Phylogenomics and the rise of the angiosperms.

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

Circadian regulation of the transcriptome in a complex polyploid crop.

The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life.

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96$\%$) and 2333 genera (17$\%$). A "first pass" angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world's natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.].

Target sequence data shed new light on the infrafamilial classification of Araceae.

PREMISE: Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of the present study was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family. METHODS: Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms 353 universal probe set. RESULTS: The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies, but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae, which has also been expanded to include Zamioculcadoideae. The tribe Aglaonemateae is newly defined to include the genera Aglaonema and Boycea. CONCLUSIONS: Our results strongly suggest that new research on African genera (Callopsis, Nephthytis, and Anubias) and Calla will be important for understanding the early evolution of the Aroideae. Also of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia, and Anchomanes, which remain only moderately supported here.

Descriptive Study of Ambulance Attendances for Older Adults with and without Dementia in Western Australia.

OBJECTIVE: To describe and compare characteristics of ambulance attendances for older adults with and without dementia. METHODS: A retrospective cohort study was conducted using electronic patient care records from the main ambulance service in Western Australia. All attendances for people aged 65 years or older in the years 2019-21 were included. Dementia status was adjudicated from the clinical history and medication lists. Patient and case characteristics of those with and without dementia were compared and stratified by type of residence. RESULTS: There were 277,996 emergency ambulance attendances made by 124,711 older adults, of whom 23.5% had dementia. The mean number of attendances per person was 3.3 in the dementia cohort vs 2.0 in those without dementia. Falls were the leading reason for ambulance attendance. People with dementia were significantly frailer, required longer at-scene intervals, were less likely to be transported as the highest priority, and had lower 30-day survival. CONCLUSIONS: Dementia is common amongst older adults attended by paramedics and is associated with higher ambulance utilization per person. People with dementia attended by paramedics have stronger signals of vulnerability, such as increased frailty. As the number of people living with dementia increases in the future, there are implications for workforce training and service planning. There are opportunities for developing alternatives to emergency department transportation for some people with dementia.

Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales.

We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality-control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality-control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality-control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad-scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.

Palliative paramedicine: Comparing clinical practice through guideline quality appraisal and qualitative content analysis.

BACKGROUND: Palliative care is an emerging scope of practice for paramedicine. The COVID-19 pandemic has highlighted the opportunity for emergency settings to deliver palliative and end-of-life care to patients wishing to avoid intensive life-sustaining treatment. However, a gap remains in understanding the scope and limitations of current ambulance services' approach to palliative and end-of-life care. AIM: To examine the quality and content of existing Australian palliative paramedicine guidelines with a sample of guidelines from comparable Anglo-American ambulance services. DESIGN: We appraised guideline quality using the AGREE II instrument and employed a collaborative qualitative approach to analyse the content of the guidelines. DATA SOURCES: Eight palliative care ambulance service clinical practice guidelines (five Australian; one New Zealand; one Canadian; one United Kingdom). RESULTS: None of the guidelines were recommended by both appraisers for use based on the outcomes of all AGREE II evaluations. Scaled individual domain percentage scores varied across the guidelines: scope and purpose (8%-92%), stakeholder involvement (14%-53%), rigour of development (0%-20%), clarity of presentation (39%-92%), applicability (2%-38%) and editorial independence (0%-38%). Six themes were developed from the content analysis: (1) audience and approach; (2) communication is key; (3) assessing and managing symptoms; (4) looking beyond pharmaceuticals; (5) seeking support; and (6) care after death. CONCLUSIONS: It is important that ambulance services' palliative and end-of-life care guidelines are evidence-based and fit for purpose. Future research should explore the experiences and perspectives of key palliative paramedicine stakeholders. Future guidelines should consider emerging evidence and be methodologically guided by AGREE II criteria.

Prehospital continuous positive airway pressure (CPAP) for acute respiratory distress: a randomised controlled trial.

