Abscisic acid biosynthesis is necessary for full auxin effects on hypocotyl elongation.

In concert with other phytohormones, auxin regulates plant growth and development. However, how auxin and other phytohormones coordinately regulate distinct processes is not fully understood. In this work, we uncover an auxin-abscisic acid (ABA) interaction module in Arabidopsis that is specific to coordinating activities of these hormones in the hypocotyl. From our forward genetics screen, we determine that ABA biosynthesis is required for the full effects of auxin on hypocotyl elongation. Our data also suggest that ABA biosynthesis is not required for the inhibitory effects of auxin treatment on root elongation. Our transcriptome analysis identified distinct auxin-responsive genes in root and shoot tissues, which is consistent with differential regulation of growth in these tissues. Further, our data suggest that many gene targets repressed upon auxin treatment require an intact ABA pathway for full repression. Our results support a model in which auxin stimulates ABA biosynthesis to fully regulate hypocotyl elongation.

A high quality, high molecular weight DNA extraction method for PacBio HiFi genome sequencing of recalcitrant plants.

BACKGROUND: PacBio HiFi sequencing provides highly accurate long-read sequencing datasets which are of great advantage for whole genome sequencing projects. One limitation of the method is the requirement for high quality, high molecular weight input DNA. This can be particularly challenging for plants that frequently contain common and species-specific secondary metabolites, which often interfere with downstream processes. Cape Primroses (genus Streptocarpus), are some of these recalcitrant plants and are selected here as material to develop a high quality, high molecular weight DNA extraction protocol for long read genome sequencing. RESULTS: We developed a DNA extraction method for PacBio HiFi sequencing for Streptocarpus grandis and Streptocarpus kentaniensis. A CTAB lysis buffer was employed to avoid guanidine, and the traditional chloroform and phenol purification steps were replaced with pre-lysis sample washes. Best cells/nucleus lysis was achieved with 4 h at 58 °C. The obtained high quality and high molecular weight DNAs were tested in PacBio SMRTBell™ library preparations, which resulted in circular consensus sequencing (CCS) reads from 17 to 27 Gb per cell, and a read length N50 from 14 to 17 kbp. To evaluate the quality of the reads for whole genome sequencing, they were assembled with HiFiasm into draft genomes, with N50 = 49 Mb and 23 Mb, and L50 = 10 and 11. The longest contigs were 95 Mb and 57 Mb respectively, showing good contiguity as these are longer than the theoretical chromosome length (genome size/chromosome number) of 78 Mb and 55 Mb, for S. grandis and S. kentaniensis respectively. CONCLUSIONS: DNA extraction is a critical step towards obtaining a complete genome assembly. Our DNA extraction method here provided the required high quality, high molecular weight DNA for successful standard-input PacBio HiFi library preparation. The contigs from those reads showed a high contiguity, providing a good starting draft assembly towards obtaining a complete genome. The results obtained here were highly promising, and demonstrated that the DNA extraction method developed here is compatible with PacBio HiFi sequencing and suitable for de novo whole genome sequencing projects of plants.

The Cultural and Commercial Value of Tulsi (Ocimum tenuiflorum L.): Multidisciplinary Approaches Focusing on Species Authentication.

Tulsi (Holy basil, Ocimum tenuiflorum L., Lamiaceae), native to Asia, has become globalised as the cultural, cosmetic, and medicinal uses of the herb have been popularised. DNA barcoding, a molecular technique used to identify species based on short regions of DNA, can discriminate between different species and identify contaminants and adulterants. This study aimed to explore the values associated with Tulsi in the United Kingdom (UK) and authenticate samples using DNA barcoding. A mixed methods approach was used, incorporating social research (i.e., structured interviews) and DNA barcoding of Ocimum samples using the ITS and trnH-psbA barcode regions. Interviews revealed the cultural significance of Tulsi: including origins, knowledge exchange, religious connotations, and medicinal uses. With migration, sharing of plants and seeds has been seen as Tulsi plants are widely grown in South Asian (SA) households across the UK. Vouchered Ocimum specimens (n = 33) were obtained to create reference DNA barcodes which were not available in databases. A potential species substitution of O. gratissimum instead of O. tenuiflorum amongst SA participants was uncovered. Commercial samples (n = 47) were difficult to authenticate, potentially due to DNA degradation during manufacturing processes. This study highlights the cultural significance of Tulsi, despite a potential species substitution, the plant holds a prestigious place amongst SA families in the UK. DNA barcoding was a reliable way to authenticate Ocimum species.

Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield.

