and environmental LCA (SELCA) methodology in light of its use in the biojet fuel product system. SELCA was developed through an extensive literature review, followed by catering it to the biojet fuel product system based on a survey and a dummy case study. The ELCA is based on unit processes while the SLCA uses organizations as its base. To reconcile these two system elements, the organizations were treated as multifunctional processes that can be allocated to the product system. The DPSIR model was used to ensure that data on interventions and economic flows were equivalent to each other and capable of being causally connected to the product system. The resulting methodology has consistent system boundaries and data for both social and environmental impacts. The majority of existing SLCA characterization methods and indicators are not compatible with SELCA. Indicators must be based on DPSIR pressure level data and be capable of being aggregated for the product system in order to be comparable to ELCA indicators. Many SLCA methodologies are based on statistical data which conceptually cannot be attributed to a particular organization or unit process. The only operational methodology is that of Hunkeler (2006) which uses quantitative labor hour data. As a methodology for assessing the biojet fuel, SELCA has several limits. The existing indicators do not address all issues considered important by academia and the industry. Also, despite that SELCA can in principle include the full biojet product system, in practice it will be limited by the lack of background databases. This results in more cut-off points and smaller system boundaries as shown in the dummy case study. However, with further research and development of characterization methods and databases, SELCA has the potential to fully integrate the environmental and social impact assessments of the biojet fuel product system.Technology, Policy and ManagementEngineering, Systems and ServicesIndustrial Ecolog

On the Origin of SERKs: Bioinformatics Analysis of the Somatic Embryogenesis Receptor Kinases

Somatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases involved in several, seemingly unrelated, plant-signaling pathways. In Arabidopsis thaliana, functional and genetic analysis of four SERK proteins has indicated that they are only partly redundant; their functions overlap but each performs a specific subset of signaling roles. The molecular basis for the functional specificity within this highly homologous protein family is currently not known. Sequence analysis of SERK proteins from different plant species indicates that the SERKs are a highly conserved protein family present in monocots, dicots, and non-vascular plants. Residues in the extracellular domain that are important for interaction with other receptor kinases are highly conserved, even among SERK members without a function in the corresponding pathways. SERK2, for instance, does not function in the brassinosteroid pathway, does not interact with BRI1, but is conserved in its BRI1-interacting domain. Further sequence analysis indicates that SERK3/BAK1 and SERK4/BKK1 have diverged from the original SERK protein in both their extracellular and cytoplasmic domains. Functional analysis of chimeric SERK proteins shows that different domains provide the SERK proteins with different functional specificity. For instance, the SERK1 or SERK2 extracellular domains are essential for SERK function in male sporogenesis, while the SERK3 extracellular and cytoplasmic domains are essential for SERK3 activity in brassinosteroid and flagellin signaling. The emerging picture is that SERKs are ancient genes, whose products have been recruited as co-receptors in the newly evolved signaling pathways. The SERK ligand-binding and protein–protein interaction domains are highly conserved, allowing all SERKs to form complexes, albeit with different affinity. However, specific functional residues must have been altered, in both the extracellular and intracellular domains, to allow for the observed differences in functionality

Decarbonising meat : Exploring greenhouse gas emissions in the meat sector

Consumption of meat is an important source of global greenhouse gas (GHG) emission and deep decarbonisation of the whole meat production chain is required to be able to meet global climate change (CC) mitigation goals. Emissions happen in different stages of meat production ranging from agricultural input production, feed production, livestock production to slaughtering, meat processing, and retail. An overview of direct emissions from processes in the meat sector themselves and indirect emissions from energy consumptions would provide a clearer picture for potential CC impact reduction. This paper explores the total GHG emissions and data availability within the meat sector of the pig, chicken, and cattle meat product system. Through statistical data provided by FAOSTAT and supplementary data from literature, the CC impacts of energy use and process GHG emissions in the pig, chicken and cattle meat life cycle are estimated. Cattle dominates, but pig and chicken meat have a sizable amount of GHG emissions with a relatively high contribution from agricultural inputs and post-farm processes. However, uncertainty and unavailability of data are large for the energy consumption, direct GHG emissions, and product flows of post-farm and agricultural input processes. In order to gain a more complete understanding of the total CC impacts of the meat sector, further research is necessary to reduce the uncertainty in the considered life cycle stages and to quantify the processes and meat products that have been excluded from this study

How much can combinations of measures reduce methane and nitrous oxide emissions from European livestock husbandry and feed cultivation?