OBJECTIVE: To compare the efficacy of continuous positive airway pressure (CPAP) versus usual care for prehospital patients with severe respiratory distress. METHODS: We conducted a parallel group, individual patient, non-blinded randomised controlled trial in Western Australia between March 2016 and December 2018. Eligible patients were aged ≥40 years with acute severe respiratory distress of non-traumatic origin and unresponsive to initial treatments by emergency medical service (EMS) paramedics. Patients were randomised (1:1) to usual care or usual care plus CPAP. The primary outcomes were change in dyspnoea score and change in RR at ED arrival, and hospital length of stay. RESULTS: 708 patients were randomly assigned (opaque sealed envelope) to usual care (n=346) or CPAP (n=362). Compared with usual care, patients randomised to CPAP had a greater reduction in dyspnoea scores (usual care -1.0, IQR -3.0 to 0.0 vs CPAP -3.5, IQR -5.2 to -2.0), median difference -2.0 (95% CI -2.5 to -1.6); and RR (usual care -4.0, IQR -9.0 to 0.0 min-1 vs CPAP -8.0, IQR -14.0 to -4.0 min-1), median difference -4.0 (95% CI -5.0 to -4.0) min-1. There was no difference in hospital length of stay (usual care 4.2, IQR 2.1 to 7.8 days vs CPAP 4.8, IQR 2.5 to 7.9 days) for the n=624 cases admitted to hospital, median difference 0.36 (95% CI -0.17 to 0.90). CONCLUSIONS: The use of prehospital CPAP by EMS paramedics reduced dyspnoea and tachypnoea in patients with acute respiratory distress but did not impact hospital length of stay. TRIAL REGISTRATION NUMBER: ACTRN12615001180505.

A predictive ambulance dispatch algorithm to the scene of a motor vehicle crash: the search for optimal over and under triage rates.

BACKGROUND: Calls for emergency medical assistance at the scene of a motor vehicle crash (MVC) substantially contribute to the demand on ambulance services. Triage by emergency medical dispatch systems is therefore important, to ensure the right care is provided to the right patient, in the right amount of time. A lights and sirens (L&S) response is the highest priority ambulance response, also known as a priority one or hot response. In this context, over triage is defined as dispatching an ambulance with lights and sirens (L&S) to a low acuity MVC and under triage is not dispatching an ambulance with L&S to those who require urgent medical care. We explored the potential for crash characteristics to be used during emergency ambulance calls to identify those MVCs that required a L&S response. METHODS: We conducted a retrospective cohort study using ambulance and police data from 2014 to 2016. The predictor variables were crash characteristics (e.g. road surface), and Medical Priority Dispatch System (MPDS) dispatch codes. The outcome variable was the need for a L&S ambulance response. A Chi-square Automatic Interaction Detector technique was used to develop decision trees, with over/under triage rates determined for each tree. The model with an under/over triage rate closest to that prescribed by the American College of Surgeons Committee on Trauma (ACS COT) will be deemed to be the best model (under triage rate of ≤ 5% and over triage rate of between 25-35%. RESULTS: The decision tree with a 2.7% under triage rate was closest to that specified by the ACS COT, had as predictors-MPDS codes, trapped, vulnerable road user, anyone aged 75 + , day of the week, single versus multiple vehicles, airbag deployment, atmosphere, surface, lighting and accident type. This model had an over triage rate of 84.8%. CONCLUSIONS: We were able to derive a model with a reasonable under triage rate, however this model also had a high over triage rate. Individual EMS may apply the findings here to their own jurisdictions when dispatching to the scene of a MVC.

An updated infra-familial classification of Sapindaceae based on targeted enrichment data.

PREMISE: The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family's complex infra-familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework. METHODS: Nuclear DNA sequence data were generated for 123 genera (86%) of Sapindaceae using target sequence capture with the Angiosperms353 universal probe set. HybPiper was used to produce aligned DNA matrices. Phylogenetic inferences were obtained using coalescence-based and concatenated methods. The clades recovered are discussed in light of both benchmark studies to identify synapomorphies and distributional evidence to underpin an updated infra-familial classification. KEY RESULTS: Coalescence-based and concatenated phylogenetic trees had identical topologies and node support, except for the placement of Melicoccus bijugatus Jacq. Twenty-one clades were recovered, which serve as the basis for a revised infra-familial classification. CONCLUSIONS: Twenty tribes are recognized in four subfamilies: two tribes in Hippocastanoideae, two in Dodonaeoideae, and 16 in Sapindoideae (no tribes are recognized in the monotypic subfamily Xanthoceratoideae). Within Sapindoideae, six new tribes are described: Blomieae Buerki & Callm.; Guindilieae Buerki, Callm. & Acev.-Rodr.; Haplocoeleae Buerki & Callm.; Stadmanieae Buerki & Callm.; Tristiropsideae Buerki & Callm.; and Ungnadieae Buerki & Callm. This updated classification provides a backbone for further research and conservation efforts on this family.

