Extensive co-operation between the Epstein-Barr virus EBNA3 proteins in the manipulation of host gene expression and epigenetic chromatin modification.

Epstein-Barr virus (EBV) is able to drive the transformation of B-cells, resulting in the generation of lymphoblastoid cell lines (LCLs) in vitro. EBV nuclear proteins EBNA3A and EBNA3C are necessary for efficient transformation, while EBNA3B is dispensable. We describe a transcriptome analysis of BL31 cells infected with a series of EBNA3-knockout EBVs, including one deleted for all three EBNA3 genes. Using Affymetrix Exon 1.0 ST microarrays analysed with the MMBGX algorithm, we have identified over 1000 genes whose regulation by EBV requires one of the EBNA3s. Remarkably, a third of the genes identified require more than one EBNA3 for their regulation, predominantly EBNA3C co-operating with either EBNA3B, EBNA3A or both. The microarray was validated by real-time PCR, while ChIP analysis of a selection of co-operatively repressed promoters indicates a role for polycomb group complexes. Targets include genes involved in apoptosis, cell migration and B-cell differentiation, and show a highly significant but subtle alteration in genes involved in mitosis. In order to assess the relevance of the BL31 system to LCLs, we analysed the transcriptome of a set of EBNA3B knockout (3BKO) LCLs. Around a third of the genes whose expression level in LCLs was altered in the absence of EBNA3B were also altered in 3BKO-BL31 cell lines.Among these are TERT and TCL1A, implying that EBV-induced changes in the expression of these genes are not required for B-cell transformation. We also identify 26 genes that require both EBNA3A and EBNA3B for their regulation in LCLs. Together, this shows the complexity of the interaction between EBV and its host, whereby multiple EBNA3 proteins co-operate to modulate the behaviour of the host cell

Student Perspectives on E-Learning in a Malaysian Medical College One Year into the COVID-19 Pandemic: A Cross-Sectional Study

Background: During the coronavirus disease 2019 (COVID-19) pandemic, physical in-person classes in Newcastle University Medicine Malaysia (NUMed) were replaced with e-learning. Teaching in NUMed was being delivered online during COVID-19 pandemic for the last one and a half academic years (18 March 2020 – June 2021) due to the strict lockdowns and physical distancing measures in place, limited in-person sessions on campus, and disrupted hospital attachments. There was concern over the effectiveness and satisfaction with e-learning amongst our students, and how this affects their overall academic performance. Our study aims to explore students’ e-learning experiences and its perceived benefits and challenges during the pandemic. Methods: 285 students participated in this cross-sectional study using a convenience sampling method. Participants completed a self-administered online questionnaire via an email invitation between July 12th and August 12th, 2021 which comprised of sociodemographic characteristics and experiences with e-learning. The data was analysed using descriptive statistics and Spearman’s correlation tests were used to identify correlation between students’ e-learning experiences, the effects of e-learning, and academic performance. Results: Most students used laptops (n=275, 96.5%) for e-learning and owned at least two electronic devices (n=245, 86%). Over half of our students (n=148, 51.9%) reported their theoretical knowledge remains unchanged, while about three-quarters (n=213, 74.7%) perceived practical skills to have worsened. Students preferred paper-based exams (n=170, 59.6%) and objectively formatted online exams (n=193, 67.7%). Since transitioning to e-learning, the majority of students (n=207, 72.6%) reported difficulties studying online and were unsatisfied with their academic performance (n=166, 58.2%). Students preferred e-learning due to the lower risk of contracting COVID-19 (n=256, 89.8%), the convenience of online classes (n=244, 85.6%) and flexible schedules (n=219, 76.8%). However, the lack of patient contact (n=236, 82.8%), lecturer and peer interactions (n=234, 82.1%), and unreliable internet (n=201, 70.5%) made e-learning challenging. Students’ experiences were generally affected by multiple factors encompassing personal, lecturer, and environmental aspects. Conclusion: E-learning during the COVID-19 pandemic has negatively impacted students’ academic performance, particularly practical skills and performance satisfaction. Therefore, the university should look towards addressing e-learning constraints and providing adequate support to improve students’ educational experiences in the ongoing pandemic

Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose.

BackgroundUnderstanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production.ResultsWe analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds.ConclusionIn this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism

Managing Local Stressors for Coral Reef Condition and Ecosystem Services Delivery Under Climate Scenarios

Coral reefs provide numerous ecosystem goods and services, but are threatened by multiple environmental and anthropogenic stressors. To identify management scenarios that will reverse or mitigate ecosystem degradation, managers can benefit from tools that can quantify projected changes in ecosystem services due to alternative management options. We used a spatially-explicit biophysical ecosystem model to evaluate socio-ecological trade-offs of land-based vs. marine-based management scenarios, and local-scale vs. global-scale stressors and their cumulative impacts. To increase the relevance of understanding ecological change for the public and decision-makers, we used four ecological production functions to translate the model outputs into the ecosystem services: “State of the Reef,” “Trophic Integrity,” “Fisheries Production,” and “Fisheries Landings.” For a case study of Maui Nui, Hawai‘i, land-based management attenuated coral cover decline whereas fisheries management promoted higher total fish biomass. Placement of no-take marine protected areas (MPAs) across 30% of coral reef areas led to a reversal of the historical decline in predatory fish biomass, although this outcome depended on the spatial arrangement of MPAs. Coral cover declined less severely under strict sediment mitigation scenarios. However, the benefits of these local management scenarios were largely lost when accounting for climate-related impacts. Climate-related stressors indirectly increased herbivore biomass due to the shift from corals to algae and, hence, greater food availability. The two ecosystem services related to fish biomass increased under climate-related stressors but “Trophic Integrity” of the reef declined, indicating a less resilient reef. “State of the Reef” improved most and “Trophic Integrity” declined least under an optimistic global warming scenario and strict local management. This work provides insight into the relative influence of land-based vs. marine-based management and local vs. global stressors as drivers of changes in ecosystem dynamics while quantifying the tradeoffs between conservation- and extraction-oriented ecosystem services

Latent Epstein-Barr Virus Can Inhibit Apoptosis in B Cells by Blocking the Induction of NOXA Expression

Latent Epstein-Barr virus (EBV) has been shown to protect Burkitt's lymphoma-derived B cells from apoptosis induced by agents that cause damage to DNA, in the context of mutant p53. This protection requires expression of the latency-associated nuclear proteins EBNA3A and EBNA3C and correlates with their ability to cooperate in the repression of the gene encoding the pro-apoptotic, BH3-only protein BIM. Here we confirm that latent EBV in B cells also inhibits apoptosis induced by two other agents – ionomycin and staurosporine – and show that these act by a distinct pathway that involves a p53-independent increase in expression of another pro-apoptotic, BH3-only protein, NOXA. Analyses employing a variety of B cells infected with naturally occurring EBV or B95.8 EBV-BAC recombinant mutants indicated that the block to NOXA induction does not depend on the well-characterized viral latency-associated genes (EBNAs 1, 2, 3A, 3B, 3C, the LMPs or the EBERs) or expression of BIM. Regulation of NOXA was shown to be at least partly at the level of mRNA and the requirement for NOXA to induce cell death in this context was demonstrated by NOXA-specific shRNA-mediated depletion experiments. Although recombinant EBV with a deletion removing the BHRF1 locus – that encodes the BCL2-homologue BHRF1 and three microRNAs – partially abrogates protection against ionomycin and staurosporine, the deletion has no effect on the EBV-mediated block to NOXA accumulation

Safety, immunogenicity, and reactogenicity of BNT162b2 and mRNA-1273 COVID-19 vaccines given as fourth-dose boosters following two doses of ChAdOx1 nCoV-19 or BNT162b2 and a third dose of BNT162b2 (COV-BOOST): a multicentre, blinded, phase 2, randomised trial

Background Some high-income countries have deployed fourth doses of COVID-19 vaccines, but the clinical need, effectiveness, timing, and dose of a fourth dose remain uncertain. We aimed to investigate the safety, reactogenicity, and immunogenicity of fourth-dose boosters against COVID-19.Methods The COV-BOOST trial is a multicentre, blinded, phase 2, randomised controlled trial of seven COVID-19 vaccines given as third-dose boosters at 18 sites in the UK. This sub-study enrolled participants who had received BNT162b2 (Pfizer-BioNTech) as their third dose in COV-BOOST and randomly assigned them (1:1) to receive a fourth dose of either BNT162b2 (30 µg in 0·30 mL; full dose) or mRNA-1273 (Moderna; 50 µg in 0·25 mL; half dose) via intramuscular injection into the upper arm. The computer-generated randomisation list was created by the study statisticians with random block sizes of two or four. Participants and all study staff not delivering the vaccines were masked to treatment allocation. The coprimary outcomes were safety and reactogenicity, and immunogenicity (antispike protein IgG titres by ELISA and cellular immune response by ELISpot). We compared immunogenicity at 28 days after the third dose versus 14 days after the fourth dose and at day 0 versus day 14 relative to the fourth dose. Safety and reactogenicity were assessed in the per-protocol population, which comprised all participants who received a fourth-dose booster regardless of their SARS-CoV-2 serostatus. Immunogenicity was primarily analysed in a modified intention-to-treat population comprising seronegative participants who had received a fourth-dose booster and had available endpoint data. This trial is registered with ISRCTN, 73765130, and is ongoing.Findings Between Jan 11 and Jan 25, 2022, 166 participants were screened, randomly assigned, and received either full-dose BNT162b2 (n=83) or half-dose mRNA-1273 (n=83) as a fourth dose. The median age of these participants was 70·1 years (IQR 51·6–77·5) and 86 (52%) of 166 participants were female and 80 (48%) were male. The median interval between the third and fourth doses was 208·5 days (IQR 203·3–214·8). Pain was the most common local solicited adverse event and fatigue was the most common systemic solicited adverse event after BNT162b2 or mRNA-1273 booster doses. None of three serious adverse events reported after a fourth dose with BNT162b2 were related to the study vaccine. In the BNT162b2 group, geometric mean anti-spike protein IgG concentration at day 28 after the third dose was 23 325 ELISA laboratory units (ELU)/mL (95% CI 20 030–27 162), which increased to 37 460 ELU/mL (31 996–43 857) at day 14 after the fourth dose, representing a significant fold change (geometric mean 1·59, 95% CI 1·41–1·78). There was a significant increase in geometric mean anti-spike protein IgG concentration from 28 days after the third dose (25 317 ELU/mL, 95% CI 20 996–30 528) to 14 days after a fourth dose of mRNA-1273 (54 936 ELU/mL, 46 826–64 452), with a geometric mean fold change of 2·19 (1·90–2·52). The fold changes in anti-spike protein IgG titres from before (day 0) to after (day 14) the fourth dose were 12·19 (95% CI 10·37–14·32) and 15·90 (12·92–19·58) in the BNT162b2 and mRNA-1273 groups, respectively. T-cell responses were also boosted after the fourth dose (eg, the fold changes for the wild-type variant from before to after the fourth dose were 7·32 [95% CI 3·24–16·54] in the BNT162b2 group and 6·22 [3·90–9·92] in the mRNA-1273 group).Interpretation Fourth-dose COVID-19 mRNA booster vaccines are well tolerated and boost cellular and humoral immunity. Peak responses after the fourth dose were similar to, and possibly better than, peak responses after the third dose

