Look away now! Defensive processing and unrealistic optimism by level of alcohol consumption

OBJECTIVE

Health risk information is insufficient as a means of reducing alcohol use, particularly when it evokes negative emotional states amongst those for whom it is most personally relevant. Appraisal biases, or 'defensive processing', may be employed to mitigate the psychological discomfort posed by such information. Few studies have evaluated the role of defensive processing in people with different levels of alcohol consumption.

DESIGN

Online participants (n = 597) completed measures of defensive processing of a health risk infographic, perceived susceptibility and severity of alcohol use, efficacy for resisting alcohol use, unrealistic optimism, the Alcohol Use Disorder Identification Test - Consumption (AUDIT-C) and demographics.

RESULTS

AUDIT-C scores were positively and linearly associated with all defensive processing measures (Pearson's correlation r from.16 to .36), threat and susceptibility (r = .16) and unrealistic optimism (r = .50). AUDIT-C scores were also negatively associated with efficacy for controlling alcohol use (r = -0.48).

CONCLUSION

People with alcohol use disorder (AUD) engaged in much more defensive processing of alcohol-related messages, offering an explanation for why such messages are limited at eliciting behaviour change. High levels of unrealistic optimism in people with alcohol use disorder may reflect low problem recognition in order to maintain a problem-free drinking identity.

Neurodevelopmental outcomes in children and adults with Fetal Valproate Spectrum Disorder: A contribution from the ConcePTION project

AIM

To describe the neurodevelopmental phenotype of older children and adults with a diagnosis of Fetal Valproate Spectrum Disorder (FVSD).

METHODS

In this cross-sectional study, 90 caregivers were recruited and completed a series of questionnaires regarding the neurodevelopmental outcomes of 146 individuals aged 7-37 years (M = 18.1), including individuals with a formal diagnosis of FVSD (n = 99), individuals exposed to Valproate but without an FVSD diagnosis (n = 24), and individuals not exposed to Valproate (N = 23). The mean dose of valproate exposure for individuals with an FVSD diagnosis was 1470 mg/day.

RESULTS

Individuals with a diagnosis of FVSD showed significantly higher levels of moderate (43.4%) and severe (14.4%) cognitive impairment than other groups (p = 0.003), high levels of required formal educational support (77.6%), and poorer academic competence than individuals not exposed to Valproate (p = 0.001). Overall psychosocial problems (p = 0.02), internalising problems (p = 0.05) and attention problems (p = 0.001), but not externalising problems, were elevated in individuals with a diagnosis of FVSD. Rates of neurodevelopmental disorders, particularly autistic spectrum disorders (62.9%) and sensory problems (80.6%) are particularly central to the FVSD phenotype. There was no evidence of a statistical dose-dependent effect, possibly due to the high mean dose of exposure having a uniformly negative impact across the sample. Individuals with FVSD had required a significant number of health and child development services.

INTERPRETATION

Children and young adults with a diagnosis of FVSD are at an increased risk of a range of altered neurodevelopmental outcomes, highlighting the need for a multidisciplinary approach to clinical management across the lifespan.

Should we promote alcohol problems as a continuum? Implications for policy and practice

The highly heterogeneous nature of alcohol use and problems has presented significant challenges to those attempting to understand, treat or prevent what is commonly termed alcohol use disorder (AUD). However, any attempts to capture this complex phenomenon, including the various current criterion of AUD, come with a number of limitations. One particular limitation has been how alcohol problems are represented or understood in ways which do not capture the broad spectrum of alcohol use and harms and the many potential routes to prevention, treatment, and recovery. One possible response to this has been proposed as more explicitly framing or conceptualizing a continuum model of alcohol use and harms. In this commentary, we attempt to identify the key implications of a continuum model for policy and practice, examining the historical and current context of alcohol problem classifications and models. We argue a continuum model of alcohol use and problems holds a number of advantages for advancing public health goals, but also some potential limitations, both of which require further examination.

Identifying plant genes shaping microbiota composition in the barley rhizosphere

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes.

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.

