Life, but not as we know it: exploring RNA viral diversity in soils through viromics

2020 ◽  
Author(s):  
Luke Hillary ◽  
Evelien Adriaenssens ◽  
Davey Jones ◽  
James McDonald
Keyword(s):  
Method Development ◽  
Viral Diversity ◽  
Dna Viruses ◽  
Holistic View ◽  
Viral Ecology ◽  
Global Context ◽  
Soil Microbial ◽  
Soil Ecosystems ◽  
Viral Communities ◽  
The Uk

<p>Viruses play a crucial and underexplored role in soil microbial ecosystems, but soil viral ecology has focused exclusively on DNA viruses. The role of RNA viruses in soil ecosystems has therefore been largely overlooked, despite their significant impact on public health and food security. Here, we report the first ever study to apply viromics to survey soil RNA viral communities from five sites along an altitudinal primary productivity gradient in the UK. We identified over 3,000 viral sequences, of which over half were unclassified, and newly identified viruses were placed in a global context by the phylogenetic comparison of their RNA-dependent RNA polymerase genes. Unlike DNA viral communities, the RNA viromes were heavily dominated by viruses of eukaryotes, including pathogens of plants, fungi, vertebrates and invertebrates. Sampling sites showed minimal similarity in viral community composition, suggesting that we have just scratched the surface of soil RNA viral diversity. Wider sequencing efforts and method development are required to further explore soil RNA viromes and understand their ecological function; however, this study represents an important step towards the characterisation of soil viral communities and interactions with their microbial hosts, which will provide a more holistic view of the biology of economically and ecologically important soils.</p>

scholarly journals Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics

2019 ◽  
Vol 93 (11) ◽  
Author(s):  
Rowena Chong ◽  
Mang Shi ◽  
Catherine E. Grueber ◽  
Edward C. Holmes ◽  
Carolyn J. Hogg ◽  
...  
Keyword(s):  
Endangered Species ◽  
Population Decline ◽  
Significant Risk ◽  
Rabbit Hemorrhagic Disease Virus ◽  
Viral Diversity ◽  
Hemorrhagic Disease ◽  
Tasmanian Devil ◽  
Dna Viruses ◽  
Viral Communities ◽  
Devil Facial Tumor Disease

ABSTRACT The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumor disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and metatranscriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from two captive and four wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses, and a gammaherpesvirus, were identified, as well as known mammalian pathogens such as rabbit hemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with metatranscriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and metatranscriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and metatranscriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample. IMPORTANCE The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.

scholarly journals Investigating the viral ecology of global bee communities with high-throughput metagenomics

2018 ◽  
Author(s):  
David A. Galbraith ◽  
Zachary L. Fuller ◽  
Axel Brockmann ◽  
Maryann Frazier ◽  
Mary W. Gikungu ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Dna Viruses ◽  
Viral Ecology ◽  
Multiple Regions ◽  
Viral Communities ◽  
Bee Communities ◽  
Ssdna Viruses ◽  
Viral Sequences ◽  
Bee Viruses

ABSTRACTBee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate the impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 5 continents and Oceania. We developed a novel pipeline to rapidly, inexpensively, and robustly screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences corresponding to (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 29 represented by >0.1 % of the reads in a given sample. These viruses and viral families were distributed across multiple regions and species. This study provides a robust pipeline for metagenomics analysis of viruses, and greatly expands our understanding of the diversity of viruses found in bee communities.

scholarly journals Diverse soil RNA viral communities have the potential to influence grassland ecosystems across multiple trophic levels

2021 ◽  
Author(s):  
Luke S. Hillary ◽  
Evelien M. Adriaenssens ◽  
David L. Jones ◽  
James E McDonald
Keyword(s):  
Phylogenetic Analyses ◽  
Soil Microbial Communities ◽  
Terrestrial Ecosystems ◽  
Trophic Levels ◽  
Soil Dna ◽  
Holistic View ◽  
Soil Microbial ◽  
Grassland Ecosystems ◽  
Viral Communities ◽  
Coastal Soils

Grassland ecosystems form 30-40% of total land cover and provide essential ecosystem services, including food production, flood mitigation and carbon storage. Their productivity is closely related to soil microbial communities, yet the role of viruses within these critical ecosystems is currently undercharacterised and in particular, our knowledge of soil RNA viruses is significantly limited. Here, we applied viromics to characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3,462 viral operational taxonomic units (vOTUs) and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited showed minimal similarity in viral community composition, but with >10-fold more vOTUs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses of viral sequences predicted broad host ranges including bacteria, plants, fungi, vertebrates and invertebrates, contrasting with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities therefore likely have the ability to influence soil ecosystems across multiple trophic levels. Our study represents an important step towards the characterisation of terrestrial RNA viral communities and the intricate interactions with their hosts, which will provide a more holistic view of the biology of economically and ecologically important terrestrial ecosystems.

