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A pinboard by Nadine Upton

Dr Nadine Upton, Post-doctoral Scientist | Curation made possible by Deep Science Ventures

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Follow this board to stay on top of trending and game-changing research papers for agritech

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48 items pinned

Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol.

Abstract: Many desired phenotypes for producing cellulosic biofuels are often observed in industrial Saccharomyces cerevisiae strains. However, many industrial yeast strains are polyploid and have low spore viability, making it difficult to use these strains for metabolic engineering applications. We selected the polyploid industrial strain S. cerevisiae ATCC 4124 exhibiting rapid glucose fermentation capability, high ethanol productivity, strong heat and inhibitor tolerance in order to construct an optimal yeast strain for producing cellulosic ethanol. Here, we focused on developing a general approach and high-throughput screening method to isolate stable haploid segregants derived from a polyploid parent, such as triploid ATCC 4124 with a poor spore viability. Specifically, we deleted the HO genes, performed random sporulation, and screened the resulting segregants based on growth rate, mating type, and ploidy. Only one stable haploid derivative (4124-S60) was isolated, while 14 other segregants with a stable mating type were aneuploid. The 4124-S60 strain inherited only a subset of desirable traits present in the parent strain, same as other aneuploids, suggesting that glucose fermentation and specific ethanol productivity are likely to be genetically complex traits and/or they might depend on ploidy. Nonetheless, the 4124-60 strain did inherit the ability to tolerate fermentation inhibitors. When additional genetic perturbations known to improve xylose fermentation were introduced into the 4124-60 strain, the resulting engineered strain (IIK1) was able to ferment a Miscanthus hydrolysate better than a previously engineered laboratory strain (SR8), built by making the same genetic changes. However, the IIK1 strain showed higher glycerol and xylitol yields than the SR8 strain. In order to decrease glycerol and xylitol production, an NADH-dependent acetate reduction pathway was introduced into the IIK1 strain. By consuming 2.4g/L of acetate, the resulting strain (IIK1A) exhibited a 14% higher ethanol yield and 46% lower byproduct yield than the IIK1 strain from anaerobic fermentation of the Miscanthus hydrolysate. Our results demonstrate that industrial yeast strains can be engineered via haploid isolation. The isolated haploid strain (4124-S60) can be used for metabolic engineering to produce fuels and chemicals.

Pub.: 22 Feb '17, Pinned: 24 Feb '17

Planning the optimal site, size, and feed of biogas plants in agricultural districts

Abstract: In agricultural districts, biogas production through anaerobic co-digestion of residual biomasses is a sustainable way to valorize agro-industry and livestock residues and integrate farm profits. Size and location of a biogas plant as well as co-digestion substrate composition strictly depend on the substrate properties and availability within the rural district. The logistical substrate chain should be optimized to assure the right size and the maximum profitability of the planned biogas plant. A simple method is proposed to site a digester and choose its power output as well as to identify the optimal substrate blend, reducing the complexity of design and management operations. The method, requiring a reduced number of easy-to-survey input parameters, has been verified by its application to an agricultural district of southern Italy. If the planned plant is fed by a prevalent substrate from a single farm, the most economical power output is 300 kW. This size depends also on the Italian subsidy system to renewable energy. However, in the case of a centralized plant, supplied by a blend of substrates, the method gives the optimal plant location, based on the district barycenter, weighed by the biogas potential production of each farm. Secondly, the method suggests the annual amounts of the different substrates in the digester blend, maximizing the plant's annual profit and complying with technical-economic constraints. Thirdly, the most economical power output of the plant is 480 kW. Finally, it indicates the related annual revenues, costs, and profits. The method can also be applied to other agricultural biomasses, such as ensiled crops or energy species available at a competitive cost, as are found in northern Europe. © 2017 Society of Chemical Industry and John Wiley & Sons, Ltd

Pub.: 06 Feb '17, Pinned: 21 Feb '17

Golden rice: scientific, regulatory and public information processes of a genetically modified organism.