The "alcoholic other": Harmful drinkers resist problem recognition to manage identity threat

OBJECTIVE

Harmful drinkers represent an important Alcohol Use Disorder (AUD) group in public health terms, accounting for significant health and social costs. However, harmful drinkers are characterized by low problem recognition; they tend to construct their drinking identity as positive and problem-free, actively setting themselves apart from the stigmatised 'alcoholic other'. As such, harmful drinkers rarely engage in treatment and represent an important opportunity for lower threshold interventions and self-change. The present study sought to explore AUD problem framing and stigma effects on problem recognition.

METHODS

Harmful drinkers without perceived addiction experience recruited online (n = 244, 54% male, 46% female, 96% British) were randomised to one of six conditions comprising beliefs about alcohol problems (control, continuum, binary disease model) and stigma (stigma, non-stigma), and completed measures relating to problem recognition.

RESULTS

As predicted, results found that harmful drinkers exposed to binary disease model beliefs and stigmatising language had significantly lower problem recognition than those in other conditions. However, no support was found for the prediction that continuum beliefs would be associated with higher problem recognition. Results suggest that the interaction of binary disease model beliefs and stigma prompted alcoholic label avoidance.

CONCLUSION

These findings suggest that problem framing has important consequences for harmful drinkers. Implications for behaviour change amongst harmful drinkers through mechanisms of problem framing and identity are discussed.

Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

Chemical Exposure-Induced Developmental Neurotoxicity in Head-Regenerating Schmidtea Mediterranea

The growing number of commercially-used chemicals that are under-evaluated for developmental neurotoxicity (DNT) combined with the difficulty in describing the etiology of exposure-related neurodevelopmental toxicity has created a reticent threat to human health. Current means of screening chemicals for DNT are limited to expensive, time-consuming, and labor-intensive traditional laboratory animal models. In this study, we hypothesize that exposed head regenerating planarian flatworms can effectively and efficiently categorize DNT in known developmental neurotoxins (ethanol and bisphenol A (BPA)). Planarian flatworms are an established alternative animal model for neurodevelopmental studies and have remarkable regenerative abilities allowing neurodevelopment to be induced via head resection. Here, we observed changes in photophobic behavior and central nervous system (CNS) morphology to evaluate the impact of exposure to low concentrations of ethanol, BPA, and BPA industry alternatives bisphenol F (BPF), and bisguaiacol (BG) on neurodevelopment. Our studies show that exposure to 1% v/v ethanol during regeneration induces a recoverable 48-hour delay in the development of proper CNS integrity, which aligns with behavioral assessments of cognitive ability. Exposure to BPA and its alternatives induced deviations to neurodevelopment in a range of severities, distinguished by suppressions, delays, or a combination of the two. These results suggest that quick and inexpensive behavioral assessments are a viable surrogate for tedious and costly immunostaining studies, equipping more utility and resolution to the planarian model for neurodevelopmental toxicity in the future of mass chemical screening. These studies demonstrate that behavioral phenotypes observed following chemical exposure are classifiable and also temporally correlated to the anatomical development of the central nervous system in planaria. This will facilitate and accelerate toxicological screening assays with this alternative animal model.

Draft genome assemblies for tree pathogens Phytophthora pseudosyringae and Phytophthora boehmeriae

Species of Phytophthora, plant pathogenic eukaryotic microbes, can cause disease on many tree species. Genome sequencing of species from this genus has helped to determine components of their pathogenicity arsenal. Here, we sequenced genomes for two widely distributed species, Phytophthora pseudosyringae and Phytophthora boehmeriae, yielding genome assemblies of 49 and 40 Mb, respectively. We identified more than 270 candidate disease promoting RXLR effector coding genes for each species, and hundreds of genes encoding candidate plant cell wall degrading carbohydrate active enzymes (CAZymes). These data boost genome sequence representation across the Phytophthora genus, and form resources for further study of Phytophthora pathogenesis.

55 Are Virtual Journal Clubs A Viable Alternative in The Covid-19 Era?

Introduction

During the COVID-19 pandemic, face to face journal clubs have been curtailed due to Governmental guidance for social distancing. We present an example of a virtual journal club set up for Orthopaedic senior house officers (SHOs) & trainees in the North West Thames (NWT) Deanery from April to August 2020.

Method

Our aims were to establish a regular online journal club for orthopaedic trainees in NWT that successfully met the objectives of the more established face to face meetings. Assessment of each session was evaluated using a post attendance survey created using an established online generator.

