Effect of dietary restriction and subsequent re-alimentation on the transcriptional profile of bovine ruminal epithelium

peer-reviewedCompensatory growth (CG) is utilised worldwide in beef production systems as a management approach to reduce feed costs. However the underlying biology regulating the expression of CG remains to be fully elucidated. The objective of this study was to examine the effect of dietary restriction and subsequent re-alimentation induced CG on the global gene expression profile of ruminal epithelial papillae. Holstein Friesian bulls (n = 60) were assigned to one of two groups: restricted feed allowance (RES; n = 30) for 125 days (Period 1) followed by ad libitum access to feed for 55 days (Period 2) or (ii) ad libitum access to feed throughout (ADLIB; n = 30). At the end of each period, 15 animals from each treatment were slaughtered and rumen papillae harvested. mRNA was isolated from all papillae samples collected. cDNA libraries were then prepared and sequenced. Resultant reads were subsequently analysed bioinformatically and differentially expressed genes (DEGs) are defined as having a Benjamini-Hochberg P value of <0.05. During re-alimentation in Period 2, RES animals displayed CG, growing at 1.8 times the rate of their ADLIB contemporary animals in Period 2 (P < 0.001). At the end of Period 1, 64 DEGs were identified between RES and ADLIB, with only one DEG identified at the end of Period 2. When analysed within RES treatment (RES, Period 2 v Period 1), 411 DEGs were evident. Genes identified as differentially expressed in response to both dietary restriction and subsequent CG included those involved in processes such as cellular interactions and transport, protein folding and gene expression, as well as immune response. This study provides an insight into the molecular mechanisms underlying the expression of CG in rumen papillae of cattle; however the results suggest that the role of the ruminal epithelium in supporting overall animal CG may have declined by day 55 of re-alimentation.SMW received financial assistance from Science Foundation Ireland (SFI) contract no 09/ RFP/GEN2447

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.This work is supported by the UK Medical Research Council (MRC); Chinese Academy of Medical Sciences(CAMS) Innovation Fund for Medical Sciences (CIFMS), China; National Institute for Health Research (NIHR)Oxford Biomedical Research Centre, and UK Researchand Innovation (UKRI)/NIHR through the UK Coro-navirus Immunology Consortium (UK-CIC). Sequencing of SARS-CoV-2 samples and collation of data wasundertaken by the COG-UK CONSORTIUM. COG-UK is supported by funding from the Medical ResearchCouncil (MRC) part of UK Research & Innovation (UKRI),the National Institute of Health Research (NIHR),and Genome Research Limited, operating as the Wellcome Sanger Institute. T.I.d.S. is supported by a Well-come Trust Intermediate Clinical Fellowship (110058/Z/15/Z). L.T. is supported by the Wellcome Trust(grant number 205228/Z/16/Z) and by theUniversity of Liverpool Centre for Excellence in Infectious DiseaseResearch (CEIDR). S.D. is funded by an NIHR GlobalResearch Professorship (NIHR300791). L.T. and S.C.M.are also supported by the U.S. Food and Drug Administration Medical Countermeasures Initiative contract75F40120C00085 and the National Institute for Health Research Health Protection Research Unit (HPRU) inEmerging and Zoonotic Infections (NIHR200907) at University of Liverpool inpartnership with Public HealthEngland (PHE), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford.L.T. is based at the University of Liverpool. M.D.P. is funded by the NIHR Sheffield Biomedical ResearchCentre (BRC – IS-BRC-1215-20017). ISARIC4C is supported by the MRC (grant no MC_PC_19059). J.C.K.is a Wellcome Investigator (WT204969/Z/16/Z) and supported by NIHR Oxford Biomedical Research Centreand CIFMS. The views expressed are those of the authors and not necessarily those of the NIHR or MRC

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

Determining the GmRIN4 Requirements of the Soybean Disease Resistance Proteins Rpg1b and Rpg1r Using a <i>Nicotiana glutinosa</i>-Based Agroinfiltration System

<div><p><i>Rpg1b</i> and <i>Rpg1r</i> are soybean disease resistance (<i>R</i>) genes responsible for conferring resistance to <i>Pseudomonas syringae</i> strains expressing the effectors AvrB and AvrRpm1, respectively. The study of these cloned genes would be greatly facilitated by the availability of a suitable transient expression system. The commonly used <i>Niciotiana benthamiana</i>-based system is not suitable for studying <i>Rpg1b</i> and <i>Rpg1r</i> function, however, because expression of AvrB or AvrRpm1 alone induces a hypersensitive response (HR), indicating that <i>N. benthamiana</i> contains endogenous <i>R</i> genes that recognize these effectors. To identify a suitable alternative host for transient expression assays, we screened 13 species of <i>Nicotiana</i> along with 11 accessions of <i>N. tabacum</i> for lack of response to transient expression of <i>AvrB</i> and <i>AvrRpm1</i>. We found that <i>N. glutinosa</i> did not respond to either effector and was readily transformable as determined by transient expression of β-glucuronidase. Using this system, we determined that <i>Rpg1b</i>-mediated HR in <i>N. glutinosa</i> required co-expression of <i>avrB</i> and a soybean ortholog of the Arabidopsis <i>RIN4</i> gene. All four soybean <i>RIN4</i> orthologs tested worked in the assay. In contrast, Rpg1r did not require co-expression of a soybean <i>RIN4</i> ortholog to recognize AvrRpm1, but recognition was suppressed by co-expression with AvrRpt2. These observations suggest that an endogenous <i>RIN4</i> gene in <i>N. glutinosa</i> can substitute for the soybean <i>RIN4</i> ortholog in the recognition of AvrRpm1 by Rpg1r.</p></div

Reconstituting the <i>Rpg1b</i>-mediated defense pathway in <i>N. glutinosa</i>.

