Exploration of wheat and pathogen transcriptomes during tan spot infection

Objectives: The fungus Pyrenophora tritici-repentis is the causal agent of tan spot, a major disease of wheat (Triticum aestivum). Here, we used RNA sequencing to generate transcriptional datasets for both the host and pathogen during infection and during in vitro pathogen growth stages. Data description: To capture gene expression during wheat infection with the P. tritici-repentis isolate M4, RNA datasets were generated for wheat inoculated with P. tritici-repentis (infection) and a mock (control) at 3 and 4 days post-infection, when scorable leaf disease symptoms manifest. The P. tritici-repentis isolate M4 was also RNA sequenced to capture gene expression in vitro at two different growth stages: 7-day old vegetative mycelia and 9-day old sporulating mycelia, to coincide with a latent growth stage and early sporulation respectively. In total, 6 RNA datasets are available to aid in the validation of predicted genes of P. tritici-repentis and wheat. The datasets generated offer an insight into the transcriptomic profile of the host-pathogen interaction and can be used to investigate the expression of a subset of transcripts or targeted genes prior to designing cost-intensive RNA sequencing experiments, that would be best further explored with replication and a time series analysis

The Hawking-Page crossover in noncommutative anti-deSitter space

We study the problem of a Schwarzschild-anti-deSitter black hole in a noncommutative geometry framework, thought to be an effective description of quantum-gravitational spacetime. As a first step we derive the noncommutative geometry inspired Schwarzschild-anti-deSitter solution. After studying the horizon structure, we find that the curvature singularity is smeared out by the noncommutative fluctuations. On the thermodynamics side, we show that the black hole temperature, instead of a divergent behavior at small scales, admits a maximum value. This fact implies an extension of the Hawking-Page transition into a van der Waals-like phase diagram, with a critical point at a critical cosmological constant size in Plank units and a smooth crossover thereafter. We speculate that, in the gauge-string dictionary, this corresponds to the confinement "critical point" in number of colors at finite number of flavors, a highly non-trivial parameter that can be determined through lattice simulations.Comment: 24 pages, 6 figure, 1 table, version matching that published on JHE

Understanding a constellation of eight COVID-19 disease prevention behaviours using the COM-B model and the theoretical domains framework: a qualitative study using the behaviour change wheel

Background: The use of behavioural science and behaviour change within local authorities and public health has supported healthful change; as evidenced by its importance and contribution to reducing harm during the COVID-19 pandemic. It can provide valuable information to enable the creation of evidence-based intervention strategies, co-created with the people they are aimed at, in an effective and efficient manner. Aim: This study aimed to use the COM-B model to understand the Capability, Opportunity and Motivation of performing a constellation of eight COVID-19 disease prevention behaviours related to the slogans of ‘Hands, Face, Space, Fresh Air’; ‘Find, Isolate, Test, (FIT), and Vaccinate’ in those employed in workplaces identified as high risk for transmission of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) to support intervention development. Methods: This qualitative study recruited twenty-three participants (16 female, 7 male), who were interviewed from three environments (schools, care homes, warehouses) across three local authorities. Semi-structured interviews were analysed using thematic analysis. Findings: Ten core themes were identified inductively; (1) knowledge and skills, (2) regulating the behaviour, (3) willingness to act, (4) necessity and concerns, (5) emotional impact, (6) conducive environment, (7) societal influence, (8) no longer united against COVID-19, (9) credible leadership, and (10) inconsistent adherence to COVID-19 prevention behaviours. Themes were then deductively mapped to the COM-B model of behaviour change and the theoretical domains framework and a logic model using the behaviour change wheel (BCW) was produced to inform intervention design. Conclusion: This study offers a novel approach to analysis that has included eight behaviours within a single thematic analysis and COM-B diagnosis. This will enable local authorities to direct limited resources to overarching priorities. Of key importance, was the need for supportive and credible leadership, alongside developing interventions collaboratively with the target audience. COVID-19 has had an emotional toll on those interviewed, however, promoting the value of disease prevention behaviours, over and above their costs, can facilitate behaviour. Developing knowledge and skills, through education, training, marketing and modelling can further facilitate behaviour. This supports guidance produced by the British Psychological Society COVID-19 behavioural science and disease prevention taskforce

Stratospheric gravity waves over the mountainous island of South Georgia: testing a high-resolution dynamical model with 3-D satellite observations and radiosondes