Results

64.4% (16/25 participants) had not attended a virtual journal club before, with 100% (33/33) reporting that they would attend another virtual journal club. 39.4% (13/33) of attendees agreed or strongly agreed that they could participate in sessions over more conventional meetings. 24.2% (8/33) of participants reported experiencing technical issues during the sessions. 90.9% (30/33) of respondents reporting the virtual model to be more convenient than standard journal clubs.

Conclusions

The potential benefits of significantly increased accessibility increased visiting expert contribution whilst still adhering to government guidelines; weighed against marginally less effective teaching nonetheless results in an overall benefit.

Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae

Phytophthora species cause some of the most serious diseases of trees and threaten forests in many parts of the world. Despite the generation of genome sequence assemblies for over 10 tree-pathogenic Phytophthora species and improved detection methods, there are many gaps in our knowledge of how these pathogens interact with their hosts. To facilitate cell biology studies of the infection cycle we examined whether the tree pathogen Phytophthora kernoviae could infect the model plant Nicotiana benthamiana. We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells. Haustoria were also formed in infected cells of natural hosts, Rhododendron ponticum and European beech (Fagus sylvatica). We analysed the transcriptome of P. kernoviae in cultured mycelia, spores, and during infection of N. benthamiana, and detected 12,559 transcripts. Of these, 1,052 were predicted to encode secreted proteins, some of which may function as effectors to facilitate disease development. From these, we identified 87 expressed candidate RXLR (Arg-any amino acid-Leu-Arg) effectors. We transiently expressed 12 of these as GFP fusions in N. benthamiana leaves and demonstrated that nine significantly enhanced P. kernoviae disease progression and diversely localized to the cytoplasm, nucleus, nucleolus, and plasma membrane. Our results show that N. benthamiana can be used as a model host plant for studying this tree pathogen, and that the interaction likely involves suppression of host immune responses by RXLR effectors. These results establish a platform to expand the understanding of Phytophthora tree diseases.

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene-zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I-tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.

Chitosan primes plant defence mechanisms against Botrytis cinerea, including expression of Avr9/Cf-9 rapidly elicited genes

Current crop protection strategies against the fungal pathogen Botrytis cinerea rely on a combination of conventional fungicides and host genetic resistance. However, due to pathogen evolution and legislation in the use of fungicides, these strategies are not sufficient to protect plants against this pathogen. Defence elicitors can stimulate plant defence mechanisms through a phenomenon known as defence priming. Priming results in a faster and/or stronger expression of resistance upon pathogen recognition by the host. This work aims to study defence priming by a commercial formulation of the elicitor chitosan. Treatments with chitosan result in induced resistance (IR) in solanaceous and brassicaceous plants. In tomato plants, enhanced resistance has been linked with priming of callose deposition and accumulation of the plant hormone jasmonic acid (JA). Large-scale transcriptomic analysis revealed that chitosan primes gene expression at early time-points after infection. In addition, two novel tomato genes with a characteristic priming profile were identified, Avr9/Cf-9 rapidly elicited protein 75 (ACRE75) and 180 (ACRE180). Transient and stable over-expression of ACRE75, ACRE180 and their Nicotiana benthamiana homologs, revealed that they are positive regulators of plant resistance against B. cinerea. This provides valuable information in the search for strategies to protect Solanaceae plants against B. cinerea.

Ingested but not perceived: Response to satiety cues disrupted by perceptual load

Selective attention research has shown that when perceptual demand is high, unattended sensory information is filtered out at early stages of processing. We investigated for the first time whether the sensory and nutrient cues associated with becoming full (satiety) would be filtered out in a similar manner. One-hundred and twenty participants consumed either a low-satiety (75 kcal) or high-satiety (272 kcal plus thicker texture) beverage, delivered via an intra-oral infusion device while participants simultaneously completed a task which was either low or high in perceptual demand. Among participants who performed the low perceptual load task, ingestion of the high-satiety beverage increased rated satiety and reduced consumption at a subsequent snack test. However, both effects were eliminated by the high perceptual load task. Therefore, the processing of satiety cues was dependent on the availability of attention, identifying a novel perceptual load mechanism of inattentive eating and supporting more recent cognitive models of appetite control.

