Publications by authors named "Kirsty L Hassall"

20 Publications

  • Page 1 of 1

Genetic Diversity in Nitrogen Fertiliser Responses and N Gas Emission in Modern Wheat.

Front Plant Sci 2022 4;13:816475. Epub 2022 May 4.

Plant Science Department, Rothamsted Research, Harpenden, United Kingdom.

Crops assimilate nitrogen (N) as ammonium via the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway which is of central importance for N uptake and potentially represents a bottle neck for N fertiliser-use efficiency. The aim of this study was to assess whether genetic diversity for N-assimilation capacity exists in wheat and could be exploited for breeding. Wheat plants rapidly, within 6 h, responded to N application with an increase in GS activity. This was not accompanied by an increase in GS gene transcript abundance and a comparison of GS1 and GS2 protein models revealed a high degree of sequence conservation. N responsiveness amongst ten wheat varieties was assessed by measuring GS enzyme activity, leaf tissue ammonium, and by a leaf-disc assay as a proxy for apoplastic ammonia. Based on these data, a high-GS group showing an overall positive response to N could be distinguished from an inefficient, low-GS group. Subsequent gas emission measurements confirmed plant ammonia emission in response to N application and also revealed emission of NO when N was provided as nitrate, which is in agreement with our current understanding that NO is a by-product of nitrate reduction. Taken together, the data suggest that there is scope for improving N assimilation capacity in wheat and that further investigations into the regulation and role of GS-GOGAT in NH emission is justified. Likewise, emission of the climate gas NO needs to be reduced, and future research should focus on assessing the nitrate reductase pathway in wheat and explore fertiliser management options.
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http://dx.doi.org/10.3389/fpls.2022.816475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9137425PMC
May 2022

Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration.

Plant Physiol 2022 May 30. Epub 2022 May 30.

Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.

Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pre-treatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pre-treatments reduced this damage. Ethylene pre-treatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.
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http://dx.doi.org/10.1093/plphys/kiac245DOI Listing
May 2022

Changes in organic carbon to clay ratios in different soils and land uses in England and Wales over time.

Sci Rep 2022 03 25;12(1):5162. Epub 2022 Mar 25.

Department of Sustainable Agriculture Sciences, Rothamsted Research, West Common, Harpenden, AL5 2JQ, Hertfordshire, UK.

Realistic targets for soil organic carbon (SOC) concentrations are needed, accounting for differences between soils and land uses. We assess the use of SOC/clay ratio for this purpose by comparing changes over time in (a) the National Soil Inventory of England and Wales, first sampled in 1978-1983 and resampled in 1994-2003, and (b) two long-term experiments under ley-arable rotations on contrasting soils in the East of England. The results showed that normalising for clay concentration provides a more meaningful separation between land uses than changes in SOC alone. Almost half of arable soils in the NSI had degraded SOC/clay ratios (< 1/13), compared with just 5% of permanent grass and woodland soils. Soils with initially large SOC/clay ratios (≥ 1/8) were prone to greater losses of SOC between the two NSI samplings than those with smaller ratios. The results suggest realistic long-term targets for SOC/clay in arable, ley grass, permanent grass and woodland soils are 1/13, 1/10, and > 1/8, respectively. Given the wide range of soils and land uses across England and Wales in the datasets used to test these targets, they should apply across similar temperate regions globally, and at national to sub-regional scales.
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http://dx.doi.org/10.1038/s41598-022-09101-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8956621PMC
March 2022

Exploring the effects of land management change on productivity, carbon and nutrient balance: Application of an Ensemble Modelling Approach to the upper River Taw observatory, UK.

Sci Total Environ 2022 Jun 16;824:153824. Epub 2022 Feb 16.

Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK. Electronic address:

Agriculture is challenged to produce healthy food and to contribute to cleaner energy whilst mitigating climate change and protecting ecosystems. To achieve this, policy-driven scenarios need to be evaluated with available data and models to explore trade-offs with robust accounting for the uncertainty in predictions. We developed a novel model ensemble using four complementary state-of-the-art agroecosystems models to explore the impacts of land management change. The ensemble was used to simulate key agricultural and environmental outputs under various scenarios for the upper River Taw observatory, UK. Scenarios assumed (i) reducing livestock production whilst simultaneously increasing the area of arable where it is feasible to cultivate (PG2A), (ii) reducing livestock production whilst simultaneously increasing bioenergy production in areas of the catchment that are amenable to growing bioenergy crops (PG2BE) and (iii) increasing both arable and bioenergy production (PG2A + BE). Our ensemble approach combined model uncertainty using the tower property of expectation and the law of total variance. Results show considerable uncertainty for predicted nutrient losses with different models partitioning the uncertainty into different pathways. Bioenergy crops were predicted to produce greatest yields from Miscanthus in lowland and from SRC-willow (cv. Endurance) in uplands. Each choice of management is associated with trade-offs; e.g. PG2A results in a significant increase of edible calories (6736 Mcal ha) but reduced soil C (-4.32 t C ha). Model ensembles in the agroecosystem context are difficult to implement due to challenges of model availability and input and output alignment. Despite these challenges, we show that ensemble modelling is a powerful approach for applications such as ours, offering benefits such as capturing structural as well as data uncertainty and allowing greater combinations of variables to be explored. Furthermore, the ensemble provides a robust means for combining uncertainty at different scales and enables us to identify weaknesses in system understanding.
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http://dx.doi.org/10.1016/j.scitotenv.2022.153824DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022088PMC
June 2022

Resolving the identification of weak-flying insects during flight: a coupling between rigorous data processing and biology.

Agric For Entomol 2021 Nov 2;23(4):489-505. Epub 2021 Jun 2.

Rothamsted Insect Survey Rothamsted Research West Common, Harpenden AL5 2JQ U.K.

Bioacoustic methods play an increasingly important role for the detection of insects in a range of surveillance and monitoring programmes.Weak-flying insects evade detection because they do not yield sufficient audio information to capture wingbeat and harmonic frequencies. These inaudible insects often pose a significant threat to food security as pests of key agricultural crops worldwide.Automatic detection of such insects is crucial to the future of crop protection by providing critical information to assess the risk to a crop and the need for preventative measures.We describe an experimental set-up designed to derive audio recordings from a range of weak-flying aphids and beetles using an LED array.A rigorous data processing pipeline was developed to extract meaningful features, linked to morphological characteristics, from the audio and harmonic series for six aphid and two beetle species.An ensemble of over 50 bioacoustic parameters was used to achieve species discrimination with a success rate of 80%. The inclusion of the dominant and fundamental frequencies improved prediction between beetles and aphids because of large differences in wingbeat frequencies.At the species level, error rates were minimized when harmonic features were supplemented by features indicative of differences in species' flight energies.
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http://dx.doi.org/10.1111/afe.12453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8596709PMC
November 2021

Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice.

Genomics 2021 11 10;113(6):4227-4236. Epub 2021 Nov 10.

Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK. Electronic address:

Seedling vigour is an important agronomic trait and is gaining attention in Asian rice (Oryza sativa) as cultivation practices shift from transplanting to forms of direct seeding. To understand the genetic control of rice seedling vigour in dry direct seeded (aerobic) conditions we measured multiple seedling traits in 684 accessions from the 3000 Rice Genomes (3K-RG) population in both the laboratory and field at three planting depths. Our data show that phenotyping of mesocotyl length in laboratory conditions is a good predictor of field performance. By performing a genome wide association study, we found that the main QTL for mesocotyl length, percentage seedling emergence and shoot biomass are co-located on the short arm of chromosome 7. We show that haplotypes in the indica subgroup from this region can be used to predict the seedling vigour of 3K-RG accessions. The selected accessions may serve as potential donors in genomics-assisted breeding programs.
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http://dx.doi.org/10.1016/j.ygeno.2021.11.006DOI Listing
November 2021

Uncovering Trait Associations Resulting in Maximal Seed Yield in Winter and Spring Oilseed Rape.

Front Plant Sci 2021 6;12:697576. Epub 2021 Sep 6.

Department of Plant Sciences, Rothamsted Research, Harpenden, United Kingdom.