In the EU28, the meat and dairy supply chains emitted 360 Mt CO2-eq or 80% of all agricultural CH4 and N2O emissions in 2016, which must be reduced to reach net-zero greenhouse gas emissions by 2050. Our research explores how far these emissions can be reduced by combining field tested mitigation measures for beef cattle, dairy cattle, swine, sheep, and synthetic fertilizers. Many mitigation measures targeting enteric fermentation, manure management, and fertilizer application have been experimentally tested; however, the impact of combining measures is relatively unexplored. To address this knowledge gap, we use graph theory to create combinations of measures for which we calculate the overall mitigation potential. From previous review studies, we identified 44 measures and formulated rules on impossible and mandatory combinations of measures. Based on the resulting sets of feasible cliques in the graphs and a simplified technological baseline, we estimate that the combinations with the highest reductions reduce CH4 and N2O emissions from beef cattle by 57%, dairy cattle by 47%, swine by 70%, sheep by 48%, and synthetic fertilizers by 44%. Together, they can reduce CH4 and N2O emissions in the EU28 from meat and dairy production by 54%, and for agriculture overall by 42%. This indicates that implementing more measures in the meat and dairy sectors can create room for further reduction than in the existing modelled pathways for the EU28. However, technical measures are incapable of fully eliminating agricultural CH4 and N2O, so there remains a need for CO2 removal technologies

Decarbonising meat : Exploring greenhouse gas emissions in the meat sector

Consumption of meat is an important source of global greenhouse gas (GHG) emission and deep decarbonisation of the whole meat production chain is required to be able to meet global climate change (CC) mitigation goals. Emissions happen in different stages of meat production ranging from agricultural input production, feed production, livestock production to slaughtering, meat processing, and retail. An overview of direct emissions from processes in the meat sector themselves and indirect emissions from energy consumptions would provide a clearer picture for potential CC impact reduction. This paper explores the total GHG emissions and data availability within the meat sector of the pig, chicken, and cattle meat product system. Through statistical data provided by FAOSTAT and supplementary data from literature, the CC impacts of energy use and process GHG emissions in the pig, chicken and cattle meat life cycle are estimated. Cattle dominates, but pig and chicken meat have a sizable amount of GHG emissions with a relatively high contribution from agricultural inputs and post-farm processes. However, uncertainty and unavailability of data are large for the energy consumption, direct GHG emissions, and product flows of post-farm and agricultural input processes. In order to gain a more complete understanding of the total CC impacts of the meat sector, further research is necessary to reduce the uncertainty in the considered life cycle stages and to quantify the processes and meat products that have been excluded from this study

Meat, dairy, and more : Analysis of material, energy, and greenhouse gas flows of the meat and dairy supply chains in the EU28 for 2016

To decarbonize the European Union, protein consumption must transition to diets low in meat and dairy which will drastically change the material and energy flows in current meat and dairy supply chains. To understand the impacts on current flows, a baseline is required. Although recent studies have improved the scope of reported greenhouse gas (GHG) emissions, no quantitative overview exists including intermediate and final product flows. To address this knowledge gap, we structured the meat and dairy supply chains into a connected set of transformation nodes and distribution nodes. The former are processes transforming inputs into outputs, whereas the latter distribute the outputs to other processes using them as inputs. Currently, livestock play a central role in agriculture and other industries through the consumption of 271 Mt fodder crops, 108 Mt grain, 85 Mt grazed biomass, 49 Mt oil meal, and 16 Mt feed by-products. This feed is transformed into 64 Mt dairy and 35 Mt meat which ensures that the EU28 is a net exporter of meat and dairy while providing 25 Mt of by-products. This production also leads to 435 Mt CO2-eq. with the main contribution from beef cattle (35%), dairy cattle (32%), and swine (20%). Thus, the lower GHG intensities of dairy products compared to meat do not imply a low contribution to the total emissions. By mapping the material, energy, and GHG emission flows, we have created a baseline suitable for identifying potential supply chain changes and their related GHG increase or decrease resulting from the protein transition