Cerro del Hierro, Spain: the largest exposed early Cambrian palaeokarst

2020 ◽  
pp. 1-14
Author(s):  
Eduardo Mayoral ◽  
María Eugenia Dies Álvarez ◽  
José Antonio Gámez Vintaned ◽  
Rodolfo Gozalo ◽  
Eladio Liñán ◽  
...  
Keyword(s):  
South America ◽  
Mediterranean Region ◽  
Early Cambrian ◽  
Karst Development ◽  
Global Context ◽  
Tectonic Events ◽  
Extensional Tectonic ◽  
Geomorphological Processes ◽  
The Uk ◽  
Regressive Events

Abstract We study the largest exposed example of an early Cambrian palaeokarst, associated with laterites and developed during rifting of the Ossa–Morena Zone. The lithostratigraphy, biostratigraphy, facies and the genesis reflect episodes of sea-level fall (Cerro del Hierro Regression) related to tectonic events and palaeoclimate. This palaeokarst can be primarily considered as the result of early Cambrian polyphase karstification in an extensional tectonic regime, later modified by Neogene–Quaternary geomorphological processes. The event may correlate with other regressive events of a similar age in Spain, Italy, United Kingdom, South America and Australia. This episode also has local names (e.g. Cerro del Hierro Regression in the Mediterranean region; Woodlands Regression in the UK). It is sometimes accompanied by additional karst development outside of Spain that is compared and interpreted in a global context.

scholarly journals Two decades of neuroscience publication trends in Africa

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
M. B. Maina ◽  
U. Ahmad ◽  
H. A. Ibrahim ◽  
S. K. Hamidu ◽  
F. E. Nasr ◽  
...  
Keyword(s):  
Accurate Data ◽  
Publication Trends ◽  
Global Context ◽  
Current State ◽  
Neuroscience Research ◽  
Research Environments ◽  
New Policies ◽  
The Uk ◽  
Extract Information

AbstractNeuroscience research in Africa remains sparse. Devising new policies to boost Africa’s neuroscience landscape is imperative, but these must be based on accurate data on research outputs which is largely lacking. Such data must reflect the heterogeneity of research environments across the continent’s 54 countries. Here, we analyse neuroscience publications affiliated with African institutions between 1996 and 2017. Of 12,326 PubMed indexed publications, 5,219 show clear evidence that the work was performed in Africa and led by African-based researchers - on average ~5 per country and year. From here, we extract information on journals and citations, funding, international coauthorships and techniques used. For reference, we also extract the same metrics from 220 randomly selected publications each from the UK, USA, Australia, Japan and Brazil. Our dataset provides insights into the current state of African neuroscience research in a global context.

scholarly journals French Bulldogs differ to other dogs in the UK in propensity for many common disorders: a VetCompass study

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Dan G. O’Neill ◽  
Rowena M.A. Packer ◽  
Peter Francis ◽  
David B. Church ◽  
Dave C. Brodbelt ◽  
...  
Keyword(s):  
Health Issues ◽  
Specific Level ◽  
Holistic View ◽  
Skin Fold ◽  
Cohort Study Design ◽  
One Year ◽  
The One ◽  
The Uk ◽  
Modelling Methods ◽  
French Bulldog