Seed yield is a complex trait for many crop species including oilseed rape (OSR) (), the second most important oilseed crop worldwide. Studies have focused on the contribution of distinct factors in seed yield such as environmental cues, agronomical practices, growth conditions, or specific phenotypic traits at the whole plant level, such as number of pods in a plant. However, how female reproductive traits contribute to whole plant level traits, and hence to seed yield, has been largely ignored. Here, we describe the combined contribution of 33 phenotypic traits within a diversity set population and their trade-offs at the whole plant and organ level, along with their interaction with plant level traits. Our results revealed that both Winter OSR (WOSR) and Spring OSR (SOSR); the two more economically important OSR groups in terms of oil production; share a common dominant reproductive strategy for seed yield. In this strategy, the main inflorescence is the principal source of seed yield, producing a good number of ovules, a large number of long pods with a concomitantly high number of seeds per pod. Moreover, we observed that WOSR opted for additional reproductive strategies than SOSR, presenting more plasticity to maximise seed yield. Overall, we conclude that OSR adopts a key strategy to ensure maximal seed yield and propose an ideal ideotype highlighting crucial phenotypic traits that could be potential targets for breeding.
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http://dx.doi.org/10.3389/fpls.2021.697576DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8450599PMC
September 2021

The potential for soybean to diversify the production of plant-based protein in the UK.

Sci Total Environ 2021 May 28;767:144903. Epub 2021 Jan 28.

Sustainable Agriculture Sciences Department, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.

Soybean (Glycine max) offers an important source of plant-based protein. Currently much of Europe's soybean is imported, but there are strong economic and agronomic arguments for boosting local production. Soybean is grown in central and eastern Europe but is less favoured in the North due to climate. We conducted field trials across three seasons and two sites in the UK to test the viability of early-maturing soybean varieties and used the data from these trials to calibrate and validate the Rothamsted Landscape Model. Once validated, the model was used to predict the probability soybean would mature and the associated yield for 26 sites across the UK based on weather data under current, near-future (2041-60) and far-future (2081-2100) climate. Two representative concentration pathways, a midrange mitigation scenario (RCP4.5) and a high emission scenario (RCP8.5) were also explored. Our analysis revealed that under current climate early maturing varieties will mature in the south of the UK, but the probability of failure increases with latitude. Of the 26 sites considered, only at one did soybean mature for every realisation. Predicted expected yields ranged between 1.39 t ha and 1.95 t ha across sites. Under climate change these varieties are likely to mature as far north as southern Scotland. With greater levels of CO yield is predicted to increase by as much as 0.5 t ha at some sites in the far future, but this is tempered by other effects of climate change meaning that for most sites no meaningful increase in yield is expected. We conclude that soybean is likely to be a viable crop in the UK and for similar climates at similar latitudes in Northern Europe in the future but that for yields to be economically attractive for local markets, varieties must be chosen to align with the growing season.
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http://dx.doi.org/10.1016/j.scitotenv.2020.144903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7938380PMC
May 2021

Plant Available Zinc Is Influenced by Landscape Position in the Amhara Region, Ethiopia.

Plants (Basel) 2021 Jan 28;10(2). Epub 2021 Jan 28.

Sustainable Agriculture Sciences Department, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK.

Zinc (Zn) is an important element determining the grain quality of staple food crops and deficient in many Ethiopian soils. However, farming systems are highly variable in Ethiopia due to different soil types and landscape cropping positions. Zinc availability and uptake by plants from soil and fertilizer sources are governed by the retention and release potential of the soil, usually termed as adsorption and desorption, respectively. The aim of this study was to characterize the amount of plant available Zn at different landscape positions. During the 2018/19 cropping season, adsorption-desorption studies were carried out on soil samples collected from on-farm trials conducted at Aba Gerima, Debre Mewi and Markuma in the Amhara Region. In all locations and landscape positions, adsorption and desorption increased with increasing Zn additions. The amount of adsorption and desorption was highly associated with the soil pH, the soil organic carbon concentration and cation exchange capacity, and these factors are linked to landscape positions. The Freundlich isotherm fitted very well to Zn adsorption (r 0.87-0.99) and desorption (r 0.92-0.99), while the Langmuir isotherm only fitted to Zn desorption (r 0.70-0.93). Multiple regression models developed by determining the most influential soil parameters for Zn availability could be used to inform Zn fertilizer management strategies for different locations and landscape positions in this region, and thereby improve plant Zn use efficiency.
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http://dx.doi.org/10.3390/plants10020254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7912194PMC
January 2021

The contribution of fiber components to water absorption of wheat grown in the UK.