Hedonic contrast and the short-term stimulation of appetite

Hedonic contrast describes how liking for one item is influenced by the recent experience of other items which differ in hedonic valence. In the context of food stimuli, there is abundant evidence that hedonic contrast alters liking, but limited information on its impact on intake, and the aim here was to further clarify how hedonic impact modifies intake. Participants (96 female volunteers) rated and consumed ad libitum a sequence of four bowls of a snack (potato crisps) in one of three conditions. In the Palatable (salted crisps) and Bland (unsalted crisps) conditions, all four bowls were the same. In the Contrast condition participants alternated between salted and unsalted crisps. In total, significantly more was consumed in the Palatable (35.0 ± 2.6 g) than Bland (26.6 ± 2.4 g) condition, but most was consumed in the Contrast condition (37.0 ± 1.6 g). The impact of hedonic contrast was seen in the third serving, where those in the Contrast condition consumed the most of any serving, and significantly more than in Palatable or Bland conditions, and at the final serving, when those in the Contrast condition consumed significantly less than in Bland or Palatable conditions. Rated liking for the foods showed a similar pattern, with liking decreasing across servings in Palatable and Bland conditions. However, liking was influenced by the preceding serving in the Contrast condition, and the change in liking produced by contrast predicted subsequent intake. Overall, these data provide clear evidence that hedonic contrast can influence consumption, with intake driven by this adjusted liking.

Student's satisfaction and intercultural competence development from a short study abroad programs: A multiple cross-sectional study

Nurses should be culturally competent to care appropriately to all patient groups. Whilst there are many opportunities to obtain clinical experiences, there are less curriculum-based opportunities to develop cultural competencies. This multiple cross-sectional study aimed to explore the development of intercultural awareness, knowledge, and competence in two different nursing students' groups (2016 and 2017 program edition) during a one-week study abroad program hosted by a European network of 14 higher education institutions. A questionnaire was designed specifically for the study and reliability established. Factor analysis confirmed three dimensions: perceived benefits, satisfaction, and acquisition of learning outcomes. Fifty-eight students (71.6%) completed the questionnaire for the April 2016 group, and 60 (88.2%) from the April 2017 group. There were minimal differences in responses between the two groups which suggested perceived benefits were retained one year later. Ratings were high for perceived satisfaction, perceived benefits; and the learning outcomes with regard to cultural competencies. Overall, the one-week program was considered a success and students would recommend it to others. This study concludes that a short, one-week study abroad program enabled nursing students to develop individually as well as develop cultural competencies in healthcare.

Implementation and evaluation of a quality improvement initiative to reduce late gestation stillbirths in Australia: Safer Baby Bundle study protocol

BACKGROUND

In 2015, the stillbirth rate after 28 weeks (late gestation) in Australia was 35% higher than countries with the lowest rates globally. Reductions in late gestation stillbirth rates have steadily improved in Australia. However, to amplify and sustain reductions, more needs to be done to reduce practice variation and address sub-optimal care. Implementing bundles for maternity care improvement in the UK have been associated with a 20% reduction in stillbirth rates. A similar approach is underway in Australia; the Safer Baby Bundle (SBB) with five elements: 1) supporting women to stop smoking in pregnancy, 2) improving detection and management of fetal growth restriction, 3) raising awareness and improving care for women with decreased fetal movements, 4) improving awareness of maternal safe going-to-sleep position in late pregnancy, 5) improving decision making about the timing of birth for women with risk factors for stillbirth.

METHODS

This is a mixed-methods study of maternity services across three Australian states; Queensland, Victoria and New South Wales. The study includes evaluation of 'targeted' implementer sites (combined total approximately 113,000 births annually, 50% of births in these states) and monitoring of key outcomes state-wide across all maternity services. Progressive implementation over 2.5 years, managed by state Departments of Health, commenced from mid-2019. This study will determine the impact of implementing the SBB on maternity services and perinatal outcomes, specifically for reducing late gestation stillbirth. Comprehensive process, impact, and outcome evaluations will be conducted using routinely collected perinatal data, pre- and post- implementation surveys, clinical audits, focus group discussions and interviews. Evaluations explore the views and experiences of clinicians embedding the SBB into routine practice as well as women's experience with care and the acceptability of the initiative.

DISCUSSION

This protocol describes the evaluation of the SBB initiative and will provide evidence for the value of a systematic, but pragmatic, approach to strategies to reduce the evidence-practice gaps across maternity services. We hypothesise successful implementation and uptake across three Australian states (amplified nationally) will be effective in reducing late gestation stillbirths to that of the best performing countries globally, equating to at least 150 lives saved annually.

