Epigenetics of Host-Pathogen Interactions: The effect of acetosyringone on Ti Plasmid methylation patterns in Agrobacterium tumefaciens C58

The plant pathogen Agrobacterium tumefaciens C58 can transfer a portion of its tumor-inducing (Ti) plasmid to plant hosts in response to the plant wound signals, including Acetosyringone. The portion transferred is aptly titled Transfer DNA (T-DNA) which encode genes involved in tumor production and biosynthesis of a unique bacterial food source called opines that provide an advantage to the inducing Agrobacterium. The Ti plasmid contains a number of genes, including the virulence region that enables T-DNA transfer. Epigenetics investigates how chemical modifications to DNA that don’t alter sequence are used to control gene expression (for example, genes involved in pathogen virulence). Epigenetic modifications can be detected by a next generation sequencing technology called Single Molecule Real Time (SMRT) sequencing. SMRT detects these modifications by tracking kinetic shifts during DNA synthesis. Given the unique inter-kingdom DNA transfer, and the importance of epigenetic regulation in other bacteria and plant species, a comparative exploration of methylation patterns of the Ti plasmid under conditions that induce virulence was undertaken. Over a dozen genes with a variety of purposes (virulence regulation, ion transport, DNA replication, etc.) lost methylation following exposure to the virulence inducing molecule acetosyringone, suggesting increased transcription. Three genes, VirD5, TraM and a phosphate/sodium symporter gained methylation throughout the gene, suggesting down regulation. The patterns discovered, while intriguing, sre limited by possible methodological flaws in SMRT sequencing due to incongruities between reported findings and those described in the literature. A further examination of the expression profiles of these genes is warranted given these findings

Partisanship, Propaganda and Post-Truth Politics: Quantifying Impact in Online Debate

The recent past has highlighted the influential role of social networks and online media in shaping public debate on current affairs and political issues. This paper is focused on studying the role of politically-motivated actors and their strategies for influencing and manipulating public opinion online: partisan media, state-backed propaganda, and post-truth politics. In particular, we present quantitative research on the presence and impact of these three `Ps' in online Twitter debates in two contexts: (i) the run up to the UK EU membership referendum (`Brexit'); and (ii) the information operations of Russia-backed online troll accounts. We first compare the impact of highly partisan versus mainstream media during the Brexit referendum, specifically comparing tweets by half a million `leave' and `remain' supporters. Next, online propaganda strategies are examined, specifically left- and right-wing troll accounts. Lastly, we study the impact of misleading claims made by the political leaders of the leave and remain campaigns. This is then compared to the impact of the Russia-backed partisan media and propaganda accounts during the referendum. In particular, just two of the many misleading claims made by politicians during the referendum were found to be cited in 4.6 times more tweets than the 7,103 tweets related to Russia Today and Sputnik and in 10.2 times more tweets than the 3,200 Brexit-related tweets by the Russian troll accounts.Comment: This is now published in the Journal of Web Science. Please cite accordingly. https://webscience-journal.net/webscience/article/view/8

Genomic characterization of two novel viruses infecting Barleria cristata L. from the genera Orthotospovirus and Polerovirus