Cereal Chem 2020 Sep-Oct;97(5):940-948. Epub 2020 Jul 16.

Rothamsted Research Harpenden UK.

Background And Objectives: The water absorption (WA) of white wheat flour is a major factor affecting processing quality, and millers, therefore, process their wheat to achieve the required level. Although it is likely that WA is determined by the amounts and compositions of three major grain components, starch, protein, and arabinoxylan, the contribution of the latter is not agreed and not recognized in the widely used Farrand equation.

Findings: We have measured a range of parameters related to fiber amount and composition and tested the ability of these to improve the prediction of WA using a modified Farrand equation. The addition of a range of single fiber traits improved the prediction of WA from a baseline of 82.98% to a maximum of 86.78%, but inclusion of all fiber traits as PCs resulted in a further improvement to 90%. Inclusion of the PCs also accounted for variation in WA between harvest years. The greatest improvement from inclusion of a single trait was observed with β-glucan, the inclusion of arabinogalactan peptide (AGP) also resulted in improved prediction of WA.

Conclusions: The study shows that fiber components contribute to variation in WA, including differences between harvest years, but that β-glucan and AGP have similar or greater impacts than AX.

Significance And Novelty: The study dissects the contributions of AX amount and composition to WA and demonstrates a contribution of b-glucan for the first time.
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http://dx.doi.org/10.1002/cche.10316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540380PMC
July 2020

Overexpression of an endogenous type 2 diacylglycerol acyltransferase in the marine diatom enhances lipid production and omega-3 long-chain polyunsaturated fatty acid content.

Biotechnol Biofuels 2020 14;13:87. Epub 2020 May 14.

1Department of Plant Sciences, Rothamsted Research, Harpenden, Herts AL5 2JQ UK.

Background: Oleaginous microalgae represent a valuable resource for the production of high-value molecules. Considering the importance of omega-3 long-chain polyunsaturated fatty acids (LC-PUFAs) for human health and nutrition the yields of high-value eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) require significant improvement to meet demand; however, the current cost of production remains high. A promising approach is to metabolically engineer strains with enhanced levels of triacylglycerols (TAGs) enriched in EPA and DHA.

Results: Recently, we have engineered the marine diatom to accumulate enhanced levels of DHA in TAG. To further improve the incorporation of omega-3 LC-PUFAs in TAG, we focused our effort on the identification of a type 2 acyl-CoA:diacylglycerol acyltransferase (DGAT) capable of improving lipid production and the incorporation of DHA in TAG. DGAT is a key enzyme in lipid synthesis. Following a diatom based in vivo screen of candidate DGATs, a native was taken forward for detailed characterisation. Overexpression of the endogenous was confirmed by qRT-PCR and the transgenic strain grew successfully in comparison to wildtype. has broad substrate specificity with preferences for C16 and LC-PUFAs acyl groups. Moreover, the overexpression of an endogenous resulted in higher lipid yields and enhanced levels of DHA in TAG. Furthermore, a combined overexpression of the endogenous and ectopic expression of a Δ5-elongase showed how iterative metabolic engineering can be used to increase DHA and TAG content, irrespective of nitrogen treatment.

Conclusion: This study provides further insight into lipid metabolism in and suggests a metabolic engineering approach for the efficient production of EPA and DHA in microalgae.
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http://dx.doi.org/10.1186/s13068-020-01726-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227059PMC
May 2020

Historical changes in the contents and compositions of fibre components and polar metabolites in white wheat flour.

Sci Rep 2020 04 3;10(1):5920. Epub 2020 Apr 3.

Plant Science Department, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.