Atmospheric gravity waves (GWs) play an important role in atmospheric dynamics but accurately representing them in general circulation models (GCMs) is challenging. This is especially true for orographic GWs generated by wind flow over small mountainous islands in the Southern Ocean. Currently, these islands lie in the “grey zone” of global model resolution, where they are neither fully resolved nor fully parameterised. It is expected that as GCMs approach the spatial resolution of current high-resolution local-area models, small-island GW sources may be resolved without the need for parameterisations. But how realistic are the resolved GWs in these high-resolution simulations compared to observations? Here, we test a high-resolution (1.5 km horizontal grid, 118 vertical levels) local-area configuration of the Met Office Unified Model over the mountainous island of South Georgia (54∘ S, 36∘ W), running without GW parameterisations. The island's orography is well resolved in the model, and real-time boundary conditions are used for two time periods during July 2013 and June–July 2015. We compare simulated GWs in the model to coincident 3-D satellite observations from the Atmospheric Infrared Sounder (AIRS) on board Aqua. By carefully sampling the model using the AIRS resolution and measurement footprints (denoted as model sampled as AIRS hereafter), we present the first like-for-like comparison of simulated and observed 3-D GW amplitudes, wavelengths and directional GW momentum flux (GWMF) over the island using a 3-D S-transform method. We find that the timing, magnitude and direction of simulated GWMF over South Georgia are in good general agreement with observations, once the AIRS sampling and resolution are applied to the model. Area-averaged zonal GWMF during these 2 months is westward at around 5.3 and 5.6 mPa in AIRS and model sampled as AIRS datasets respectively, but values directly over the island can exceed 50 mPa. However, up to 35 % of the total GWMF in AIRS is actually found upwind of the island compared to only 17 % in the model sampled as AIRS, suggesting that non-orographic GWs observed by AIRS may be underestimated in our model configuration. Meridional GWMF results show a small northward bias (∼20 %) in the model sampled as AIRS that may correspond to a southward wind bias compared to coincident radiosonde measurements. Finally, we present one example of large-amplitude (T′≈15–20 K at 45 km altitude) GWs at short horizontal wavelengths (λH≈30–40 km) directly over the island in AIRS measurements that show excellent agreement with the model sampled as AIRS. This suggests that orographic GWs in the full-resolution model with T′≈45 K and λH≈30–40 km can occur in reality. Our study demonstrates that not only can high-resolution local-area models simulate realistic stratospheric GWs over small mountainous islands but the application of satellite sampling and resolution to these models can also be a highly effective method for their validation

How do we get there? Effects of cognitive aging on route memory

© 2017 The Author(s) Research into the effects of cognitive aging on route navigation usually focuses on differences in learning performance. In contrast, we investigated age-related differences in route knowledge after successful route learning. One young and two groups of older adults categorized using different cut-off scores on the Montreal Cognitive Assessment (MoCA), were trained until they could correctly recall short routes. During the test phase, they were asked to recall the sequence in which landmarks were encountered (Landmark Sequence Task), the sequence of turns (Direction Sequence Task), the direction of turn at each landmark (Landmark Direction Task), and to identify the learned routes from a map perspective (Perspective Taking Task). Comparing the young participant group with the older group that scored high on the MoCA, we found effects of typical aging in learning performance and in the Direction Sequence Task. Comparing the two older groups, we found effects of early signs of atypical aging in the Landmark Direction and the Perspective Taking Tasks. We found no differences between groups in the Landmark Sequence Task. Given that participants were able to recall routes after training, these results suggest that typical and early signs of atypical aging result in differential memory deficits for aspects of route knowledge

Monoubiquitination of syntaxin 3 leads to retrieval from the basolateral plasma membrane and facilitates cargo recruitment to exosomes

Syntaxin 3 (Stx3), a SNARE protein located and functioning at the apical plasma membrane of epithelial cells, is required for epithelial polarity. A fraction of Stx3 is localized to late endosomes/lysosomes, although how it traffics there and its function in these organelles is unknown. Here we report that Stx3 undergoes monoubiquitination in a conserved polybasic domain. Stx3 present at the basolateral—but not the apical—plasma membrane is rapidly endocytosed, targeted to endosomes, internalized into intraluminal vesicles (ILVs), and excreted in exosomes. A nonubiquitinatable mutant of Stx3 (Stx3-5R) fails to enter this pathway and leads to the inability of the apical exosomal cargo protein GPRC5B to enter the ILV/exosomal pathway. This suggests that ubiquitination of Stx3 leads to removal from the basolateral membrane to achieve apical polarity, that Stx3 plays a role in the recruitment of cargo to exosomes, and that the Stx3-5R mutant acts as a dominant-negative inhibitor. Human cytomegalovirus (HCMV) acquires its membrane in an intracellular compartment and we show that Stx3-5R strongly reduces the number of excreted infectious viral particles. Altogether these results suggest that Stx3 functions in the transport of specific proteins to apical exosomes and that HCMV exploits this pathway for virion excretion

