Research Repository

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DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples (2019)
Journal Article
Shaw, L. M., Blanchard, A., Chen, Q., An, X., Davies, P., Totemeyer, S., …Stekel, D. J. (2019). DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples. Scientific Reports, 9, doi:10.1038/s41598-019-38873-4

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test... Read More

Development and validation of an exome-based SNP marker set for identification of the St, Jr and Jvs genomes of Thinopyrym intermedium in a wheat background (2019)
Journal Article
Cseh, A., Yang, C., Hubbart-Edwards, S., Scholefield, D., Ashling, S. S., Burridge, A. J., …Grewal, S. (2019). Development and validation of an exome-based SNP marker set for identification of the St, Jr and Jvs genomes of Thinopyrym intermedium in a wheat background. TAG Theoretical and Applied Genetics, doi:10.1007/s00122-019-03300-9

Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic d... Read More

Gsmodutils: A python based framework for test-driven genome scale metabolic model development (2019)
Journal Article
Gilbert, J., Pearcy, N., Norman, R., Millat, T., Winzer, K., King, J., …Twycross, J. (2019). Gsmodutils: A python based framework for test-driven genome scale metabolic model development. Bioinformatics, doi:10.1093/bioinformatics/btz088

Motivation Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include th... Read More

The commercial pig as a model of spontaneously-occurring osteoarthritis (2019)
Journal Article
Macfadyen, M. A., Daniel, Z., Kelly, S., Parr, T., Brameld, J. M., Murton, A. J., & Jones, S. W. (2019). The commercial pig as a model of spontaneously-occurring osteoarthritis. BMC Musculoskeletal Disorders, 20, doi:10.1186/s12891-019-2452-0

Background: Preclinical osteoarthritis models where damage occurs spontaneously may better reflect the initiation and development of human osteoarthritis. The aim was to assess the commercial pig as a model of spontaneous osteoarthritis development b... Read More

Development of stable homozygous wheat/Amblyopyrum muticum (Aegilops mutica) introgression lines and their cytogenetic and molecular characterization (2019)
Journal Article
King, J., Newell, C., Grewal, S., Hubbart-Edwards, S., Yang, C., Scholefield, D., …King, I. P. (2019). Development of stable homozygous wheat/Amblyopyrum muticum (Aegilops mutica) introgression lines and their cytogenetic and molecular characterization. Frontiers in Plant Science, 10, 1-10. doi:10.3389/fpls.2019.00034

Wheat is one of the world’s most important sources of food. However, due to its evolution its genetic base has narrowed, which is severely limiting the ability of breeders to develop new higher yielding varieties that can adapt to the changing enviro... Read More

Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis (2019)
Journal Article
Ramos-Ibeas, P., Sang, F., Zhu, Q., Wang, W. W., Withey, S., Klisch, D., …Alberio, R. (2019). Pluripotency and X chromosome dynamics revealed in pig pre-gastrulating embryos by single cell analysis. Nature Communications, 10, doi:10.1038/s41467-019-08387-8

High-resolution molecular programmes delineating the cellular foundations of mammalian embryogenesis have emerged recently. Similar analysis of human embryos is limited to pre-implantation stages, since early post-implantation embryos are largely ina... Read More

Sex allocation, sex ratios and reproduction (2019)
Book Chapter
Hardy, I. C., & Boulton, R. A. (2019). Sex allocation, sex ratios and reproduction. In J. Choe (Ed.), Encyclopedia of Animal Behavior, 464-471. (2nd edition). Elsevier

Sex allocation theory provides a powerful framework for understanding a range of reproductive behavior, including the numerical sex ratio of the progeny that parents produce. Starting with evolutionary explanations for why many species have unbiased... Read More

A loop-mediated isothermal amplification (LAMP) assay for rapid and specific detection of airborne inoculum of Uromyces betae (sugar beet rust) (2019)
Journal Article
Kaczmarek, A., King, K., West, J., Stevens, M., Sparkes, D., & Dickinson, M. (2019). A loop-mediated isothermal amplification (LAMP) assay for rapid and specific detection of airborne inoculum of Uromyces betae (sugar beet rust). Plant Disease, doi:10.1094/PDIS-02-18-0337-RE

Sugar beet rust disease (causal agent Uromyces betae) represents a serious threat to worldwide sugar beet (Beta vulgaris) crops, causing yield losses of up to 10% in the UK. Currently, the disease is managed mainly by application of fungicides after... Read More

Uncertainty in geological interpretations: effectiveness of expert elicitations (2019)
Journal Article
Randle, C. H., Bond, C. E., Lark, R. M., & Monaghan, A. A. (2019). Uncertainty in geological interpretations: effectiveness of expert elicitations. Geosphere, 15(1), doi:10.1130/GES01586.1

Uncertainty in geological interpretations creates and often unquantified risk for sub- surface industries. The challenge of quantifying interpretation uncertainty has been addressed using various methods. For interpretation of borehole data, empirica... Read More

Infestation by Myzus persicae increases susceptibility of Brassica napus cv. “Canard” to Rhizoctonia solani AG 2-1 (2018)
Journal Article
Drizou, F., Bruce, T. J. A., Ray, R. V., & Graham, N. S. (2018). Infestation by Myzus persicae increases susceptibility of Brassica napus cv. “Canard” to Rhizoctonia solani AG 2-1. Frontiers in Plant Science, 9, 1-14. doi:10.3389/fpls.2018.01903