Barleria cristata L. has become naturalized in South Africa, where it is commonly used as an ornamental. In 2019, plants of B. cristata showing putative viral symptoms were collected from two locations in Gauteng, South Africa. RNAtag-seq libraries were prepared and sequenced using an Illumina HiSeq 2500 platform. De novo assembly of the resulting data revealed the presence of a novel member of the family Tospoviridae associated with the plants from both locations, and this virus was given the tentative name "barleria chlorosis-associated virus". Segments L, M, and S have lengths of 8752, 4760, and 2906 nt, respectively. Additionally, one of the samples was associated with a novel polerovirus, provisionally named "barleria polerovirus 1", with a complete genome length of 6096 nt. This is the first study to show the association of viruses with a member of the genus Barleria.SUPPLEMENTARY INFORMATION : Supplementary Figure 1: Foliar symptoms associated with Barleria cristata plants that were sampled in this study. Large, diffuse chlorotic spots were associated with the single infection of barleria severe mosaic virus (BSMoV) (19-3031), while a more defined mosaic was associated with the mixed involving both BSMoV and barleria polerovirus 1 (19-3037).Supplementary Figure 2: Maximum likelihood phylogeny based on the amino acid sequences of the N-protein of barleria chlorosis-associated virus (indicated by solid circle markers) and selected members of the Tospoviridae family. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the best-fit (Le Gascuel) model with gamma distribution (n=4). Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. The cognate amino acid sequence of Guaroa virus was used as an outgroup.Supplementary Figure 3: Maximum likelihood phylogeny based on the amino acid sequences of the RNA-dependant RNA polymerase of barleria polero virus 1 (indicated by solid circle markers) and selected members of the Luteoviridae family. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the best-fit (Jones-Taylor-Thornton) model. Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. The cognate amino acid sequences of two enamoviruses were used as outgroups.http://link.springer.com/journal/7052022-07-01hj2022Forestry and Agricultural Biotechnology Institute (FABI

HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase

Poly(ADP-ribose) polymerase 1 (PARP1) is an important player in the response to DNA damage. Recently, Histone PARylation Factor (HPF1) was shown to be a critical modulator of the activity of PARP1 by facilitating PARylation of histones and redirecting the target amino acid specificity from acidic to serine residues. Here, we investigate the mechanism and specific consequences of HPF1-mediated PARylation using nucleosomes as both activators and substrates for PARP1. HPF1 provides that catalytic base Glu284 to substantially redirect PARylation by PARP1 such that the histones in nucleosomes become the primary recipients of PAR chains. Surprisingly, HPF1 partitions most of the reaction product to free ADP-ribose (ADPR), resulting in much shorter PAR chains compared to reactions in the absence of HPF1. This HPF1-mediated switch from polymerase to hydrolase has important implications for the PARP1-mediated response to DNA damage and raises interesting new questions about the role of intracellular ADPR and depletion of NAD+. </div

Will they be back? A framework to guide rare macrophyte conservation decisions in lakes

Shallow lake restoration typically focusses on the re-establishment of macrophytes. The likelihood of a species returning to a site is contingent on dispersal, proximity to propagule sources, and the on-site propagule-bank viability. We explore the potential of palaeoecological records in combination with botanical surveys and distribution maps, to ascertain the loss of three submerged macrophytes (Littorella uniflora, Najas flexilis, and Elatine hydropiper) from, respectively, two lakes (Barton Broad, Norfolk and Esthwaite Water, Cumbria) and one lake landscape (Greater Glasgow, Scotland). We discuss re-establishment likelihood when accounting for species' autoecology and current water-chemistry conditions. L. uniflora is widespread in the United Kingdom but absent locally in Norfolk without known seed bank, hence is unlikely to naturally recolonise Barton Broad. Furthermore, current conditions are unsuitable for this species suggesting that nutrient reduction is required prior to translocation. N. flexilis is extinct in Cumbria and the long distances involved (>100 km) for recolonisation of Esthwaite Water suggest that spatial dispersal is unlikely, rendering the seed bank the last chance of natural recovery. Alternatively, translocation may be feasible. E. hydropiper is a nationally scarce species in the United Kingdom yet would have only a short dispersal distance (~10 km) to recolonise Loch Libo, hence there being no requirement for translocation. In exploring the recovery possibilities for the three focal plant species, we develop a time–space integrated framework that can be employed to guide conservation decisions for other species, enabling a more rational use of translocations in the future, in line with international guidelines

The ZERO: Zip-Tie Revolver

The Boise State University Microgravity Team has been challenged with designing a mechanical Zip-tie tool to be used during EVA missions on the ISS. NASA is looking for a new tool that will allow astronauts to fasten zip-ties to secure wires and hoses. This tool would need to have a number of zip-ties stored internally, be quickly reusable, and would need to be easily and safely operated by an astronaut in a single handed operation