Aidong Yang

• University of Oxford

The food supply chain is currently challenged by the imperative to sustainably feed the increasingly expanding population while simultaneously striving to meet global net-zero emission targets. The dairy sector is widely considered as a carbon-intensive industry, contributing to significant greenhouse gas (GHG) emissions thereby exacerbating global...

An accurate deep learning predictor of enzyme optimal pH is essential to quantitatively describe how pH influences the enzyme catalytic activity. Seq2pHopt-2.0, developed in this study, outperformed existing predictors of enzyme optimal pH (RMSE=0.833 and R2=0.479), and could provide good interpretability with informative residue attention weights....

Microbes compete and cooperate with each other via a variety of chemicals and circuits. Recently, to decipher, simulate or reconstruct microbial communities, many researches have been engaged in engineering microbiomes with bottom-up synthetic biology approaches for diverse applications. However, they have been separately focused on individual pers...

An accurate deep learning predictor is needed for enzyme optimal temperature (Topt), which quantitatively describes how temperature affects the enzyme catalytic activity. Seq2Topt, developed in this study, reached a superior accuracy on Topt prediction just using protein sequences (RMSE = 13.3℃ and R2=0.48) in comparison with existing models, and c...

The exopolysaccharide (EPS) produced by Lactiplantibacillus plantarum is a high-value bioproduct in food and health industries, and its biosynthesis has been found as a secondary metabolic pathway to mediate acid stress. To quantitatively investigate acid stress response in L. plantarum and model EPS production, this study measured metabolomics, pr...

Lactiplantibacillus plantarum is a probiotic bacterium widely used in food and health industries, but its gene regulatory information is limited in existing databases, which impedes the research of its physiology and its applications. To obtain a better understanding of the transcriptional regulatory network of L. plantarum, independent component a...

Background Microbes in diverse natural communities communicate via quorum sensing (QS) signals that act as microbial languages. However, earlier work on the investigation on microbial interactions and systematic stability mostly based on the diverse modelling-assistant ecological pairwise interactions (such as cooperation and competition) or metabo...

The enzyme turnover rate, ${k}_{cat}$, quantifies enzyme kinetics by indicating the maximum efficiency of enzyme catalysis. Despite its importance, ${k}_{cat}$ values remain scarce in databases for most organisms, primarily because of the cost of experimental measurements. To predict ${k}_{cat}$ and account for its strong temperature dependence, DL...

Lactobacillus plantarum is a probiotic bacteria widely used in food and health industries, but its gene regulatory information is limited in existing databases, which impedes the research of its physiology and its applications. To obtain a better understanding of the transcriptional regulatory network of L. plantarum, independent component analysis...

In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of...

The enzyme turnover rate, kcat, quantifies enzyme kinetics by indicating the maximum efficiency of enzyme catalysis. Despite its importance, kcat values remain scarce in databases for most organisms, primarily due to the cost of experimental measurements. To predict kcat and account for its strong temperature dependence, DLTKcat was developed in th...

Genome‐scale metabolic models and flux balance analysis (FBA) have been extensively used for modeling and designing bacterial fermentation. However, FBA‐based metabolic models that accurately simulate the dynamics of coculture are still rare, especially for lactic acid bacteria used in yogurt fermentation. To investigate metabolic interactions in y...

The steel sector currently accounts for 7% of global energy-related CO2 emissions and requires deep reform to disconnect from fossil fuels. Here, we investigate the market competitiveness of one of the widely considered decarbonisation routes for primary steel production: green hydrogen-based direct reduction of iron ore followed by electric arc fu...

Genome-scale metabolic models (GSMMs) and flux balance analysis (FBA) have been extensively used to model and design bacterial fermentation. However, FBA-based metabolic models designed for simulating the dynamics of co-culture with quantitative accuracy are still uncommon, which is particularly true for lactic acid bacteria (LAB) used for yogurt f...

Significant loss of valuable resources and increasing burdens on landfills are often associated with a lack of proper planning in waste management and resource recovery strategy. A sustainable waste management model is thus urgently needed to improve resource efficiency and divert more waste from landfills. This paper proposes a comprehensive syste...