TRIAL REGISTRATION

The Safer Baby Bundle Study was retrospectively registered on the ACTRN12619001777189 database, date assigned 16/12/2019.

Effects on health and process outcomes of physiotherapist-led orthopaedic triage for patients with musculoskeletal disorders: a systematic review of comparative studies

BACKGROUND

Physiotherapist-led (PT-led) orthopaedic triage is an evolving model of care for patients with musculoskeletal disorders. Objectives for this study were to establish the current evidence body on the impact of PT-led orthopaedic triage on health, quality, and service outcomes for patients referred for orthopaedic consultation, compared with standard (orthopaedic surgeon) care.

METHODS

Medline, EMBASE, Scopus and CINAHL were searched from inception until 7 May 2018; search updated 24 April 2020. Search terms (including derivatives) included physiotherapy, advanced/extended scope, musculoskeletal/orthopaedic, triage. The search was framed as Population = patients referred for orthopaedic consultation; Intervention = PT-led orthopaedic triage; Comparison = standard care; Outcomes = health, quality and process outcomes. Only randomised controlled trials (RCTs) and prospective comparative cohort studies were eligible for inclusion. Screening, study selection, data extraction, and assessment of methodological quality were performed independently by reviewer pairs. Quality was scored with the Downs and Black checklist. Certainty of evidence was determined using GRADE. PROSPERO registration number CRD42017070950.

RESULTS

We included two RCTs and eleven cohort studies (n = 1357 participants) of variable methodological quality (range 14-23 of possible 28). Certainty of evidence was low to moderate. There was no difference between PT-led orthopaedic triage and standard care for patient-reported outcomes (two RCTs). Perceived quality of care with PT-led orthopaedic triage was higher (two RCTs, four cohort studies) or equal (one cohort study) compared with standard care. PT-led orthopaedic triage had higher surgery conversion rates (one RCT, three cohort studies) (55-91% vs 22-38%), lower (two RCTs) or equal rate (two cohort studies) of referral for investigations, shorter waiting times (one RCT, one cohort study), and lower costs (one RCT). Furthermore, there was high agreement between physiotherapists' and orthopaedic surgeons' treatment approach (eight cohort studies), referral for investigation (five cohort studies), and diagnosis (nine cohort studies). Study limitations were the low number of RCTs, and variable methodological quality.

CONCLUSIONS

Evidence of low to moderate certainty suggests that PT-led orthopaedic triage leads to similar diagnostic decisions as standard care, has a higher conversion-to-surgery rate, reduces waiting times, is cost effective and valued by patients, and that health outcomes are equivalent.

A composite neonatal adverse outcome indicator using population-based data: an update

Introduction

Severe morbidity rates in neonates can be estimated using diagnosis and procedure coding in linked routinely collected retrospective data as a cost-effective way to monitor quality and safety of perinatal services. Coding changes necessitate an update to the previously published composite neonatal adverse outcome indicator for identifying infants with severe or medically significant morbidity.

Objectives

To update the neonatal adverse outcome indicator for identifying neonates with severe or medically significant morbidity, and to investigate the validity of the updated indicator.

Methods

We audited diagnosis and procedure codes and used expert clinician input to update the components of the indicator. We used linked birth, hospital and death data for neonates born alive at 24 weeks or more in New South Wales, Australia (2002–2014) to describe the incidence of neonatal morbidity and assess the validity of the updated indicator.

Results

The updated indicator included 28 diagnostic and procedure components. In our population of 1,194,681 live births, 5.44% neonates had some form of morbidity. The rate of morbidity was greater for higher-risk pregnancies and was lowest for those born at 39–40 weeks’ gestation. Incidence increased over the study period for overall neonatal morbidity, and for individual components: intravenous infusion, respiratory diagnoses, and non-invasive ventilation. Severe or medically significant neonatal morbidity was associated with double the risk of hospital readmission and 10 times the risk of death within the first year of life.

Conclusion

The updated composite indicator has maintained concurrent and predictive validity and is a standardised, economic way to measure neonatal morbidity when using population-based data. Changes within individual components should be considered when examining longitudinal data.