Abstract: Historically, agricultural development evolved in three phases. During the first phase the plants were selected on the basis of the availability of a plant with desirable properties at a specific location. The second phase provided the agricultural community with crossbreeding plants to achieve improvement in agricultural production. The evolution of biological knowledge has provided the ability to genetically engineer (GE) crops, one of the key processes within genetically modified organisms (GMO). This article uses golden rice, a species of transgenic Asian rice which contains a precursor of vitamin A in the edible part of the plant as an example of GE/GMO emphasizing Chinese experience in agricultural evolution. It includes a brief review of agricultural evolution to be followed by a description of golden rice development. Golden rice was created as a humanitarian project and has received positive comments by the scientific community and negative voices from certain environmental groups. In this article, we use the Best Available Science (BAS) Concept and Metrics for Evaluation of Scientific Claims (MESC) derived from it to evaluate claims and counter claims on scientific aspects of golden rice. This article concludes that opposition to golden rice is based on belief rather than any of its scientifically derived nutritional, safety or environmental properties.

Pub.: 22 Jan '15, Pinned: 18 Feb '17

Manipulation of Carotenoid Content in Plants to Improve Human Health.

Abstract: Carotenoids are essential components for human nutrition and health, mainly due to their antioxidant and pro-vitamin A activity. Foods with enhanced carotenoid content and composition are essential to ensure carotenoid feasibility in malnourished population of many countries around the world, which is critical to alleviate vitamin A deficiency and other health-related disorders. The pathway of carotenoid biosynthesis is currently well understood, key steps of the pathways in different plant species have been characterized and the corresponding genes identified, as well as other regulatory elements. This enables the manipulation and improvement of carotenoid content and composition in order to control the nutritional value of a number of agronomical important staple crops. Biotechnological and genetic engineering-based strategies to manipulate carotenoid metabolism have been successfully implemented in many crops, with Golden rice as the most relevant example of β-carotene improvement in one of the more widely consumed foods. Conventional breeding strategies have been also adopted in the bio-fortification of carotenoid in staple foods that are highly consumed in developing countries, including maize, cassava and sweet potatoes, to alleviate nutrition-related problems. The objective of the chapter is to summarize major breakthroughs and advances in the enhancement of carotenoid content and composition in agronomical and nutritional important crops, with special emphasis to their potential impact and benefits in human nutrition and health.

Pub.: 04 Aug '16, Pinned: 18 Feb '17

Golden bananas in the field: elevated fruit pro-vitamin A from the expression of a single banana transgene.

Abstract: Vitamin A deficiency remains one of the world's major public health problems despite food fortification and supplements strategies. Biofortification of staple crops with enhanced levels of pro-vitamin A (PVA) offers a sustainable alternative strategy to both food fortification and supplementation. As a proof of concept, PVA-biofortified transgenic Cavendish bananas were generated and field trialed in Australia with the aim of achieving a target level of 20 μg/g of dry weight (dw) β-carotene equivalent (β-CE) in the fruit. Expression of a Fe'i banana-derived phytoene synthase 2a (MtPsy2a) gene resulted in the generation of lines with PVA levels exceeding the target level with one line reaching 55 μg/g dw β-CE. Expression of the maize phytoene synthase 1 (ZmPsy1) gene, used to develop "Golden Rice 2", also resulted in increased fruit PVA levels although many lines displayed undesirable phenotypes. Constitutive expression of either transgene with the maize polyubiquitin promoter increased PVA accumulation from the earliest stage of fruit development. In contrast, PVA accumulation was restricted to the late stages of fruit development when either the banana 1-aminocyclopropane-1-carboxylate oxidase or the expansin 1 promoters were used to drive the same transgenes. Wild-type plants with the longest fruit development time had also the highest fruit PVA concentrations. The results from this study suggest that early activation of the rate-limiting enzyme in the carotenoid biosynthetic pathway, as well as extended fruit maturation time, are essential factors to achieve optimal PVA concentrations in banana fruit. This article is protected by copyright. All rights reserved.