Modulation of apoptotic pathways in B cells by Epstein-Barr virus

Epstein-Barr virus (EBV) is a gammaherpesvirus associated with several human malignancies including Burkitt’s lymphoma (BL). Latent EBV infection protects BL cell lines from apoptosis induced by genotoxic drugs including cisplatin, roscovitine and nocodazole. This protection is dependent on the co-expression of EBNA3A and EBNA3C, which downregulate the pro-apoptotic Bim, but is independent of the tumour suppressor p53 (Anderton et at., Oncogene (2008) 27, 421-33). However, using the calcium ionophore ionomycin as the apoptosis-inducing agent, another pathway by which BL cells undergo apoptosis has been identified. This is independent of both Bim and p53, but can also be blocked by latent EBV. By assessing the response of a panel BL cells expressing restricted sets of viral latent genes to ionomycin, it was shown that EBNA1, EBNA2, LMP2A and LMP2B, full-length EBNA-LP, EBNA3A, EBNA3B, EBNA3C and EBERs are not required for ionomycin-resistance although LMP1 can provide partial protection. Recombinant and revertant EBV-BACs were constructed to investigate the contribution of the EBNA3 locus and the BHRF1 locus to ionomycin-resistance. It was determined that the EBNA3 locus is not involved in rescue from ionomycin. However, loss of the BHRF1 locus partially abrogates protection against ionomycin-induced apoptosis. The pro-apoptotic BH3-only protein Noxa is consistently induced at the level of protein and mRNA in BL cells sensitive to ionomycin irrespective of p53 status. Suppression of Noxa by shRNA-expressing lentiviruses attenuates ionomycin- induced apoptosis, indicating that EBV confers resistance at least in part by inhibiting the accumulation of Noxa through a yet to be identified mechanism. This Noxa- associated apoptotic pathway is also activated by the protein kinase inhibitor staurosporine. Further investigation using the DNA topoisomerase II inhibitor etoposide indicates that in addition EBNA3A and EBNA3C, EBV can also confer resistance against genotoxic agents through the BHRF1 locus in a Bim-independent manner.Open Acces

Modulation of apoptotic pathways in B cell by Epstein-Barr virus

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Supporting Academic Self-Efficacy, Academic Motivation, and Information Literacy for Students in Tertiary Institutions

Academic self-efficacy, academic motivation, and information literacy are considered crucial to fostering student learning in tertiary institutions. The aim of this study was to examine the information literacy self-efficacy and academic motivation of college students and to identify the predictors of information literacy self-efficacy. The participants included students in their junior and senior years studying nursing, healthcare, and non-healthcare disciplines at a self-financing institution. Data were collected through a quota sampling method using a questionnaire. In total, 504 valid questionnaires were returned. The results indicated a moderate positive correlation between the two variables. The nursing students were found to have lower information literacy self-efficacy scores than those from the other disciplines. The results from a multiple regression analysis showed that the following factors are predictors of information literacy self-efficacy: being a nursing student, total scores for academic motivation, and owning a personal computer. Nurse educators are encouraged to strengthen the information literacy skills of nursing students, as this is an essential component in the application of evidence-based practices in the nursing profession