Dataset of Escherichia coli O157: H7 genes enriched in adherence to spinach root tissue

A high-throughput positive-selection approach was taken to generate a dataset of Shigatoxigenic Escherichia coli (STEC) O157:H7 genes enriched in adherence to plant tissue. The approach generates a differential dataset based on BAC clones enriched in the output, after adherence, compared to the inoculum used as the input. A BAC clone library derived from STEC isolate ‘Sakai’ was used since this isolate is associated with a very large-scale outbreak of human disease from consumption of contaminated fresh produce; white radish sprouts. Spinach was used for the screen since it is associated with STEC outbreaks, and the roots provide a suitable site for bacterial colonisation. Four successive of rounds of Sakai BAC clone selection and amplification were applied for spinach root adherence, in parallel to a non-plant control. Genomic DNA was obtained from a total of 7.17 × 10⁸ cfu/ml of bacteria from the plant treatment and 1.13 × 10⁹ cfu/ml of bacteria from the no-plant control. Relative gene abundance of the output compared to the input pools was obtained using an established E. coli DNA microarray chip for STEC. The dataset enables screening for genes enriched under the treatment condition and informs on genes that may play a role in plant-microbe interactions.

A footprint of plant eco-geographic adaptation on the composition of the barley rhizosphere bacterial microbiota

The microbiota thriving in the rhizosphere, the thin layer of soil surrounding plant roots, plays a critical role in plant’s adaptation to the environment. Domestication and breeding selection have progressively differentiated the microbiota of modern crops from the ones of their wild ancestors. However, the impact of eco-geographical constraints faced by domesticated plants and crop wild relatives on recruitment and maintenance of the rhizosphere microbiota remains to be fully elucidated. Here we performed a comparative 16S rRNA gene survey of the rhizosphere of 4 domesticated and 20 wild barley (Hordeum vulgare) genotypes grown in an agricultural soil under controlled environmental conditions. We demonstrated the enrichment of individual bacteria mirrored the distinct eco-geographical constraints faced by their host plants. Unexpectedly, Elite varieties exerted a stronger genotype effect on the rhizosphere microbiota when compared with wild barley genotypes adapted to desert environments with a preferential enrichment for members of Actinobacteria. Finally, in wild barley genotypes, we discovered a limited, but significant, correlation between microbiota diversity and host genomic diversity. Our results revealed a footprint of the host’s adaptation to the environment on the assembly of the bacteria thriving at the root–soil interface. In the tested conditions, this recruitment cue layered atop of the distinct evolutionary trajectories of wild and domesticated plants and, at least in part, is encoded by the barley genome. This knowledge will be critical to design experimental approaches aimed at elucidating the recruitment cues of the barley microbiota across a range of soil types.

Use of public water supply fluoride concentration as an indicator of population exposure to fluoride in England 1995-2015

Public health monitoring of Community Water Fluoridation (CWF) schemes requires estimates of exposure to fluoride in public water supplies (PWS). We aimed to use routine data to estimate population exposure to PWS-fluoride in England and to determine whether PWS-fluoride exposure from 2005 to 2015 could be used as a proxy for exposure for 1995-2004, when fluoride concentration data that could be linked to population health data were unavailable. We calculated annual mean water supply zone PWS-fluoride concentrations from monitoring data for 1995-2015, stratified by fluoridation scheme-flagging. We allocated annual 2005-2015 mean PWS-fluoride concentrations to small area boundaries to describe population exposure within five concentration categories (< 0.1 to ≥ 0.7 mg/L). We compared zone-level 1995-2004 and 2005-2015 mean PWS-fluoride concentrations using Spearman correlation. Most (72%) of the population received PWS with < 0.2 mg/L fluoride and 10% with ≥ 0.7 mg/L. Fluoride concentrations in 1995-2004 and 2005-2015 were similar (median 0.11 mg/L (lower quartile-upper quartile (LQ-UQ) 0.06-0.17) and 0.11 mg/L (LQ-UQ 0.07-0.17), respectively) and highly correlated (coefficient 0.93) if un-fluoridated but differed (1995-2004 median 0.78 mg/L (LQ-UQ 0.59-0.92); 2005-2015 0.84 mg/L (LQ-UQ 0.72-0.95)) and correlated weakly (coefficient 0.31) if fluoridated. Fluoride concentrations in 2005-2015 approximate those in 1995-2004 but with a greater risk of misclassification in fluoridation schemes.