Pub.: 14 Oct '16, Pinned: 18 Feb '17

A Randomized, Controlled Trial of ZMapp for Ebola Virus Infection.

Abstract: Background Data from studies in nonhuman primates suggest that the triple monoclonal antibody cocktail ZMapp is a promising immune-based treatment for Ebola virus disease (EVD). Methods Beginning in March 2015, we conducted a randomized, controlled trial of ZMapp plus the current standard of care as compared with the current standard of care alone in patients with EVD that was diagnosed in West Africa by polymerase-chain-reaction (PCR) assay. Eligible patients of any age were randomly assigned in a 1:1 ratio to receive either the current standard of care or the current standard of care plus three intravenous infusions of ZMapp (50 mg per kilogram of body weight, administered every third day). Patients were stratified according to baseline PCR cycle-threshold value for the virus (≤22 vs. >22) and country of enrollment. Oral favipiravir was part of the current standard of care in Guinea. The primary end point was mortality at 28 days. Results A total of 72 patients were enrolled at sites in Liberia, Sierra Leone, Guinea, and the United States. Of the 71 patients who could be evaluated, 21 died, representing an overall case fatality rate of 30%. Death occurred in 13 of 35 patients (37%) who received the current standard of care alone and in 8 of 36 patients (22%) who received the current standard of care plus ZMapp. The observed posterior probability that ZMapp plus the current standard of care was superior to the current standard of care alone was 91.2%, falling short of the prespecified threshold of 97.5%. Frequentist analyses yielded similar results (absolute difference in mortality with ZMapp, -15 percentage points; 95% confidence interval, -36 to 7). Baseline viral load was strongly predictive of both mortality and duration of hospitalization in all age groups. Conclusions In this randomized, controlled trial of a putative therapeutic agent for EVD, although the estimated effect of ZMapp appeared to be beneficial, the result did not meet the prespecified statistical threshold for efficacy. (Funded by the National Institute of Allergy and Infectious Diseases and others; PREVAIL II ClinicalTrials.gov number, NCT02363322 .).

Pub.: 13 Oct '16, Pinned: 17 Feb '17

Satellite-based assessment of yield variation and its determinants in smallholder African systems

Abstract: The emergence of satellite sensors that can routinely observe millions of individual smallholder farms raises possibilities for monitoring and understanding agricultural productivity in many regions of the world. Here we demonstrate the potential to track smallholder maize yield variation in western Kenya, using a combination of 1-m Terra Bella imagery and intensive field sampling on thousands of fields over 2 y. We find that agreement between satellite-based and traditional field survey-based yield estimates depends significantly on the quality of the field-based measures, with agreement highest (<mml:math><mml:msup><mml:mi mathvariant="normal">R</mml:mi><mml:mn>2</mml:mn></mml:msup></mml:math>R2 up to 0.4) when using precise field measures of plot area and when using larger fields for which rounding errors are smaller. We further show that satellite-based measures are able to detect positive yield responses to fertilizer and hybrid seed inputs and that the inferred responses are statistically indistinguishable from estimates based on survey-based yields. These results suggest that high-resolution satellite imagery can be used to make predictions of smallholder agricultural productivity that are roughly as accurate as the survey-based measures traditionally used in research and policy applications, and they indicate a substantial near-term potential to quickly generate useful datasets on productivity in smallholder systems, even with minimal or no field training data. Such datasets could rapidly accelerate learning about which interventions in smallholder systems have the most positive impact, thus enabling more rapid transformation of rural livelihoods.