Activation of plant defense pathways can be influenced by the presence of different species of attacking organisms. Understanding the complicated interactions triggering plant defense mechanisms is of great interest as it may allow the development of... Read More

Productivity framework (2018)
Journal Article
Wagstaff, C., Kendrick, F., Dennis, C., Hollington, P., Hess, T., Brameld, J., …Mason, B. (2018). Productivity framework. 00 Journal not listed, 32(4), 52-57

A canopy conundrum: can wind-induced movement help to increase crop productivity by relieving photosynthetic limitations? (2018)
Journal Article
Burgess, A. J., Gibbs, J. A., & Murchie, E. H. (2018). A canopy conundrum: can wind-induced movement help to increase crop productivity by relieving photosynthetic limitations?. Journal of Experimental Botany, doi:10.1093/jxb/ery424

Wind-induced movement is a ubiquitous occurrence for all plants grown in natural or agricultural settings and in the context of high, damaging wind speeds it has been well studied. However, the impact of lower wind speeds (that do not cause any damag... Read More

Spatial variability of organic matter properties determines methane fluxes in a tropical forested peatland (2018)
Journal Article
Girkin, N. T., Vane, C. H., Cooper, H. V., Moss-Hayes, V., Craigon, J., Turner, B. L., …Sjögersten, S. (2019). Spatial variability of organic matter properties determines methane fluxes in a tropical forested peatland. Biogeochemistry, 142(2), 231-245. doi:10.1007/s10533-018-0531-1

Tropical peatland ecosystems are a significant component of the global carbon cycle and feature a range of distinct vegetation types, but the extent of links between contrasting plant species, peat biogeochemistry and greenhouse gas fluxes remains un... Read More

Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice (2018)
Journal Article
Yang, M., Lu, K., Zhao, F., Xie, W. X., Ramakrishna, P., Wang, G., …Lian, X. (2018). Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. Plant Cell, 30(11), 2720–2740. doi:10.1105/tpc.18.00375

Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we des... Read More

A modified high-throughput analysis of PLFAs in soil (2018)
Journal Article
Ellis, S., & Ritz, K. (2018). A modified high-throughput analysis of PLFAs in soil. MethodsX, 5, 1491-1497. doi:10.1016/j.mex.2018.10.022

Microbial community profiling via phospholipid fatty-acid (PLFA) analysis is an insightful technique which elucidates the phenotypic structure of microbial assemblages within soil. Previous iterations of PLFA analysis have used large quantities of ch... Read More

Putative regulatory candidate genes for QTL linked to fruit traits in oil palm (Elaeis guineensis Jacq.) (2018)
Journal Article
Ting, N., Mayes, S., Massawe, F., Sambanthamurthi, R., Jansen, J., Shahrul Rabiah Syed Alwee, S., …Singh, R. (2018). Putative regulatory candidate genes for QTL linked to fruit traits in oil palm (Elaeis guineensis Jacq.). Euphytica, doi:10.1007/s10681-018-2296-y

Palm oil is among the most important vegetable oils, contributing to a quarter of the world’s oils and fats market. The oil palm (Elaeis guineensis Jacq.) fruitlets, which are the source of palm oil, vary from 8eight to 20 g in weight. Palm oil conte... Read More

The beta-adrenergic agonist, Ractopamine increases skeletal muscle expression of Asparagine Synthetase as part of an integrated stress response gene program (2018)
Journal Article
Brown, D., Ryan, K., Daniel, Z., Mareko, M., Talbot, R., Moreton, J., …Brameld, J. M. (2018). The beta-adrenergic agonist, Ractopamine increases skeletal muscle expression of Asparagine Synthetase as part of an integrated stress response gene program. Scientific Reports, 8, doi:10.1038/s41598-018-34315-9

Synthetic beta-adrenergic agonists (BA) have broad biomedical and agricultural application for increasing lean body mass, yet a poor understanding of the biology underpinning these agents is limiting further drug discovery potential. Growing female p... Read More

Evidence for carbon cycling in a large freshwater lake in the Balkans over the last 0.5 million years using the isotopic composition of bulk organic matter (2018)
Journal Article
Zanchetta, G., Baneschi, I., Francke, A., Boschi, C., Regattieri, E., Wagner, B., …Sadori, L. (2018). Evidence for carbon cycling in a large freshwater lake in the Balkans over the last 0.5 million years using the isotopic composition of bulk organic matter. Quaternary Science Reviews, 202, 154-165. doi:10.1016/j.quascirev.2018.10.022

In the DEEP core from the Lake Ohrid ICDP drilling project, the carbon isotope composition of bulk organic matter (δ13CTOC) over the last 516 ka shows a negative correlation with total organic carbon (TOC) and total inorganic carbon (TIC). This relat... Read More

Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedling establishment (2018)
Journal Article
Zhang, H., Gannon, L., Jones, P. D., Rundle, C. A., Hassall, K. L., Gibbs, D. J., …Theodoulou, F. L. (2018). Genetic interactions between ABA signalling and the Arg/N-end rule pathway during Arabidopsis seedling establishment. Scientific Reports, 8(1), doi:10.1038/s41598-018-33630-5

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... Read More