A high-throughput genomic screen identifies a role for the plasmid-borne type II secretion system of Escherichia coli O157:H7 (Sakai) in plant-microbe interactions

Shiga-toxigenic Escherichia coli (STEC) is often transmitted into food via fresh produce plants, where it can cause disease. To identify early interaction factors for STEC on spinach, a high-throughput positive-selection system was used. A bacterial artificial chromosome (BAC) clone library for isolate Sakai was screened in four successive rounds of short-term (2 h) interaction with spinach roots, and enriched loci identified by microarray. A Bayesian hierarchical model produced 115 CDS credible candidates, comprising seven contiguous genomic regions. Of the two candidate regions selected for functional assessment, the pO157 plasmid-encoded type two secretion system (T2SS) promoted interactions, while a chaperone-usher fimbrial gene cluster (loc6) did not. The T2SS promoted bacterial binding to spinach and appeared to involve the EtpD secretin protein. Furthermore, the T2SS genes, etpD and etpC, were expressed at a plant-relevant temperature of 18 °C, and etpD was expressed in planta by E. coli Sakai on spinach plants.

Immunogenicity of the hepatitis A vaccine 20 years after infant immunization

To determine the duration of immunity provided by the Hepatitis A vaccination (HepA), we evaluated a cohort of participants in Alaska 20 years after being immunized as infants. At recruitment, participants received two doses of inactivated HepA vaccine on one of three schedules. We conducted hepatitis A antibody (anti-HAV) testing for participants at the 20-year time-point. Seventy-five of the original 183 participants (41%) were available for follow-up. The overall anti-HAV geometric mean concentration was 29.9 mIU/mL (95% CI 22.4 mIU/mL, 39.7 mIU/mL) and 50 participants (68%) remained seropositive (titer ≥ 20 mIU/mL). Using a fractional polynomial model, the predicted percent seropositive at 25 years was 55.3%, 49.8% at 30 years and 45.7% at 35 years, suggesting that the percent sero-positive could drop below 50% earlier than previously expected. Further research is necessary to understand if protection continues after seropositivity diminishes or if a HepA booster dose may become necessary.

Continuum beliefs are associated with higher problem recognition than binary beliefs among harmful drinkers without addiction experience

Low problem recognition may be an important barrier to opportunities for self-change or help-seeking in harmful drinkers. Little is known about how the beliefs harmful drinkers hold about the nature and causes of alcohol problems affect problem recognition and subsequent behaviour change processes. Participants (n = 597) recruited online were randomised to one of two conditions designed to promote beliefs according to (a) a continuum model of alcohol problems or (b) a binary disease model, or (c) a control condition. Participants completed measures of alcohol problem beliefs, problem recognition and other indices including the Alcohol Use Disorder Identification Test (AUDIT), addiction beliefs, addiction experience and demographics. Results showed that harmful drinkers without addiction experience exposed to the continuum condition had significantly higher problem recognition than those in binary disease model or control conditions. Continuum beliefs appear to offer self-evaluative benefits for harmful drinkers with low alcohol problem recognition, thus potentially facilitating help-seeking or self-change regarding alcohol use. Further research to understand the mechanisms by which continuum beliefs may promote more accurate drinking self-evaluation and its potential for behaviour change is warranted. The role of continuum beliefs may have important consequences for alcohol-related messaging and interventions seeking to promote self-change or help-seeking.

Editorial - Child oral health; is there anything more to know?

It seems a strange thing to be writing about child oral health in the middle of a virus pandemic that has, in the UK at least, paused all routine dental care. Perhaps not; as thoughts turn to the return of "normal" opera- tion there are concerns over potential ongoing impacts from COVID-19 on health services including stricter infection-control requirements and economic impacts from the lockdown. It invites ridicule to try and predict what will happen in the coming years, but the economic and social impacts are likely to increase vulnerability among the already vulnerable and the delivery of dental care is likely to be more problematic and more expensive. More than ever we need to reduce the burden of avoidable dental disease.

Greater child dental health inequality in England compared to Wales and Northern Ireland, despite lower average disease levels

INTRODUCTION

Dental caries and inequalities in dental health are major public health concerns.

AIM

To report variation in dental caries experience across deprivation quintiles and the magnitude of inequalities between countries.