Pub.: 15 Feb '17, Pinned: 17 Feb '17

Farming ethics in practice: from freedom to professional moral autonomy for farmers

Abstract: Food production, water management, land use, and animal and public health are all topics of extensive public debate. These themes are linked to the core activities of the agricultural sector, and more specifically to the work of farmers. Nonetheless, the ethical discussions are mostly initiated by interest groups in society rather than by farmers. At least in Europe, consumer organizations and animal welfare and environmental organizations are more present in the public debate than farmers. This is not how it should be. First, because consumers often cannot but rely on agriculture. Second, because recent research shows that farmers have moral beliefs and convictions that appear to be broader than economic considerations and that are—to a certain extent—specific to their profession. This raises the question how to make input from farmers operational in the public debates on the future of farming. We discuss one option: entrusting farmers with professional autonomy concerning moral matters related to farming. We sketch the historical background of the current situation in which farmers are relatively silent on moral matters and we present some clear indications that farmers have values and moral beliefs that are relevant for the public debate. Next the concepts of professionalism and professional autonomy are discussed and applied to the practice of farming. Finally, we discuss the relevance and limits of professional moral autonomy for the agricultural profession. We close with an overview of what this moral autonomy implies for and requires from farmers in practice. We conclude that if some preconditions are met by farmers, then this type of moral autonomy can be relevant for farmers and for society, and contributes to the quality of the public debate on the future of farming.

Pub.: 04 Aug '15, Pinned: 17 Feb '17

Planting seeds for the future of food.

Abstract: The health and wellbeing of future generations will depend on humankind's ability to deliver sufficient nutritious food to a world population in excess of 9 billion. Feeding this many people by 2050 will require science-based solutions that address sustainable agricultural productivity and enable healthful dietary patterns in a more globally equitable way. This topic was the focus of a multi-disciplinary international conference hosted by Nestlé in June 2015, and provides the inspiration for the present article. The conference brought together a diverse range of expertise and organisations from the developing and industrialised world, all with a common interest in safeguarding the future of food. This article provides a snapshot of three of the recurring topics that were discussed during this conference: soil health, plant science and the future of farming practice. Crop plants and their cultivation are the fundamental building blocks for a food secure world. Whether these are grown for food or feed for livestock, they are the foundation of food and nutrient security. Many of the challenges for the future of food will be faced where the crops are grown: on the farm. Farmers need to plant the right crops and create the right conditions to maximise productivity (yield) and quality (e.g. nutritional content), whilst maintaining the environment, and earning a living. New advances in science and technology can provide the tools and know-how that will, together with a more entrepreneurial approach, help farmers to meet the inexorable demand for the sustainable production of nutritious foods for future generations. © 2015 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Pub.: 02 Dec '15, Pinned: 17 Feb '17

Potential of plants to produce recombinant protein products

Abstract: Abstract Plants have great potential as photosynthetic factories to produce pharmaceutically important and commercially valuable biomedicines and industrial proteins at low cost. The U.S. Food and Drug Administration (U.S. FDA) has approved the drug Elelyso (taliglucerase alfa) produced by carrot cells for treatment of type 1 Gaucher’s disease in 2012. The commercial potential of biomedicines produced by molecular farming has dramatically improved due to the success of an experimental drug called ZMapp, which has immunological activity in Ebola patients. A cocktail of three monoclonal antibodies was produced in tobacco (Nicotiana benthamiana) plants (Chen and Davis 2016). At present, very few drugs made by this technology have been approved by worldwide authorities such as the U.S. FDA. However, plants have been proposed as a novel paradigm for commercial production of proteins over the next decade. In recent years, leading researchers on molecular farming have given more priority to the area of animal-free therapeutic proteins such as parenteral and oral vaccines. Although plant-based platforms have considerable advantages over traditional systems such as bacterial and animal systems, there are several obstacles to commercial-scale production, especially with regards to improving the quality and quantity of plant-produced biologics and industrial materials. One of the biggest barriers to commercialization of this technology is the intense scrutiny of these new plant varieties by regulatory agencies and the public as well as the high costs associated with their regulatory approval.AbstractPlants have great potential as photosynthetic factories to produce pharmaceutically important and commercially valuable biomedicines and industrial proteins at low cost. The U.S. Food and Drug Administration (U.S. FDA) has approved the drug Elelyso (taliglucerase alfa) produced by carrot cells for treatment of type 1 Gaucher’s disease in 2012. The commercial potential of biomedicines produced by molecular farming has dramatically improved due to the success of an experimental drug called ZMapp, which has immunological activity in Ebola patients. A cocktail of three monoclonal antibodies was produced in tobacco (Nicotiana benthamiana) plants (Chen and Davis 2016). At present, very few drugs made by this technology have been approved by worldwide authorities such as the U.S. FDA. However, plants have been proposed as a novel paradigm for commercial production of proteins over the next decade. In recent years, leading researchers on molecular farming have given more priority to the area of animal-free therapeutic proteins such as parenteral and oral vaccines. Although plant-based platforms have considerable advantages over traditional systems such as bacterial and animal systems, there are several obstacles to commercial-scale production, especially with regards to improving the quality and quantity of plant-produced biologics and industrial materials. One of the biggest barriers to commercialization of this technology is the intense scrutiny of these new plant varieties by regulatory agencies and the public as well as the high costs associated with their regulatory approval.Nicotiana benthamiana