Genome-Wide Mutagenesis Reveals That ORF7 Is a Novel VZV Skin-Tropic Factor

The Varicella Zoster Virus (VZV) is a ubiquitous human alpha-herpesvirus that is the causative agent of chicken pox and shingles. Although an attenuated VZV vaccine (v-Oka) has been widely used in children in the United States, chicken pox outbreaks are still seen, and the shingles vaccine only reduces the risk of shingles by 50%. Therefore, VZV still remains an important public health concern. Knowledge of VZV replication and pathogenesis remains limited due to its highly cell-associated nature in cultured cells, the difficulty of generating recombinant viruses, and VZV's almost exclusive tropism for human cells and tissues. In order to circumvent these hurdles, we cloned the entire VZV (p-Oka) genome into a bacterial artificial chromosome that included a dual-reporter system (GFP and luciferase reporter genes). We used PCR-based mutagenesis and the homologous recombination system in the E. coli to individually delete each of the genome's 70 unique ORFs. The collection of viral mutants obtained was systematically examined both in MeWo cells and in cultured human fetal skin organ samples. We use our genome-wide deletion library to provide novel functional annotations to 51% of the VZV proteome. We found 44 out of 70 VZV ORFs to be essential for viral replication. Among the 26 non-essential ORF deletion mutants, eight have discernable growth defects in MeWo. Interestingly, four ORFs were found to be required for viral replication in skin organ cultures, but not in MeWo cells, suggesting their potential roles as skin tropism factors. One of the genes (ORF7) has never been described as a skin tropic factor. The global profiling of the VZV genome gives further insights into the replication and pathogenesis of this virus, which can lead to improved prevention and therapy of chicken pox and shingles

C4b Binding Protein Binds to CD154 Preventing CD40 Mediated Cholangiocyte Apoptosis: A Novel Link between Complement and Epithelial Cell Survival

Activation of CD40 on hepatocytes and cholangiocytes is critical for amplifying Fas-mediated apoptosis in the human liver. C4b-Binding Protein (C4BP) has been reported to act as a potential surrogate ligand for CD40, suggesting that it could be involved in modulating liver epithelial cell survival. Using surface plasmon resonance (BiaCore) analysis supported by gel filtration we have shown that C4BP does not bind CD40, but it forms stable high molecular weight complexes with soluble CD40 ligand (sCD154). These C4BP/sCD154 complexes bound efficiently to immobilised CD40, but when applied to cholangiocytes they failed to induce apoptosis or proliferation or to activate NFkB, AP-1 or STAT 3, which are activated by sCD154 alone. Thus C4BP can modulate CD40/sCD154 interactions by presenting a high molecular weight multimeric sCD154/C4BP complex that suppresses critical intracellular signalling pathways, permitting cell survival without inducing proliferation. Immunohistochemistry demonstrated co-localisation and enhanced expression of C4BP and CD40 in human liver cancers. These findings suggest a novel pathway whereby components of the complement system and TNF ligands and receptors might be involved in modulating epithelial cell survival in chronic inflammation and malignant disease

Time-resolved crystallography using the Hadamard transform

YesWe describe a method for performing time-resolved X-ray crystallographic experiments based on the Hadamard transform, in which time resolution is defined by the underlying periodicity of the probe pulse sequence, and signal/noise is greatly improved over that for the fastest pump-probe experiments depending on a single pulse. This approach should be applicable on standard synchrotron beamlines and will enable high-resolution measurements of protein and small-molecule structural dynamics. It is also applicable to other time-resolved measurements where a probe can be encoded, such as pump-probe spectroscopy.Wellcome Trust 4-year PhD program “The Molecular Basis of Biological Mechanisms” 089312/Z/09/Z. This work was also supported by the EPSRC Award “Dynamic Structural Science at the Research Complex at Harwell” EP/I01974X/1 and by BBSRC Award BB/H001905/1

Dual Infection and Superinfection Inhibition of Epithelial Skin Cells by Two Alphaherpesviruses Co-Occur in the Natural Host

Hosts can be infected with multiple herpesviruses, known as superinfection; however, superinfection of cells is rare due to the phenomenon known as superinfection inhibition. It is believed that dual infection of cells occurs in nature, based on studies examining genetic exchange between homologous alphaherpesviruses in the host, but to date, this has not been directly shown in a natural model. In this report, gallid herpesvirus 2 (GaHV-2), better known as Marek’s disease virus (MDV), was used in its natural host, the chicken, to determine whether two homologous alphaherpesviruses can infect the same cells in vivo. MDV shares close similarities with the human alphaherpesvirus, varicella zoster virus (VZV), with respect to replication in the skin and exit from the host. Recombinant MDVs were generated that express either the enhanced GFP (eGFP) or monomeric RFP (mRFP) fused to the UL47 (VP13/14) herpesvirus tegument protein. These viruses exhibited no alteration in pathogenic potential and expressed abundant UL47-eGFP or -mRFP in feather follicle epithelial cells in vivo. Using laser scanning confocal microscopy, it was evident that these two similar, but distinguishable, viruses were able to replicate within the same cells of their natural host. Evidence of superinfection inhibition was also observed. These results have important implications for two reasons. First, these results show that during natural infection, both dual infection of cells and superinfection inhibition can co-occur at the cellular level. Secondly, vaccination against MDV with homologous alphaherpesvirus like attenuated GaHV-2, or non-oncogenic GaHV-3 or meleagrid herpesvirus (MeHV-1) has driven the virus to greater virulence and these results implicate the potential for genetic exchange between homologous avian alphaherpesviruses that could drive increased virulence. Because the live attenuated varicella vaccine is currently being administered to children, who in turn could be superinfected by wild-type VZV, this could potentiate recombination events of VZV as well