Thirty-nine UK adapted wheat cultivars dating from between 1790 and 2012 were grown in replicated randomised field trials for three years, milled, and white flour analysed for the contents of dietary fibre components (arabinoxylan and β-glucan) and polar metabolites (sugars, amino acids, organic acids, choline and betaine) to determine whether the composition had changed due to the effects of intensive breeding. The concentrations of components varied between study years, indicating strong effects of environment. Nevertheless, some trends were observed, with the concentrations of arabinoxylan fibre and soluble sugars (notably sucrose, maltose and fructose) increasing and most amino acids (including asparagine which is the precursor of acrylamide formed during processing) decreasing between the older and newer types. The concentration of betaine, which is beneficial for cardio-vascular health, also increased. The study therefore provided no evidence for adverse effects of intensive breeding on the contents of beneficial components in wheat flour.
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http://dx.doi.org/10.1038/s41598-020-62777-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7125105PMC
April 2020

Functional QTL mapping and genomic prediction of canopy height in wheat measured using a robotic field phenotyping platform.

J Exp Bot 2020 03;71(6):1885-1898

Department of Computational & Analytical Sciences, Rothamsted Research, Harpenden, UK.

Genetic studies increasingly rely on high-throughput phenotyping, but the resulting longitudinal data pose analytical challenges. We used canopy height data from an automated field phenotyping platform to compare several approaches to scanning for quantitative trait loci (QTLs) and performing genomic prediction in a wheat recombinant inbred line mapping population based on up to 26 sampled time points (TPs). We detected four persistent QTLs (i.e. expressed for most of the growing season), with both empirical and simulation analyses demonstrating superior statistical power of detecting such QTLs through functional mapping approaches compared with conventional individual TP analyses. In contrast, even very simple individual TP approaches (e.g. interval mapping) had superior detection power for transient QTLs (i.e. expressed during very short periods). Using spline-smoothed phenotypic data resulted in improved genomic predictive abilities (5-8% higher than individual TP prediction), while the effect of including significant QTLs in prediction models was relatively minor (<1-4% improvement). Finally, although QTL detection power and predictive ability generally increased with the number of TPs analysed, gains beyond five or 10 TPs chosen based on phenological information had little practical significance. These results will inform the development of an integrated, semi-automated analytical pipeline, which will be more broadly applicable to similar data sets in wheat and other crops.
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http://dx.doi.org/10.1093/jxb/erz545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094083PMC
March 2020

Accounting for data sparsity when forming spatially coherent zones.

Appl Math Model 2019 Aug;72:537-552

Sustainable Agricultural Systems, Rothamsted Research, Harpenden, AL5 2JQ, UK.

Efficient farm management can be aided by the identification of zones in the landscape. These zones can be informed from different measured variables by ensuring a sense of spatial coherence. Forming spatially coherent zones is an established method in the literature, but has been found to perform poorly when data are sparse. In this paper, we describe the different types of data sparsity and investigate how this impacts the performance of established methods. We introduce a set of methodological advances that address these shortcomings to provide a method for forming spatially coherent zones under data sparsity.
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http://dx.doi.org/10.1016/j.apm.2019.03.030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6559136PMC
August 2019

The contribution of spatial mass effects to plant diversity in arable fields.

J Appl Ecol 2019 Jul 3;56(7):1560-1574. Epub 2019 Jun 3.

Sustainable Agricultural Sciences Rothamsted Research Harpenden Hertfordshire UK.

In arable fields, plant species richness consistently increases at field edges. This potentially makes the field edge an important habitat for the conservation of the ruderal arable flora (or 'weeds') and the invertebrates and birds it supports. Increased diversity and abundance of weeds in crop edges could be owing to either a reduction in agricultural inputs towards the field edge and/or spatial mass effects associated with dispersal from the surrounding landscape.We contend that the diversity of weed species in an arable field is a combination of species, that can persist under the intense selection pressure of regular cultivation and agrochemical inputs (typically more ruderal species), and species that rely on regular dispersal from neighbouring habitats (characterised by a more 'competitive' ecological strategy).We analysed a large dataset of conventionally managed arable fields in the UK to study the effect of the immediate landscape on in-field plant diversity and abundance and to quantify the contribution of spatial mass effects to plant diversity in arable fields in the context of the ecological strategy of the resulting community.We demonstrated that the decline in diversity with distance into an arable field is highly dependent on the immediate landscape, indicating the important role of spatial mass effects in explaining the increased species richness at field edges in conventionally managed fields.We observed an increase in the proportion of typical arable weeds away from the field edge towards the centre. This increase was dependent on the immediate landscape and was associated with a higher proportion of more competitive species, with a lower fidelity to arable habitats, at the field edge. . Conserving the ruderal arable plant community, and the invertebrates and birds that use it as a resource, in conventionally managed arable fields typically relies on the targeted reduction of fertilisers and herbicides in so-called 'conservation headlands'. The success of these options will depend on the neighbouring habitat and boundary. They should be placed along margins where the potential for ingress of competitive species, that may become dominant in the absence of herbicides, is limited. This will enhance ecosystem services delivered by the ruderal flora and reduce the risk of competitive species occurring in the crop.
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http://dx.doi.org/10.1111/1365-2664.13414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6618144PMC
July 2019