DESIGN

Secondary analyses of cross-sectional data from the 2013 Child Dental Health Survey (CDHS) in England, Wales, and Northern Ireland.

MATERIALS AND METHODS

Distribution of dental caries across deprivation quintiles were estimated using as proportions and means. The magnitude of inequalities was calculated using the Relative Index of Inequality (RII).

MAIN OUTCOMES

Dental caries experience as indicated by the prevalence (%dmft/DMFT>0) and severity (dmft/DMFT) of 'obvious' and 'clinical' decay experience in both primary and permanent dentitions.

RESULTS

Children from more deprived quintiles showed higher prevalence and severity of dental caries. RIIs for dental caries were greater in England than Wales or Northern Ireland, indicating greater relative inequalities despite lower average dental caries experience. The prevalence and severity of dental caries among the most deprived children in England were 1.7 to 3.7 times greater than those of the least deprived.

CONCLUSION

There is a deprivation gradient in child dental caries in all three countries, with England showing the greatest inequalities.

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

BACKGROUND

The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.

RESULTS

A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427-433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20-28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5' and 3' UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage.

CONCLUSION

A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.

BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq

BACKGROUND

The time required to analyse RNA-seq data varies considerably, due to discrete steps for computational assembly, quantification of gene expression and splicing analysis. Recent fast non-alignment tools such as Kallisto and Salmon overcome these problems, but these tools require a high quality, comprehensive reference transcripts dataset (RTD), which are rarely available in plants.

RESULTS

A high-quality, non-redundant barley gene RTD and database (Barley Reference Transcripts - BaRTv1.0) has been generated. BaRTv1.0, was constructed from a range of tissues, cultivars and abiotic treatments and transcripts assembled and aligned to the barley cv. Morex reference genome (Mascher et al. Nature; 544: 427-433, 2017). Full-length cDNAs from the barley variety Haruna nijo (Matsumoto et al. Plant Physiol; 156: 20-28, 2011) determined transcript coverage, and high-resolution RT-PCR validated alternatively spliced (AS) transcripts of 86 genes in five different organs and tissue. These methods were used as benchmarks to select an optimal barley RTD. BaRTv1.0-Quantification of Alternatively Spliced Isoforms (QUASI) was also made to overcome inaccurate quantification due to variation in 5' and 3' UTR ends of transcripts. BaRTv1.0-QUASI was used for accurate transcript quantification of RNA-seq data of five barley organs/tissues. This analysis identified 20,972 significant differentially expressed genes, 2791 differentially alternatively spliced genes and 2768 transcripts with differential transcript usage.

CONCLUSION

A high confidence barley reference transcript dataset consisting of 60,444 genes with 177,240 transcripts has been generated. Compared to current barley transcripts, BaRTv1.0 transcripts are generally longer, have less fragmentation and improved gene models that are well supported by splice junction reads. Precise transcript quantification using BaRTv1.0 allows routine analysis of gene expression and AS.

A highly mutagenised barley (cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing

BACKGROUND

We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Golden Promise is the 'reference' genotype for barley transformation and a primary objective of using this cultivar was to be able to genetically complement observed mutations directly in order to prove gene function. Importantly, a reference genome assembly of Golden Promise has also recently been developed. As our primary interest was to identify mutations in genes involved in meiosis and recombination, to characterise the population we focused on a set of 46 genes from the literature that are possible meiosis gene candidates.

RESULTS

Sequencing 20 plants from the population using whole exome capture revealed that the mutation density in this population is high (one mutation every 154 kb), and consequently even in this small number of plants we identified several interesting mutations. We also recorded some issues with seed availability and germination. We subsequently designed and applied a simple two-dimensional pooling strategy to identify mutations in varying numbers of specific target genes by Illumina short read pooled-amplicon sequencing and subsequent deconvolution. In parallel we assembled a collection of semi-sterile mutants from the population and used a custom exome capture array targeting the 46 candidate meiotic genes to identify potentially causal mutations.

CONCLUSIONS

We developed a highly mutagenised barley TILLING population in the transformation competent cultivar Golden Promise. We used novel and cost-efficient screening approaches to successfully identify a broad range of potentially deleterious variants that were subsequently validated by Sanger sequencing. These resources combined with a high-quality genome reference sequence opens new possibilities for efficient functional gene validation.