Many diseases and health conditions are closely related to various microbes, which participate in complex interactions with diverse drugs; nonetheless, the detailed targets of such drugs remain to be elucidated. Many existing studies have reported causal associations among drugs, gut microbes, or diseases, calling for a workflow to reveal their int...

Quorum sensing (QS) is a cell-cell communication mechanism that connects members in various microbial systems. Conventionally, a small number of QS entries are collected for specific microbes, which is far from being able to fully depict communication-based complex microbial interactions in human gut microbiota. In this study, we propose a systemat...

Modern greenhouses and vertical farming projects promise increased food output per unit area relative to open-field farming. However, their high energy consumption calls for a low-carbon power supply such as solar photovoltaic and wind, which adds to cost and overall land footprint. Here we use geospatial and mathematical modelling to compare open-...

Background: Regulatory authorities around the world have introduced incentives to improve the speed-to-market of innovative therapies. Aim & methods: To better understand the capacity and portfolio planning decisions of autologous cell therapies and particularly the impact of fast-tracking designations, this paper describes a mixed-integer linear p...

Chemically reactive mine tailings are a potential resource for drawing down carbon dioxide out of the atmosphere in mineral weathering schemes. Such carbon dioxide removal (CDR) systems, applied on a large scale, could help to meet internationally agreed targets for minimising climate change, but crucially we need to identify what materials could r...

Enhanced weathering of minerals is one option being considered for removing CO2 from the atmosphere to help combat climate change. In this work, we consider the weathering of calcite with seawater in a reactor using air enriched with CO2. A mathematical model of the packed bubble column reactor was constructed with the key mass transfer and chemica...

Over the coming years, the world is projected to witness an upsurge in “drop-in” aviation biofuel production as part of the renewable energy and bioeconomy developments. This paper presents a comprehensive review of the current status of biojet fuel development and uptake in global commercial aviation industry, including state-of-the-art certified...

Background The rising consensus that the cell can dynamically allocate its resources provides an interesting angle for discovering the governing principles of cell growth and metabolism. Extensive efforts have been made in the past decade to elucidate the relationship between resource allocation and phenotypic patterns of microorganisms. Despite th...

The trend to localise food production promises reduced reliance on increasingly uncertain global supply chains. Controlled-environment agriculture, in particular indoor vertical farming, is developing as part of this trend, to ensure a year-round supply of healthy food and protection from extreme weather events. However, high energy consumption is...

Chemical production using renewable energies is an important element on the roadmap of industry decarbonisation. This work investigates the optimisation of renewable power supply for a fully electrified methanol process, with a focus on the interplay between renewable fix, storage sizing and the use of backup dispatchable power source. The analysis...

Background aims Decentralized, or distributed, manufacturing that takes place close to the point of care has been a manufacturing paradigm of heightened interest within the cell therapy domain because of the product's being living cell material as well as the need for a highly monitored and temperature-controlled supply chain that has the potential...

Enhanced weathering (EW) of alkaline minerals can potentially capture CO2 from the atmosphere at gigaton scale, but the reactor design presents great challenges. We model EW with fresh water in a counter‐current trickle flow packed bed batch of 1–10 mm calcite particles. Weathering kinetics are integrated with the mass transfer of CO2 incorporating...

Chemical process electrification and renewable energy integration facilitate one another along the pathway towards a greener industry. However, integrating intermittent and variable renewable power into large-scale chemical processes, which conventionally are preferred to operate at a steady-state with a constant load, could lead to prohibitive cos...

The increasing concern with greenhouse gas emissions and nutrients cycling creates a need for cost-effective, practical and environmentally sensible biowaste management strategies. Centralized systems have struggled to comply with those needs. Decentralized systems, treating waste at source, promise local nutrient circularity and increased resource...

Formation and vitrification of the capillary bridges is believed critical to matrix assisted room temperature drying of biologics. In this paper, a Capillary Bridge number (CB number) is derived to predict the wetting morphology with CB > 0 to form capillary bridges, otherwise, form droplets. To simulate the drying of the formed capillary bridge wi...