A higher-level nuclear phylogenomic study of the carrot family (Apiaceae).

PREMISE: The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. METHODS: Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. RESULTS: We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysace resolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study. CONCLUSIONS: We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.

Motor Vehicle Crash Characteristics That Are Predictive of High Acuity Patients: An Analysis of Linked Ambulance and Crash Data.

BACKGROUND: Motor vehicle crashes (MVCs) comprise a significant component of emergency medical service workload. Due to the potential for life-threatening injuries, ambulances are often dispatched at the highest priority to MVCs. However, previous research has shown that only a small proportion of high-priority ambulance responses to MVCs encounter high acuity patients. Alternative methods for triaging patients over the phone are required to reduce the burden of over-triage. One method is to use information readily available at the scene (e.g. whether a person was a motorcyclist, ejection status or whether an airbag deployed) as potential predictors of high acuity. Methods: A retrospective cohort study was conducted of all MVC patients in Perth attended by St John Western Australia between 2014 and 2016. Ambulance data was linked with Police crash data. The outcome variable of interest was patient acuity, where high acuity was defined as where a patient (1) died on-scene or (2) was transported by ambulance on priority one (lights & sirens) from the scene to hospital. Crash characteristics that are predictive of high acuity patients were identified by estimating crude odds ratios and 95% confidence intervals. Results: Of the 18,917 MVC patients attended by SJ-WA paramedics, 6.4% were classified as high acuity patients. The odds of being a high acuity patient was greater for vulnerable road users (motorcyclists, pedestrians and cyclists) than for motor vehicle occupants (OR 3.19, 95% CI, 2.80-3.64). A 'not ambulant patient' (one identified by paramedics as unable to walk or having an injury incompatible with being able to walk) had 15 times the odds of being high acuity than ambulant patients (OR 15.34, 95% CI, 11.48-20.49). Those who were trapped in a vehicle compared to those not trapped (OR 4.68, 95% CI, 3.95-5.54); and those who were ejected (both partial and full) from the vehicle compared to those not ejected (OR 6.49, 95% CI, 4.62-9.12) had higher odds of being high acuity patients. Discussion: There were two important findings from this study: (1) few MVC patients were deemed to be high acuity; and (2) several crash scene characteristics were strong predictors of high acuity patients.

The Effects of Caffeine and Citrus Aurantium on Performance During Repeated Maximal Anaerobic Exercise Bouts in Habitual Caffeine Users.

ABSTRACT: McLester, CN, Bailey, P, Bechke, EE, Williamson, CM, McLester, JR, and Kliszczewicz, B. The effects of caffeine and Citrus aurantium on performance during repeated maximal anaerobic exercise bouts in habitual caffeine users. J Strength Cond Res 35(12): 3394-3399, 2021-The combination of caffeine (CAF) and Citrus aurantium (CA) have demonstrated the potential to improve various types of performance. To date, few studies have explored this relationship in purely anaerobic-based exercise. Therefore, the purpose of this study was to examine the influence of an acute dose of CAF + CA on peak anaerobic performance and the attenuation of power over multiple anaerobic bouts and to determine any differences in perceived effort or fatigue. Ten active men (25.1 ± 3.9 years) who habitually consumed caffeine volunteered to perform repeated anaerobic bouts on a cycle ergometer on 2 separate days, consuming either a placebo or 100 mg CAF + 100 mg CA. Significance was set at p ≤ 0.05 and repeated measures analysis of variance showed no main effects for peak power p = 0.520, mean power p = 0.926, minimum power p = 0.321, total work p = 0.924, time to peak power p = 0.536, or rate of fatigue p = 0.284. There was a time effect for all variables (p ≤ 0.05) with the exception of time to peak power (p = 0.181). There were no differences in any measures of perceived effort or fatigue between conditions (p ≥ 0.05), but there were time-dependent differences observed each day (p ≤ 0.05). Overall, an acute dosage of 100 mg CAF and 100 mg CA did not elicit any differences in anaerobic performance or in perceived measures of effort and fatigue in young males who habitually consume caffeine. Therefore, caution should be used when pairing CAF and CA for the goal of improving anaerobic performance, because no clear benefit was realized in this population at this dosage.