Abstract Background The French Bulldog is a highly popular dog breed but is linked with many serious health issues. A holistic view of breed health in French Bulldogs would assist efforts to appreciate the overall health strengths and weaknesses in the French Bulldog and to take appropriate steps to mitigate these. Based on random sampling of French Bulldogs and non-French Bulldogs under primary veterinary care during 2016 within the VetCompass Programme, a cohort study design was used to estimate the one-year (2016) period prevalence of the most commonly diagnosed disorders in each group. Risk factor analysis used multivariable logistic regression modelling methods. Results The analysis included 2,781 French Bulldogs and 21,850 non-French Bulldogs. French Bulldogs were younger (1.51 years, IQR 0.86 – 2.77 vs. 4.48 years, IQR 1.94 – 8.14) (p < 0.001) and lighter (12.45 kg, IQR 11.00 – 14.03 versus 13.80 kg, IQR 8.10 – 25.12) (p < 0.001) than non-French Bulldogs. Of 43 common specific-level disorders across both groups, French Bulldogs had significantly increased adjusted odds of 20/43 (46.5 %) disorders and significantly reduced adjusted odds of 11/43 (25.6 %) disorders compared to non-French Bulldogs. Highly predisposed disorders in French Bulldogs included stenotic nares (OR 42.14; 95 % CI 18.50 to 95.99; p < 0.001), Brachycephalic Obstructive Airway Syndrome (OR 30.89; 95 % CI 20.91 to 45.64; p < 0.001), aural discharge (OR 14.40; 95 % CI 9.08 to 22.86; p < 0.001), skin fold dermatitis (OR 11.18; 95 % CI 7.19 to 17.40; p < 0.001) and dystocia (OR 9.13; 95 % CI 5.17 to 16.13; p < 0.001). At a grouped-level of diagnostic precision, French Bulldogs had increased adjusted odds of 12/32 (37.5 %) disorders and reduced adjusted odds of 6/32 (18.8 %) disorders compared to non-French Bulldogs. Conclusions These results identified ultra-predispositions with worryingly higher odds in French Bulldogs for several disorders, suggesting that the health of French Bulldogs has diverged substantially from, and may be lower than, the health of the wider non-French Bulldog population. Many of these predispositions are closely associated with the conformational extremes that define the French Bulldog breed. Shifting the typical conformation of the French Bulldog population towards a more moderate phenotype is proposed as a logical opportunity to reduce the serious health issues endemic in the French Bulldog breed.

scholarly journals Validation of the English Version of the Scale for Psychosocial Factors in Food Allergy and the Relationship with Mental Health, Quality of Life, and Self-Efficacy

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Rebecca C. Knibb ◽  
Aaron Cortes ◽  
Christopher Barnes ◽  
Carol Stalker
Keyword(s):  
Quality Of Life ◽  
Mental Health ◽  
Food Allergy ◽  
Psychosocial Factors ◽  
Self Efficacy ◽  
Holistic View ◽  
Parental Quality ◽  
The Uk ◽  
The Impact

Background. The Scale for Psychosocial Factors in Food Allergy (SPS-FA) is based on the biopsychosocial model of health and was developed and validated in Chile to measure the interaction between psychological variables and allergy symptoms in the child. We sought to validate this scale in an English speaking population and explore its relationship with parental quality of life, self-efficacy, and mental health. Methods. Parents (n=434) from the general population in the UK, who had a child with a clinical diagnosis of food allergy, completed the SPS-FA and validated scales on food allergy specific parental quality of life (QoL), parental self-efficacy, and general mental health. Findings. The SPS-FA had good internal consistency (alphas = .61–.86). Higher scores on the SPS-FA significantly correlated with poorer parental QoL, self-efficacy, and mental health. All predictors explained 57% of the variance in SPS-FA scores with QoL as the biggest predictor (β=.52). Discussion. The SPS-FA is a valid scale for use in the UK and provides a holistic view of the impact of food allergy on the family. In conjunction with health-related QoL measures, it can be used by health care practitioners to target care for patients and evaluate psychological interventions for improvement of food allergy management.