Pub.: 01 Dec '16, Pinned: 16 Feb '17

Robotic weeding's false dawn? Ten requirements for fully autonomous mechanical weed management

Abstract: While machines called weeding robots are now commercially available and many more designs are being actively researched, I contend that current machines are not truly robotic weeders, rather they are essentially self‐guiding vehicles carrying weeding tools. I consider true robotic weeders to be a far more difficult objective. While advances in robotics have been outstanding, the weeding component often appears to be an afterthought. I contend that the weeding is as complex as the robotics. A genuine weeding robot should be able to: (i) monitor the crop, weeds, weather and soil, (ii) decide when the crop should be weeded, (iii) choose the optimal weeder, (iv) take the weeder to the field, (v) adjust the weeder for optimal performance, (vi) continuously monitor the entire weeder for blockages and mechanical breakages and fix them in the field, (vii) continuously monitor and adjust the weeder's performance, (viii) return the weeder to the farmyard and (ix) clean, maintain and store the weeder, that is replace all human intervention. This ten‐point list both defines and is a guide to what is required for completely autonomous robotic weeding. Currently, this list is far beyond current technology and it may be decades before it is realisable. The aim of this study therefore was not to disparage the achievements of agricultural roboticists, rather it is to highlight the complexity and demands of mechanical weeding and therefore describe what is really required to create a true robotic weeder. I therefore hope it will guide and expedite research and lead to more rapid success for robotic weeding.

Pub.: 06 Jul '16, Pinned: 16 Feb '17

Developing science–industry collaborations into a transdisciplinary process: a case study on improving sustainability of pork production

Abstract: Sustainability of livestock farming is not only part of intensive public debate, but also refers to a multi-stakeholder field comprising many different interests and worldviews. Beyond the environmental, economic and social dimensions of livestock farming, especially animal welfare should be considered as an essential aspect of sustainability. Such sustainability issues may be successfully addressed by transdisciplinary research. Science–industry collaborations in the realm of livestock sciences do have the potential for becoming successful transdisciplinary projects if project partners are aware of the challenges and limitations. In the light of this situation the University of Natural Resources and Life Sciences, Vienna and an Austrian food retailer launched a collaborative research project. The main objective of the project was to develop measures to improve sustainability of current pig fattening systems with a special focus on animal welfare. These measures were subsequently implemented on three pig fattening farms in Austria and the effects on animal welfare, economic and environmental performance as well as the farmers’ perception were evaluated. In this paper, the research process will be analysed from a transdisciplinary perspective, identifying differences between transdisciplinarity and different forms of applied research. This is followed by a discussion of challenges and failures as well as opportunities and achievements of the project concluding with a presentation of recommendations for further research projects. Finally, it is discussed to which extent industry-funded research offers suitable conditions for transdisciplinary research projects in pork production using the present project as a case study.

Pub.: 03 Sep '15, Pinned: 16 Feb '17