<p>(<b>A</b>) Activation of Rpg1b by AvrB requires co-expression of a <i>GmRIN4</i> gene. The images shown are of typical responses displayed by <i>N. glutinosa</i> leaves expressing the combination of genes labeled on each image. (<b>B</b>) Quantification of <i>Rpg1b</i>-mediated HR when co-expressed with various combinations of <i>AvrB</i> and <i>GmRIN4</i> genes. The strength of Rpg1b-mediated HR was determined by the extent of leaf collapse in the infiltrated area. Based on the extent of leaf collapse in the infiltrated area, plant leaves were categorized into 4 classes: 0 (no collapse); 1 (less than one third collapsed); 2 (one third to two thirds collapsed); 3 (greater than two thirds collapsed). Images were taken and plant leaves were scored approximately 2 days after transgene induction. The number of leaves infiltrated and scored for each combination (n) is listed above each bar. This experiment was repeated 3 times with similar results.</p

<i>Nicotiana</i> accessions used in this study and their responses to AvrB and AvrRpm1.

<p>A (+) sign indicates that leaves expressing a given effector gave a stronger response than leaves expressing <i>GUS</i>, while a (-) sign indicates there was no difference between leaves expressing an effector and those expressing <i>GUS.</i> The observed morphologies in response to <i>Agrobacterium</i>-mediated transformation were leaf browning (b), shininess on the abaxial surface (s), leaf collapse (lc), and no response (nr). See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108159#pone.0108159.s001" target="_blank">Figure S1</a> for photographs of phenotypes. Each plant species/accession was tested at least 3 times with similar results.</p><p><i>Nicotiana</i> accessions used in this study and their responses to AvrB and AvrRpm1.</p

Reconstituting the <i>Rpg1r</i>-mediated defense pathway in <i>N. glutinosa</i>.

<p>(<b>A</b>) <i>Rpg1r</i>-<i>sYFP</i>-mediated HR does not require co-expression of a <i>GmRIN4</i> gene, but is suppressed by <i>avrRpt2</i>. The images shown are of typical responses displayed by <i>N. glutinosa</i> leaves expressing the combination of genes labeled on each image. (<b>B</b>) Quantification of <i>Rpg1r</i>-<i>sYFP</i> mediated HR. Responses were categorized as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108159#pone-0108159-g002" target="_blank">Figure 2</a>. C122A indicates the protease inactive form of AvrRpt2. Images were taken and plant leaves were scored approximately 2 days after transgene induction. The number of leaves infiltrated and scored for each combination (n) is listed above each bar. This experiment was repeated 3 times with similar results.</p

Localised invertebrate grazing moderates the effect of warming on competitive fungal interactions

Outcomes of competitive mycelial interactions determine saprotrophic fungal community composition and are regulated by biotic (e.g. invertebrate grazing) and abiotic (e.g. climate) factors. Selective grazing can moderate the effects of elevated temperature on fungal interactions. In natural systems, however, patchy and aggregative distributions of invertebrates exert unequal grazing pressures on competing fungi. We explored whether restricting grazing to the territory of one fungal competitor affected the potential of Oniscus asellus (Isopoda) to control the outcomes of interactions and mediate responses to elevated temperature. Restricted grazing prevented the dominance of any one fungal species in the majority of interactions and, indirectly, altered the influence of warming. The location of grazer restriction was, however, only important during certain interactions. Selective pressures reflected feeding preferences, but grazer location determined the extent of selective grazing pressure exerted. Aggregation of macro-invertebrate grazers appears important in maintaining multi-species assemblages of wood-decomposer fungi in a changing climate

Localised invertebrate grazing moderates the effect of warming on competitive fungal interactions

Outcomes of competitive mycelial interactions determine saprotrophic fungal community composition and are regulated by biotic (e.g. invertebrate grazing) and abiotic (e.g. climate) factors. Selective grazing can moderate the effects of elevated temperature on fungal interactions. In natural systems, however, patchy and aggregative distributions of invertebrates exert unequal grazing pressures on competing fungi. We explored whether restricting grazing to the territory of one fungal competitor affected the potential of Oniscus asellus (Isopoda) to control the outcomes of interactions and mediate responses to elevated temperature. Restricted grazing prevented the dominance of any one fungal species in the majority of interactions and, indirectly, altered the influence of warming. The location of grazer restriction was, however, only important during certain interactions. Selective pressures reflected feeding preferences, but grazer location determined the extent of selective grazing pressure exerted. Aggregation of macro-invertebrate grazers appears important in maintaining multi-species assemblages of wood-decomposer fungi in a changing climate