Empirical kinetic models such as the Monod equation have been widely applied to relate the cell growth with substrate availability. The Monod equation shares a similar form with the mechanistically-based Michaelis-Menten kinetics for enzymatic processes, which has provoked long-standing and un-concluded conjectures on their relationship. In this wo...

A type of chromosome-free cell called SimCells (simple cells) has been generated from Escherichia coli , Pseudomonas putida , and Ralstonia eutropha. The removal of the native chromosomes of these bacteria was achieved by double-stranded breaks made by heterologous I-CeuI endonuclease and the degradation activity of endogenous nucleases. We have sh...

Making better-informed decisions throughout the lifecycle of the development of cell- and gene-based therapies is crucial for their successful translation to the market. At the research and development phase, the choice of cell source can have a major impact on subsequent regulatory hurdles. The chosen indication will have substantial impact on the...

Background The formation of acetate by fast-growing Escherichia coli (E. coli) is a commonly observed phenomenon, often referred to as overflow metabolism. Among various studies that have been carried over decades, a recent work (Basan, M. et al. Nature528, 99–104, 2015) suggested and validated that it is the differential proteomic efficiencies in...

The authors wish to make the following correction to this paper [...]

Re-distributed manufacturing (RDM) is of high economic and political interest and is associated with rapid technological, environmental, political, regulatory and social changes in the UK. RDM of food raises opportunities and questions around the local nexus of food, energy and water. Considering these together can provide opportunities for rationa...

Large scale urban agriculture (UA) has been considered as a potential contributor to the sustainability and the resilience of the food system. However, its synergy with the tackling of another main challenge in cities, namely the management of organic wastes, has previously not been extensively explored. The aim of this work is to understand the po...

Introduction Following recent regulatory approvals of two chimeric antigen receptor T-cell (CAR-T) therapies, the field now faces a number of post-approval challenges. These challenges are in some respects defined and, in others, uncertain due to the nascence of the field. At present, information pertaining to such post-approval challenges are scat...

Culturing human Mesenchymal stromal cells (hMSCs) in vitro in hypoxic conditions resulted in reduced senescence, enhanced pluripotency and altered proliferation rate. It has been known that in vitro hypoxia affects expression of cell surface proteins. However, the impact of culture surfaces on the hypoxia-regulated genes (HRG) have not yet been rep...

The UK is facing tremendous challenges in tackling food waste diversion from landfill. Whilst much effort has been made to prevent food waste, there is still a lack of attention and strategic approach in dealing with resource recovery and valorisation of food waste. This paper presents a systematic framework for sustainable organic waste management...

Addressing the intersection of two important emerging research areas, re-distributed manufacturing (RDM) and the food-energy-water (FEW) nexus, this work combines insights from engineering, business and policy perspectives and explores opportunities and challenges towards a more localized and sustainable food system. Analysis centred on two specifi...

Background and objectives: The International Society for Cellular Therapy (ISCT) proposed a set of minimal markers for identifying human mesenchymal stromal cells (hMSCs) in 2007. Since then, with the growing interest of better characterising hMSCs, various additional surface markers have been proposed. However, the impact of how culture condition...

Escherichia coli has been the host organism most frequently investigated for efficient recombinant protein production. However, the production of a foreign protein in recombinant E. coli often leads to growth deterioration and elevated secretion of acetic acid. Such observed phenomena have been widely linked with cell stress responses and metabolic...

Bioreactors that employ a synthetic microbial community hold potential to overcome limitations of those based on a single species, which embrace a higher level of complexity due to the inter-species interactions. In this work, a number of generic system structures involving two cross-feeding species and various types of inhibition have been studied...

Several recent experiments of microalgal polyculture have observed an increased yield compared to monocultures, leading to the suggestion that improved use of the available light resource due to complementary light absorption spectra may be among the underlying reasons. Using numerical simulation, this work explores the impact of conditions (includ...

