Plant DNA Barcodes Can Accurately Estimate Species Richness in Poorly Known Floras

Extent: 9p.BACKGROUND: Widespread uptake of DNA barcoding technology for vascular plants has been slow due to the relatively poor resolution of species discrimination (~70%) and low sequencing and amplification success of one of the two official barcoding loci, matK. Studies to date have mostly focused on finding a solution to these intrinsic limitations of the markers, rather than posing questions that can maximize the utility of DNA barcodes for plants with the current technology. METHODOLOGY/PRINCIPAL FINDINGS: Here we test the ability of plant DNA barcodes using the two official barcoding loci, rbcLa and matK, plus an alternative barcoding locus, trnH-psbA, to estimate the species diversity of trees in a tropical rainforest plot. Species discrimination accuracy was similar to findings from previous studies but species richness estimation accuracy proved higher, up to 89%. All combinations which included the trnH-psbA locus performed better at both species discrimination and richness estimation than matK, which showed little enhanced species discriminatory power when concatenated with rbcLa. The utility of the trnH-psbA locus is limited however, by the occurrence of intraspecific variation observed in some angiosperm families to occur as an inversion that obscures the monophyly of species. CONCLUSIONS/SIGNIFICANCE: We demonstrate for the first time, using a case study, the potential of plant DNA barcodes for the rapid estimation of species richness in taxonomically poorly known areas or cryptic populations revealing a powerful new tool for rapid biodiversity assessment. The combination of the rbcLa and trnH-psbA loci performed better for this purpose than any two-locus combination that included matK. We show that although DNA barcodes fail to discriminate all species of plants, new perspectives and methods on biodiversity value and quantification may overshadow some of these shortcomings by applying barcode data in new ways.Craig Costion, Andrew Ford, Hugh Cross, Darren Crayn, Mark Harrington and Andrew Low

The relationship between international trade and non-nutritional health outcomes : A systematic review of quantitative studies

Markets throughout the world have been reducing barriers to international trade and investment in recent years. The resulting increases in levels of international trade and investment have subsequently generated research interest into the potential population health impact. We present a systematic review of quantitative studies investigating the relationship between international trade, foreign direct investment and non-nutritional health outcomes. Articles were systematically collected from the SCOPUS, PubMed, EconLit and Web of Science databases. Due to the heterogeneous nature of the evidence considered, the 16 included articles were subdivided into individual level data analyses, selected country analyses and international panel analyses. Articles were then quality assessed using a tool developed as part of the project. Nine of the studies were assessed to be high quality, six as medium quality, and one as low quality. The evidence from the quantitative literature suggests that overall, there appears to be a beneficial association between international trade and population health. There was also evidence of the importance of foreign direct investment, yet a lack of research considering the direction of causality. Taken together, quantitative research into the relationship between trade and non-nutritional health indicates trade to be beneficial, yet this body of research is still in its infancy. Future quantitative studies based on this foundation will provide a stronger basis on which to inform relevant national and international institutions about the health consequences of trade policies

Intestinal intraepithelial lymphocyte-enterocyte crosstalk regulates production of bactericidal angiogenin 4 by Paneth cells upon microbial challenge

Antimicrobial proteins influence intestinal microbial ecology and limit proliferation of pathogens, yet the regulation of their expression has only been partially elucidated. Here, we have identified a putative pathway involving epithelial cells and intestinal intraepithelial lymphocytes (iIELs) that leads to antimicrobial protein (AMP) production by Paneth cells. Mice lacking γδ iIELs (TCRδ(-/-)) express significantly reduced levels of the AMP angiogenin 4 (Ang4). These mice were also unable to up-regulate Ang4 production following oral challenge by Salmonella, leading to higher levels of mucosal invasion compared to their wild type counterparts during the first 2 hours post-challenge. The transfer of γδ iIELs from wild type (WT) mice to TCRδ(-/-) mice restored Ang4 production and Salmonella invasion levels were reduced to those obtained in WT mice. The ability to restore Ang4 production in TCRδ(-/-) mice was shown to be restricted to γδ iIELs expressing Vγ7-encoded TCRs. Using a novel intestinal crypt co-culture system we identified a putative pathway of Ang4 production initiated by exposure to Salmonella, intestinal commensals or microbial antigens that induced intestinal epithelial cells to produce cytokines including IL‑23 in a TLR-mediated manner. Exposure of TCR-Vγ7(+) γδ iIELs to IL-23 promoted IL‑22 production, which triggered Paneth cells to secrete Ang4. These findings identify a novel role for γδ iIELs in mucosal defence through sensing immediate epithelial cell cytokine responses and influencing AMP production. This in turn can contribute to the maintenance of intestinal microbial homeostasis and epithelial barrier function, and limit pathogen invasion

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

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

The methodologies, geographies, and technologies of energy justice: a systematic and comprehensive review

The energy justice literature has seen a rapid surge in both academic and practical popularity. However, there has been less systematic reflection on the research conducted so far, its scope or contribution, nor what it might mean for the future of the concept. To provide insights, this paper presents the results of a systematic and comprehensive review of 155 peer-reviewed articles published across eight databases between January 2008 and December 2019. The aim is firstly to review the current state of the art in the energy justice literature and, secondly, to present findings that support novel recommendations with the potential to enhance the impact of energy justice research, including applications in the economic and planning policy sectors. Critically, our study demonstrates that the literature lacks diversity in its author basis and research design. By contrast, conceptual frameworks and the geographies and technologies of global energy injustice are proliferating. These results illustrate that energy justice has power and agency as a tool. It can act as a protagonist in energy research, provoking researchers to remain reflexively normative and active in identifying injustices and vulnerabilities, and it can act as a promising progenitor, creating new research methods and themes

The cost-effectiveness of pulmonary maintenance schedules

BACKGROUND: Chronic obstructive pulmonary disease (COPD) affects approximately 3 million people in the UK. An 8-week pulmonary rehabilitation (PR) course is recommended under current guidelines. However, studies show that initial benefits diminish over time. OBJECTIVE: We present here an economic evaluation conducted alongside a randomised controlled trial (RCT) of a low-intensity maintenance programme over a time horizon of 1 year delivered in UK primary and secondary care settings. METHODS: Patients with COPD who completed at least 60 % of a standard 8-week PR programme were randomised to a 2-h maintenance session at 3, 6 and 9 months (n = 73) or treatment as usual (n = 75). Outcomes were change in Chronic Respiratory Questionnaire (CRQ) score, EQ-5D-based QALYs, cost (price year 2014) to the UK NHS and social services over the 12 months following initial PR, and incremental cost-effectiveness ratios (ICERs). RESULTS: At 12 months, incremental cost to the NHS and social services was -£204.04 (95 % CI -£1522 to £1114). Incremental CRQ and QALY gains were -0.007 (-0.461 to 0.447) and +0.015 (-0.050 to 0.079), respectively. Based on point estimates, PR maintenance therefore dominates treatment as usual from the perspective of the NHS and social services in terms of cost per QALY gained. Whether it is cost effective in terms of CRQ depends on whether the £204 per patient could be reinvested elsewhere to a CRQ gain of greater than 0.007. However, there is much decision uncertainty: 95 % CIs around increments did not exclude zero, and there is a 72.9 % (72.5 %) probability that the ICER is below £20,000 (£30,000) per QALY. CONCLUSION: Future research should explore whether more intensive maintenance regimens offer benefit to patients at reasonable cost.This paper presents independent research funded by the National Institute for Health Research (NIHR) under its Research for Patient Benefit (RfPB) Programme (Grant Reference Number PB-PG-0408-16225).This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s40258-015-0199-