Uncovering hidden variation in polyploid wheat.

Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.

Impact of the Four-Hour Rule policy on emergency medical services delays in Australian EDs: a longitudinal cohort study.

INTRODUCTION: Delayed handover of emergency medical services (EMS) patients to EDs is a major issue with hospital crowding considered a primary cause. We explore the impact of the 4-hour rule (the Policy) in Australia, focusing on ambulance and ED delays. METHODS: EMS (ambulance), ED and hospital data of adult patients presenting to 14 EDs from 2002 to 2013 in three jurisdictions were linked. Interrupted time series 'Before-and-After' trend analysis was used for assessing the Policy's impact. Random effects meta-regression analysis was examined for associations between ambulance delays and Policy-associated ED intake, throughput and output changes. RESULTS: Before the Policy, the proportion of ED ambulances delayed increased between 1.1% and 1.7% per quarter across jurisdictions. After Policy introduction, Western Australia's increasing trend continued but Queensland decreased by 5.1% per quarter. In New South Wales, ambulance delay decreased 7.1% in the first quarter after Policy introduction. ED intake (triage delay) improved only in New South Wales and Queensland. Each 1% ambulance delay reduction was significantly associated with a 0.91% reduction in triage delay (p=0.014) but not ED length of stay ≤4 hours (p=0.307) or access-block/boarding (p=0.605) suggesting only partial improvement in ambulance delay overall. CONCLUSION: The Policy was associated with reduced ambulance delays over time in Queensland and only the immediate period in New South Wales. Associations may be due to local jurisdictional initiatives to improve ambulance performance. Strategies to alleviate ambulance delay may need to focus on the ED intake component. These should be re-examined with longer periods of post-Policy data.

Longer Prehospital Time was not Associated with Mortality in Major Trauma: A Retrospective Cohort Study.

Objective: The objective of this study was to determine the association between prehospital time and outcomes in adult major trauma patients, transported by ambulance paramedics. Methods: A retrospective cohort study of major trauma patients (Injury Severity Score >15) attended by St John Ambulance paramedics in Perth, Western Australia, who were transported to hospital between January 1, 2013 and December 31, 2016. Inverse probability of treatment weighting (IPTW) using the propensity score was performed to limit selection bias and confounding. The primary outcome was 30-day mortality and the secondary outcome was the length of hospital stay (LOS) for 30-day survivors. Multivariate logistic and log-linear regression analyses with IPTW were used to determine if prehospital time of more than the one hour (from receipt of the emergency call to arrival at hospital) or any individual prehospital time interval (response, on-scene, transport, or total time) was associated with 30-day mortality or LOS. Results: A total of 1,625 major trauma patients were included and 1,553 included in the IPTW sample. No significant association between prehospital time of one hour and 30-day mortality was found (adjusted odds ratio 1.10, 95% confidence interval (CI) 0.71-1.69). No association between any individual prehospital time interval and 30-day mortality was identified. In the 30-day survivors, one-minute increase of on-scene time was associated with 1.16 times (95% CI 1.03-1.31) longer LOS. Conclusion: Longer prehospital times were not associated with an increased likelihood of 30-day mortality in major trauma patients transported to hospital by ambulance paramedics. We found no evidence to support the hypothesis that prehospital time longer than one hour resulted in an increased risk of 30-day mortality. However, longer on-scene time was associated with longer hospital LOS (for 30-day survivors). Our recommendation is that prehospital care is delivered in a timely fashion and delivery of the patient to hospital is reasonably prompt.

Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges.

Traditionally, Sicilian blood oranges (Citrus sinensis) have been associated with cardiovascular health, and consumption has been shown to prevent obesity in mice fed a high-fat diet. Despite increasing consumer interest in these health-promoting attributes, production of blood oranges remains unreliable due largely to a dependency on cold for full color formation. We show that Sicilian blood orange arose by insertion of a Copia-like retrotransposon adjacent to a gene encoding Ruby, a MYB transcriptional activator of anthocyanin production. The retrotransposon controls Ruby expression, and cold dependency reflects the induction of the retroelement by stress. A blood orange of Chinese origin results from an independent insertion of a similar retrotransposon, and color formation in its fruit is also cold dependent. Our results suggest that transposition and recombination of retroelements are likely important sources of variation in Citrus.