Urban agriculture is of increasing interest for tackling a range of environmental and social issues of the current food systems. However, many questions remain unanswered regarding upscaling, the balancing of its multipurpose nature, and how it should be embedded into the broader urban system. This review looks at a breadth of novel insights that a...

Waste heat is a major source of recoverable loss in societal energy use, offering significant potential for reduction in greenhouse gas emissions. A number of studies have been carried out to determine the size of the available resource but have been limited in scope or confined to the status quo. This work reports a method to quantify future globa...

BACKGROUND Decisional tools or decision-support tools are tools that can be used to support complex decision making and problem-solving. Since their advent in the 1970s, these tools have been used to support evidence-based decision-making in various industries, including healthcare, agriculture and the environment. OBJECTIVE The review aims to pro...

Background Decisional tools have demonstrated their importance in informing manufacturing and commercial decisions in the monoclonal antibody domain. Recent approved therapies in regenerative medicine have shown great clinical benefits to patients. Objective The objective of this review was to investigate what decisional tools are available and wh...

Variations in substrate chemistry and the micro-structure were shown to have a significant effect on the biology of human mesenchymal stromal cells (hMSCs). This occurs when differences in the surface properties indirectly modulate pathways within numerous signaling networks that control cell fate. To understand how the surface features affect hMSC...

Background: Existing experimental data have shown hypoxia to be an important factor affecting the proliferation of mesenchymal stromal cells (MSCs), but the contrasting observations made at various hypoxic levels raise the questions of whether hypoxia accelerates proliferation, and how. On the other hand, in order to meet the increasing demand of...

This study evaluates the impact of decentralisation on the reliability of electricity networks, particularly under stressed conditions. By applying four strategies to add decentralised generators to the grid, the impact on network reliability has been assessed, where the blackout impact has been defined as the product of the relative blackout size...

Sustainable use and management of nutrients is an important issue for food, energy and water systems. The close connections between the three systems, reflected by the "nexus" concept, warrant an integrated approach to nutrients management across the nexus. In this paper, dynamic modelling of nutrient flows in a local food-energy-water system is pr...

Three-dimensional (3D) printing has been widely identified as an emerging disruptive technology. This study examines how this technology could enable the circular economy by disrupting the existing materials value chain. Specifically, could this novel technology be used to locally manufacture new goods from local sources of recycled plastic waste,...

This paper presents the first environmental life cycle analysis for a range of different confectionery products. A proposed Life Cycle Assessment (LCA) approach and multi-criteria decision analysis (MCDA) was developed to characterise and identify the environmental profiles and hotspots for five different confectionery products; milk chocolate, dar...

Mathematical modelling and optimisation at both household and energy supply network levels were developed to study the transformation of the natural gas-based domestic energy supply system with the introduction of biomethane generation, processing and utilisation based on a range of feedstock and conversion technologies. Biomethane processing inclu...

Abstract The water-energy-food (WEF) nexus concept highlights the importance of integrative solutions that secure resource supplies and meet demands sustainably. There is a need for translating the nexus concept into clear frameworks and tools that can be applied to decision making. A simulation and analytics framework, and a concomitant Nexus Simu...

Optimisation of regional and local food–energy–water systems that takes into account the connections between the three sectors is classified into ‘integration based on footprint’ and ‘integration based on co-decision’. Footprint-based approaches focus on the decision on one main system while using static footprint data to account for the links with...

Industrial ovens consume a considerable amount of energy and have a significant impact on product quality; therefore, improving ovens should be an important objective for manufacturers. This paper presents a novel and practical approach to oven improvement that emphasises both energy reduction and enhanced process performance. The three-phased appr...

Industrial ovens play a significant role in many manufacturing and process industries. Despite the desire to enhance sustainability throughout this sector, research looking to improve the sustainability of industrial ovens is in its infancy. This paper presents seven sustainability indicators to assess potential oven investment; these include syste...

At the local scale, interconnected production, consumption, waste management and other man-made technological components interact with local ecosystem components to form a local production system. The purpose of this work is to develop a framework for the conceptual characterization and mathematical modeling of a local production system to support...

