The role of spatial structure in the infection spread models: population density map of England example

The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license: https://creativecommons.org/licenses/by-nc-nd/4.0/.In the current situation of a pandemic caused by COVID-19 developing models accurately predicting the dynamics of the outbreaks in time and space became extremely important. Individual-based models (IBM) simulating the spread of infection in a population have a few advantages compared to classical equation-based approach. First, they use individuals as units, which represent the population, and reflect the local variations happening in real life. Second, the simplicity of modelling the interactions between the individuals, which may not be the case when using differential equations.We propose to use freely available population density maps to simulate the infection spread in the human population on the scale of an individual country or a city. We explore the effect of social distancing and show that it can reduce the outbreak when applied before or during peak time, but it can also inflict the second wave when relaxed after the peak. This can be explained by a large proportion of susceptible individuals, even in the large cities, after the first wave.The model can be adapted to any spatial scale from a single hospital to multiple countries.Final Published versio

Genomic evidence for genes encoding leucine-rich repeat receptors linked to resistance against the eukaryotic extra- and intracellular Brassica napus pathogens Leptosphaeria maculans and Plasmodiophora brassicae

© 2018 Stotz et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) control resistance against intracellular (cell-penetrating) pathogens. However, evidence for a role of genes coding for proteins with LRR domains in resistance against extracellular (apoplastic) fungal pathogens is limited. Here, the distribution of genes coding for proteins with eLRR domains but lacking kinase domains was determined for the Brassica napus genome. Predictions of signal peptide and transmembrane regions divided these genes into 184 coding for receptor-like proteins (RLPs) and 121 coding for secreted proteins (SPs). Together with previously annotated NLRs, a total of 720 LRR genes were found. Leptosphaeria maculans-induced expression during a compatible interaction with cultivar Topas differed between RLP, SP and NLR gene families; NLR genes were induced relatively late, during the necrotrophic phase of pathogen colonization. Seven RLP, one SP and two NLR genes were found in Rlm1 and Rlm3/Rlm4/Rlm7/Rlm9 loci for resistance against L. maculans on chromosome A07 of B. napus. One NLR gene at the Rlm9 locus was positively selected, as was the RLP gene on chromosome A10 with LepR3 and Rlm2 alleles conferring resistance against L. maculans races with corresponding effectors AvrLm1 and AvrLm2, respectively. Known loci for resistance against L. maculans (extracellular hemi-biotrophic fungus), Sclerotinia sclerotiorum (necrotrophic fungus) and Plasmodiophora brassicae (intracellular, obligate biotrophic protist) were examined for presence of RLPs, SPs and NLRs in these regions. Whereas loci for resistance against P. brassicae were enriched for NLRs, no such signature was observed for the other pathogens. These findings demonstrate involvement of (i) NLR genes in resistance against the intracellular pathogen P. brassicae and a putative NLR gene in Rlm9-mediated resistance against the extracellular pathogen L. maculans.Peer reviewe

Heterogeneity of cell membrane structure studied by single molecule tracking

© The Royal Society of Chemistry 2021. his article is licensed under a Creative Commons Attribution 3.0 Unported Licence. https://creativecommons.org/licenses/by/3.0/Heterogeneity in cell membrane structure, typified by microdomains with different biophysical and biochemical properties, is thought to impact on a variety of cell functions. Integral membrane proteins act as nanometre-sized probes of the lipid environment and their thermally-driven movements can be used to report local variations in membrane properties. In the current study, we have used total internal reflection fluorescence microscopy (TIRFM) combined with super-resolution tracking of multiple individual molecules, in order to create high-resolution maps of local membrane viscosity. We used a quadrat sampling method and show how statistical tests for membrane heterogeneity can be conducted by analysing the paths of many molecules that pass through the same unit area of membrane. We describe experiments performed on cultured primary cells, stable cell lines and ex vivo tissue slices using a variety of membrane proteins, under different imaging conditions. In some cell types, we find no evidence for heterogeneity in mobility across the plasma membrane, but in others we find statistically significant differences with some regions of membrane showing significantly higher viscosity than others. This journal isPeer reviewedFinal Published versio