A subcellular tug of war involving three MYB-like proteins underlies a molecular antagonism in Antirrhinum flower asymmetry.

The establishment of meristematic domains with different transcriptional activity is essential for many developmental processes. The asymmetry of the Antirrhinum majus flower is established by transcription factors with an asymmetric pattern of activity. To understand how this asymmetrical pattern is established, we studied the molecular mechanism through which the dorsal MYB protein RADIALIS (RAD) restricts the activity of the MYB transcription factor DIVARICATA (DIV) to the ventral region of the flower meristem. We show that RAD competes with DIV for binding with other MYB-like proteins, termed DRIF1 and DRIF2 (DIV- and-RAD-interacting-factors). DRIF1 and DIV interact to form a protein complex that binds to the DIV-DNA consensus region, suggesting that the DRIFs act as co-regulators of DIV transcriptional activity. In the presence of RAD, the interaction between DRIF1 and DIV bound to DNA is disrupted. Moreover, the DRIFs are sequestered in the cytoplasm by RAD, thus, preventing or reducing the formation of DRIF-DIV heterodimers in the nuclei. Our results suggest that in the dorsal region of the Antirrhinum flower meristem the dorsal protein RAD antagonises the activity of the ventral identity protein DIV in a subcellular competition for a DRIF protein promoting the establishment of the asymmetric pattern of gene activity in the Antirrhinum flower.

Reflecting on activities which support public involvement within an evaluation of public involvement reports from facilities funded by the national institute for health and care research: a co-produced commentary.

Although including public contributors as members of research teams is becoming common, there are few reflections on how they have been incorporated, and almost none of these reflections are co-produced with public contributors. This commentary, written by both academics and a public contributor, reflects on Patient and Public Involvement (PPI) activities when undertaking a framework analysis of PPI sections of annual reports from the National Institute for Health and care Research (NIHR) funded research centres. The UK Standards for Public Involvement (inclusive opportunities, working together, support and learning, communications, impact and governance) were used to structure our reflections. Key topics of reflection were: how difficult it is, in practice, to incorporate PPI into all aspects of the research cycle, especially when completing a commissioned research project on a short time-frame, and the complexities of incorporating PPI into qualitative analysis. Although useful when reflecting upon our own PPI practices, ways in which the UK Standards for Public Involvement could be improved were suggested. We hope that the co-produced recommendations can be used by other teams engaging with public contributors.

Although including public contributors as members of research teams is becoming common, there are few reflections on how they have been incorporated, and almost none of these reflections are co-produced with public contributors. This commentary, written by both academics and a public contributor, reflects on Patient and Public Involvement (PPI) activities when undertaking an evaluation of PPI sections of annual reports from the National Institute for Health and care Research (NIHR) funded research centres. The UK Standards for Public Involvement (inclusive opportunities, working together, support and learning, communications, impact and governance) were used to structure our reflections. Key topics of reflection were: how difficult it is, in practice, to incorporate PPI into all aspects of the research cycle, especially when completing a commissioned research project within a short time-frame, and the complexities of incorporating PPI into qualitative analysis. Although useful when reflecting upon our own PPI practices, ways in which the UK Standards for Public Involvement could be improved were suggested. We hope that the co-produced recommendations can be used by other teams engaging with public contributors.

Light-sensitive short hypocotyl genes confer symbiotic nodule identity in the legume Medicago truncatula.

Legumes produce specialized root nodules that are distinct from lateral roots in morphology and function, with nodules intracellularly hosting nitrogen-fixing bacteria. We have previously shown that a lateral root program underpins nodule initiation, but there must be additional developmental regulators that confer nodule identity. Here, we show two members of the LIGHT-SENSITIVE SHORT HYPOCOTYL (LSH) transcription factor family, predominantly known to define shoot meristem complexity and organ boundaries, function as regulators of nodule organ identity. In parallel to the root initiation program, LSH1/LSH2 recruit a program into the root cortex that mediates the divergence into nodules, in particular with cell divisions in the mid-cortex. This includes regulation of auxin and cytokinin, promotion of NODULE ROOT1/2 and Nuclear Factor YA1, and suppression of the lateral root program. A principal outcome of LSH1/LSH2 function is the production of cells able to accommodate nitrogen-fixing bacteria, a key feature unique to nodules.