The Local Nexus Network is addressing the intersection of two important emerging research areas, re-distributed manufacturing and the food-energy-water nexus. It is an on-going initiative which aims to develop an evidence-based comprehensive research agenda and foster an inclusive community of researchers and stakeholders for sustainable local food...

Improving industrial ovens is an important objective for sustainable manufacturing due to their significant energy consumption and impact on final product quality. A generic approach for sustainable oven development is presented that focuses on reducing the environmental impact of the oven and manufacturing superior product. The approach focuses on...

With increasing resource scarcity and environmental impacts resulting from inefficient resource utilisation, accounting for resource consumption along the life cycle of a product or service becomes critical for designing production–consumption systems. This work aims at developing a coherent framework for resource accounting to support the evaluati...

The recovery of heat has long been a key measure to improving energy efficiency and maximising the heat recovery of factories by Pinch analysis. However, a substantial amount of research has been dedicated to conventional heat integration where low grade heat is often ignored. Despite this, the sustainability challenges facing the process manufactu...

Integrated Process Analysis and Design for Sustainable Local Resource Management. This paper reports a systems engineering approach for the integration of local processes or activities, as a way to use locally available resources (biomass, solar irradiation, water, etc.) in a more efficient manner to meet local population needs. System dynamics mo...

This paper uses the biorefinery concept as a way to approach the problem for integrated municipal solid waste management. The design of an urban biorefinery, integrating the plastics and paper recycling processes, was performed using a superstructure optimisation approach. The objective function was the maximisation of before-tax profit. The approa...

The rise and uncertainty in energy prices in recent years has widened the solution search space by industry to understand the full impacts on operations and to develop a range of workable solutions to reduce risk. This has involved companies exploring alternative approaches to co-create solutions with different groups comprising varying intellectua...

Carbon dioxide (CO2) emitted from conventional coal-based power plants is a growing concern for the environment. Chemical looping combustion (CLC), pre-combustion and oxy-fuel combustion are promising CO2 capture technologies which allow clean electricity generation from coal in an integrated gasification combined cycle (IGCC) power plant. This wor...

The paper introduces a new paradigm for Industrial Symbiosis by pioneering the use of ontology engineering in the field. Semantics are used to model Industrial Symbiosis flows, to model enabling technologies and to systematise the development of a matching service. Combined with a systems engineering approach, semantics further combine tacit knowle...

Centralised production of essential products and services based on fossil fuels and large scale distribution infrastructures have contributed to a plethora of issues such as deterioration of ecosystems, social-economic injustice and depletion of resources. The establishment of localised production systems can potentially reduce unsustainable resour...

The integration of renewable biomass feedstocks is receiving primal attention in energy and process industries. The conversion of biomass is typically faced with multiple options with respect to feedstocks, processing paths and product portfolios. The options for sustainable bio-based material have been highlighted in Association for the Advances o...

The Integrated Gasification Combined Cycle coupled with chemical looping combustion (IGCC-CLC) is one of the most promising technologies that allow generation of cleaner energy from coal by capturing carbon dioxide (CO2). It is essential to compare and evaluate the performances of various oxygen carriers (OC), used in the CLC system; these are cruc...

Free access link: http://pubs.acs.org/articlesonrequest/AOR-ZcByUtm68StRd39fsPZB For sustainability's sake, the establishment of bioenergy production can no longer overlook the interactions between ecosystem and technological processes, to ensure the preservation of ecosystem functions that provide energy and other goods and services to the human...

Many manufacturing companies recognise the need to produce products that are cleaner, greener, and environmentally sustainable, yet they are only at the early stages of this transition in addressing the symptoms of unsustainability at their direct operations by reducing waste and the use of energy, water and material. The implementation of reductio...

One of the key challenges in the area of biorefining is to screen over the multiple possibilities and combinations among the numerous bio-based sources, processes and products that form a biorefinery. The methodology proposed in the current paper makes use of the systems technology to deal with the overflow of degrees of freedom originated from dif...