‘British Values Are Also Values All Around the World’: Teaching Fundamental British Values through a Human Rights Lens

2020 ◽  
Author(s):  
Alison E C Struthers ◽  
Julie Mansuy
Keyword(s):  
Human Rights ◽  
Primary Schools ◽  
Formal Education ◽  
National Level ◽  
Formal Schooling ◽  
Desire For Children ◽  
Global Citizens ◽  
Global Context ◽  
National Values ◽  
The Uk

Abstract Since 2014, the promotion of Fundamental British Values (FBV) has been a requirement across formal schooling in England. The agenda has, however, faced criticism from various stakeholders. Much of this denunciation has been directed at the opaque nature of FBV, but the agenda is problematic for more concerning reasons. It is arguable that, in light of the current threat from ethno-nationalism, frameworks such as FBV that focus on a particular definition and formulation of national values run the risk of being interpreted in a manner that is exclusionary and liable to ‘other’ different ethnic groups in the classroom. The FBV framework furthermore overlooks the fact that the UK isalready subject to numerous international human rights obligations, including many that mandate the provision of holistic and effective human rights education at all levels of formal education. This article therefore draws upon the findings of a pilot study conducted with Year 5 learners in four primary schools in the West Midlands showing that teaching about human rights through the FBV agenda is possible, by linking discussion of values at the national level to broader human rights principles. Such an approach satisfies the government’s desire for children to learn about FBV, whilst highlighting that these values also exist in a global context. This, in turn, is likely to be a more effective way of encouraging learners to be global citizens who will contribute to the building of a broader culture that is respectful of human rights.

scholarly journals Managing risk for auto warranties

2019 ◽  
Vol 36 (7) ◽  
pp. 1088-1105
Author(s):  
Ahmed M. Aljazea ◽  
Shaomin Wu
Keyword(s):  
Human Error ◽  
Decision Makers ◽  
Holistic View ◽  
Content Type ◽  
Related Data ◽  
Customer Dissatisfaction ◽  
Managing Risk ◽  
Warranty Costs ◽  
Warranty Service ◽  
The Uk

Purpose The purpose of this paper is threefold: first, to analyse the existing work of warranty risk management (WaRM); second, to develop a generic WaRM framework; and third, to design a generic taxonomy for warranty hazards from a warranty chain perspective. Design/methodology/approach To understand the top warranty hazards, the authors designed a questionnaire, received 40 responses from the warranty decision makers (WDM) in the automotive industry in the UK and then analysed the responses. Findings The assembly process capability at suppliers is the top contributor to warranty incidents from the suppliers’ and original equipment manufacturers’ (OEMs’) viewpoints. The human error at different stages of the product lifecycle contributes to the occurrence of warranty incidents. The collaboration among parties, particularly, the accessibility to warranty-related data between parties (i.e. suppliers, OEM and dealers), is limited. Customers’ fraud contributes more to warranty costs than warranty services providers’ fraud. The top contributors to customer dissatisfaction relating to warranty are the warranty service time and service quality. Research limitations/implications The questionnaires were used to collect data in the UK, which implies the research outcomes of this paper may only reflect the UK area. Practical implications The WaRM framework and taxonomy proposed in this paper provide WDM with a holistic view to identifying the top contributors to warranty incidents. With them, the decision makers will be able to allocate the required fund and efforts more effectively. Originality/value This paper contributes to the literature by providing the first work of systematically analysing the top contributors to warranty incidents and costs and by providing a WaRM framework.

Comparative viromes of Culicoides and mosquitoes reveal their consistency and diversity in viral profiles

2020 ◽  
Author(s):  
Lin Liu ◽  
Qin Shen ◽  
Nan Li ◽  
Yuwen He ◽  
Na Han ◽  
...  
Keyword(s):  
Spatiotemporal Distribution ◽  
Viral Diversity ◽  
Emerging Viruses ◽  
Biting Midges ◽  
Viral Ecology ◽  
Pathogenic Viruses

Abstract The genus Culicoides includes biting midges, some of which are vectors for viruses that cause diseases in humans and animals. Knowledge of the roles of Culicoides in viral ecology is inadequate. We collected ~300 000 samples of Culicoides and mosquitoes in 15 representative regions within Yunnan, China. Using mosquitoes as reference vectors, we designed a comparative virome strategy to study the viral composition, diversity, hosts and spatiotemporal distribution of Culicoides. A map of viromes in Culicoides and mosquitoes in Yunan province, China, was constructed. At the same locations, Culicoides and mosquitoes usually share a similar viral diversity. At least 10 important pathogenic viruses were detected from Culicoides. Many novel viruses were discovered, including 21 segmented viruses of Flaviviridae, 180 viruses of Monjiviricetes and 130 viruses of Bunyavirales. The findings demonstrate that Culicoides is an important part of viral ecology and should be studied and monitored for potentially emerging viruses.

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