Disentangling juxtacrine from paracrine signalling in dynamic tissue.

PLoS Comput Biol 2019 06 13;15(6):e1007030. Epub 2019 Jun 13.

Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom, Mathematics Institute, University of Warwick, Coventry, United Kingdom.

Prolactin is a major hormone product of the pituitary gland, the central endocrine regulator. Despite its physiological importance, the cell-level mechanisms of prolactin production are not well understood. Having significantly improved the resolution of real-time-single-cell-GFP-imaging, the authors recently revealed that prolactin gene transcription is highly dynamic and stochastic yet shows space-time coordination in an intact tissue slice. However, it still remains an open question as to what kind of cellular communication mediates the observed space-time organization. To determine the type of interaction between cells we developed a statistical model. The degree of similarity between two expression time series was studied in terms of two distance measures, Euclidean and geodesic, the latter being a network-theoretic distance defined to be the minimal number of edges between nodes, and this was used to discriminate between juxtacrine from paracrine signalling. The analysis presented here suggests that juxtacrine signalling dominates. To further determine whether the coupling is coordinating transcription or post-transcriptional activities we used stochastic switch modelling to infer the transcriptional profiles of cells and estimated their similarity measures to deduce that their spatial cellular coordination involves coupling of transcription via juxtacrine signalling. We developed a computational model that involves an inter-cell juxtacrine coupling, yielding simulation results that show space-time coordination in the transcription level that is in agreement with the above analysis. The developed model is expected to serve as the prototype for the further study of tissue-level organised gene expression for epigenetically regulated genes, such as prolactin.
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http://dx.doi.org/10.1371/journal.pcbi.1007030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6592563PMC
June 2019

Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedling establishment.

Sci Rep 2018 10 12;8(1):15192. Epub 2018 Oct 12.

Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK.

The Arg/N-end rule pathway of ubiquitin-mediated proteolysis has multiple functions throughout plant development, notably in the transition from dormant seed to photoautotrophic seedling. PROTEOLYSIS6 (PRT6), an N-recognin E3 ligase of the Arg/N-end rule regulates the degradation of transcription factor substrates belonging to Group VII of the Ethylene Response Factor superfamily (ERFVIIs). It is not known whether ERFVIIs are associated with all known functions of the Arg/N-end rule, and the downstream pathways influenced by ERFVIIs are not fully defined. Here, we examined the relationship between PRT6 function, ERFVIIs and ABA signalling in Arabidopsis seedling establishment. Physiological analysis of seedlings revealed that N-end rule-regulated stabilisation of three of the five ERFVIIs, RAP2.12, RAP2.2 and RAP2.3, controls sugar sensitivity of seedling establishment and oil body breakdown following germination. ABA signalling components ABA INSENSITIVE (ABI)4 as well as ABI3 and ABI5 were found to enhance ABA sensitivity of germination and sugar sensitivity of establishment in a background containing stabilised ERFVIIs. However, N-end rule regulation of oil bodies was not dependent on canonical ABA signalling. We propose that the N-end rule serves to control multiple aspects of the seed to seedling transition by regulation of ERFVII activity, involving both ABA-dependent and independent signalling pathways.
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http://dx.doi.org/10.1038/s41598-018-33630-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6185960PMC
October 2018

New insights in the composition of wax and sterol esters in common and mutant sunflower oils revealed by ESI-MS/MS.

Food Chem 2018 Dec 28;269:70-79. Epub 2018 Jun 28.

Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK. Electronic address:

Wax esters (WEs) and steryl esters (SEs) are minor components of sunflower oils formed by the esterification of long chain fatty alcohols and sterols to fatty acids. These compounds have similar carbon numbers and polarities making them difficult to separate using conventional chromatographic methods. In this study, electrospray ionisation-tandem mass spectrometry (ESI-MS/MS) allowed the rapid and accurate profiling of WEs and SEs acyl moieties in total ester fractions of common and mutant sunflower oils with different fatty acid profiles. The acyl composition of both WEs and SEs partially reflected that of the oil and the high oleic background displayed the lowest level of crystallisable waxes. ESI-MS/MS complemented by GC-MS analyses revealed that SEs contain 17-30% of previously unreported methylsterol moieties. We demonstrated that these compounds are overlooked by official sterol analytical methods which may have consequences for quality control and authentication of vegetable oils prior to commercialisation.
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http://dx.doi.org/10.1016/j.foodchem.2018.06.135DOI Listing
December 2018

Beyond the one-way ANOVA for 'omics data.

BMC Bioinformatics 2018 07 9;19(Suppl 7):199. Epub 2018 Jul 9.

Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK.

Background: With ever increasing accessibility to high throughput technologies, more complex treatment structures can be assessed in a variety of 'omics applications. This adds an extra layer of complexity to the analysis and interpretation, in particular when inferential univariate methods are applied en masse. It is well-known that mass univariate testing suffers from multiplicity issues and although this has been well documented for simple comparative tests, few approaches have focussed on more complex explanatory structures.

Results: Two frameworks are introduced incorporating corrections for multiplicity whilst maintaining appropriate structure in the explanatory variables. Within this paradigm, a choice has to be made as to whether multiplicity corrections should be applied to the saturated model, putting emphasis on controlling the rate of false positives, or to the predictive model, where emphasis is on model selection. This choice has implications for both the ranking and selection of the response variables identified as differentially expressed. The theoretical difference is demonstrated between the two approaches along with an empirical study of lipid composition in Arabidopsis under differing levels of salt stress.

Conclusions: Multiplicity corrections have an inherent weakness when the full explanatory structure is not properly incorporated. Although a unifying 'single best' recommendation is not provided, two reasonable alternatives are provided and the applicability of these approaches is discussed for different scenarios where the aims of analysis will differ. The key result is that the point at which multiplicity is incorporated into the analysis will fundamentally change the interpretation of the results, and the choice of approach should therefore be driven by the specific aims of the experiment.
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http://dx.doi.org/10.1186/s12859-018-2173-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069693PMC
July 2018

N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway.

New Phytol 2018 05 23;218(3):1106-1126. Epub 2017 Nov 23.

Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK.

The N-end rule pathway of targeted protein degradation is an important regulator of diverse processes in plants but detailed knowledge regarding its influence on the proteome is lacking. To investigate the impact of the Arg/N-end rule pathway on the proteome of etiolated seedlings, we used terminal amine isotopic labelling of substrates with tandem mass tags (TMT-TAILS) for relative quantification of N-terminal peptides in prt6, an Arabidopsis thaliana N-end rule mutant lacking the E3 ligase PROTEOLYSIS6 (PRT6). TMT-TAILS identified over 4000 unique N-terminal peptides representing c. 2000 protein groups. Forty-five protein groups exhibited significantly increased N-terminal peptide abundance in prt6 seedlings, including cruciferins, major seed storage proteins, which were regulated by Group VII Ethylene Response Factor (ERFVII) transcription factors, known substrates of PRT6. Mobilisation of endosperm α-cruciferin was delayed in prt6 seedlings. N-termini of several proteases were downregulated in prt6, including RD21A. RD21A transcript, protein and activity levels were downregulated in a largely ERFVII-dependent manner. By contrast, cathepsin B3 protein and activity were upregulated by ERFVIIs independent of transcript. We propose that the PRT6 branch of the pathway regulates protease activities in a complex manner and optimises storage reserve mobilisation in the transition from seed to seedling via control of ERFVII action.
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Source
http://dx.doi.org/10.1111/nph.14909DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5947142PMC
May 2018
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