Intrinsic and extrinsic factors influencing large African herbivore movements

This document is the Accepted Manuscript version of the following article: Jan A. Venter, Herbert H. T. Prins, Alla Mashanova, Willem F. de Boer, and Rob Slotow, 'Intrinsic and extrinsic factors influencing large African herbivore movements', Ecological Informatics, Vol. 30: 257-262, November 2015, doi: https://doi.org/10.1016/j.ecoinf.2015.05.006. This manuscript version is made available under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or built upon in any way.Understanding environmental as well as anthropogenic factors that influence large herbivore ecological patterns and processes should underpin their conservation and management. We assessed the influence of intrinsic, extrinsic environmental and extrinsic anthropogenic factors on movement behaviour of eight African large herbivore species. A cumulative odds ordinal logistic regression was used to determine the effect of season, feeding niche, number of vegetation types, home range size, and fences on the number of exponential distributions observed. When animals faced the trade-off between forage quality and quantity during the dry season, they moved further between forage areas and water sources in order to get to better forage, which added to the number of movement scales observed. Elephants had a lower number of movement scales, compared to all the other feeding types, which could be attributed to them being able to switch between browse and graze. The number of movement scales increased in more heterogeneous areas. Animals with larger home ranges, which are also larger species, and animals more restricted by fences, had fewer movement scales. In order for managers to effectively manage protected areas and associated biodiversity they need take cognisance of the different scales animals operate under, and the different factors that may be important for different species.Peer reviewe

Effects of a penthiopyrad and picoxystrobin fungicide mixtureon phoma stem canker (Leptosphaeria spp.) on UK winteroilseed rape

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2016. This is a pre-copyedited, author-produced PDF of an article accepted for publication in European Journal of Plant Pathology following peer review. The final publication [Sewell, T.R., Moloney, S., Ashworth, M. et al., European Journal of Plant Pathology (2016) 145: 675-685, first published online April 5, 2016] is available at Springer via doi: http://dx.doi.org/10.1007/s10658-016-0916-8In the UK, fungicides are often used to controlphoma stem canker on winter oilseed rape. Field trialswere established near Boxworth, Cambridgeshire for fourcropping seasons (2011/2012, 2012/2013, 2013/2014 and2014/15) to test the efficacy of a new fungicide mixtureRefinzar® (penthiopyrad + picoxystrobin) by comparisonto an existing fungicide Proline 275® (prothioconazole)against phoma stem canker (Leptosphaeria spp.) andthe effect on winter oilseed rape (cv. Catana) yield. Ineach season, weather data were collected from a weatherstation at Boxworth and the release of ascospores wasmonitored using a nearby Burkard spore sampler. Thepatterns of ascospore release differed between seasonsand related to weather conditions. Fungicidespenthiopyrad + picoxystrobin and prothioconazole wereapplied in October/November when 10 % of plants hadphoma leaf spotting (T1, early), 4/8 weeks after T1 (T2,late) or at both T1 and T2 (combined). When phoma leafspot symptoms were assessed in autumn/winter,penthiopyrad + picoxystrobin and prothioconazole bothdecreased numbers of phoma leaf spots caused byL. maculans; there were few leaf spots caused byL. biglobosa. Penthiopyrad + picoxystrobin andprothioconazole both reduced phoma stem canker severitybefore harvest compared to the untreated control butdid not increase yield in these seasons when epidemicswere not severe. In 2013/2014, the presence ofL. maculans and L. biglobosa in upper stem lesions orstem base cankers was determined by species-specificPCR. The proportions of stems with L. maculans DNAwere much greater than those with L. biglobosa DNA forboth upper stem lesions and basal stem cankers. Theseresults suggest that both penthiopyrad + picoxystrobinand prothioconazole can decrease phoma stem cankerseverity on winter oilseed rape in severe disease seasons.Peer reviewe

Plant species in flower during the year

This note presents a graph showing numbers of plant species in flower observed by BNA members during walks through the year.Final Published versio

Recording of higher plants 2017-2019

© 2020 The Author(s).The most recent report of flora recording in Herts was published by Trevor James in the 2017 issue of The Hertfordshire Naturalist (James, 2017). This covered the years 2015 and 2016 and so an update is overdue. Here we summarise botanical activities and notable developments between 2017 and 2019, a period during which Trevor sadly encountered serious health problems and was unable to participate to the extent he would have liked.Non peer reviewe

Recording of higher plants 2020

Peer reviewe