Artemisia annua is the major natural source of artemisinin, an anti-malarial medicine commonly used worldwide. Here, we present chromosome-level haploid maps for two A. annua strains with different artemisinin contents to explore the relationships between genomic organization and artemisinin production. High-fidelity sequencing, optical mapping, and chromatin conformation capture sequencing were used to assemble the heterogeneous and repetitive genome and resolve the haplotypes of A. annua. Approximately 50,000 genes were annotated for each haplotype genome, and a triplication event that occurred approximately 58.12 million years ago was examined for the first time in this species. A total of 3,903,467-5,193,414 variants (SNPs, indels, and structural variants) were identified in the 1.5-Gb genome during pairwise comparison between haplotypes, consistent with the high heterozygosity of this species. Genomic analyses revealed a correlation between artemisinin concents and the copy number of amorpha-4,11-diene synthase genes. This correlation was further confirmed by resequencing of 36 A. annua samples with varied artemisinin contents. Circular consensus sequencing of transcripts facilitated the detection of paralog expression. Collectively, our study provides chromosome-level allele-aware genome assemblies for two A. annua strains and new insights into the biosynthesis of artemisinin and its regulation, which will contribute to conquering malaria worldwide.

Challenges in Medicinal and Aromatic Plants DNA Barcoding-Lessons from the Lamiaceae.

The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples.

A customised target capture sequencing tool for molecular identification of Aloe vera and relatives.

Plant molecular identification studies have, until recently, been limited to the use of highly conserved markers from plastid and other organellar genomes, compromising resolution in highly diverse plant clades. Due to their higher evolutionary rates and reduced paralogy, low-copy nuclear genes overcome this limitation but are difficult to sequence with conventional methods and require high-quality input DNA. Aloe vera and its relatives in the Alooideae clade (Asphodelaceae, subfamily Asphodeloideae) are of economic interest for food and health products and have horticultural value. However, pressing conservation issues are increasing the need for a molecular identification tool to regulate the trade. With > 600 species and an origin of ± 15 million years ago, this predominantly African succulent plant clade is a diverse and taxonomically complex group for which low-copy nuclear genes would be desirable for accurate species discrimination. Unfortunately, with an average genome size of 16.76 pg, obtaining high coverage sequencing data for these genes would be prohibitively costly and computationally demanding. We used newly generated transcriptome data to design a customised RNA-bait panel targeting 189 low-copy nuclear genes in Alooideae. We demonstrate its efficacy in obtaining high-coverage sequence data for the target loci on Illumina sequencing platforms, including degraded DNA samples from museum specimens, with considerably improved phylogenetic resolution. This customised target capture sequencing protocol has the potential to confidently indicate phylogenetic relationships of Aloe vera and related species, as well as aid molecular identification applications.

Management of non-traumatic epistaxis in adults in the emergency department.

BACKGROUND/AIMS: Despite epistaxis being a common presentation to emergency departments there is a lack of guidelines, both nationally and internationally, for its management. The authors reviewed the current management of epistaxis and then introduced a new pathway for management to see if care could be improved. The aims were to evaluate the impact of the pathway on reduction of emergency department breaches, emergency ambulance transfers and hospital admissions. METHODS: The study was an interrupted time series analysis over 29 months and included 903 participants. A pathway for the management of adults with non-traumatic epistaxis was designed and implemented in a university teaching hospital with an emergency department annual attendance rate of 105 495 in 2019-20. RESULTS: The pathway led to a 14-minute longer stay in the emergency department, a 5% increase in emergency department breaches, an 8.2% reduction in admissions, a 3.6% reduction in emergency ambulance transfers, a 14.1% increase in nasal cautery and a 3.2% reduction in nasal packing. CONCLUSIONS: The authors calculate that these results equate to roughly 56 hospital bed days saved, providing better care closer to home for patients, in addition to beneficial knock-on effects for other emergency department and admitted patients.

Array-based dynamic allele specific hybridization (Array-DASH): Optimization-free microarray processing for multiple simultaneous genomic assays.

We report proof-of-principle experiments regarding a dynamic microarray protocol enabling accurate and semi-quantitative DNA analysis for re-sequencing, fingerprinting and genotyping. Single-stranded target molecules hybridise to surface-bound probes during initial gradual cooling with high-fidelity. Real-time tracking of target denaturation (via fluorescence) during a 'dynamic' gradual heating phase permits 'melt-curve' analysis. The probe most closely matching the target sequence is identified based on the highest melting temperature. We demonstrated a >99% re-sequencing accuracy and a potential detection rate of 1% for SNPs. Experiments employing Hypericum ribosomal ITS regions and HIV genomes illustrated a reliable detection level of 5% plus simultaneous re-sequencing and genotyping. Such performance suggests a range of potential real-world applications involving rapid sequence interrogation, for example, in the Covid-19 pandemic. Guidance is offered towards the development of a commercial platform and dedicated software required to bring this technique into mainstream science.

Applied Barcoding: The Practicalities of DNA Testing for Herbals.

DNA barcoding is a widely accepted technique for the identification of plant materials, and its application to the authentication of commercial medicinal plants has attracted significant attention. The incorporation of DNA-based technologies into the quality testing protocols of international pharmacopoeias represents a step-change in status, requiring the establishment of standardized, reliable and reproducible methods. The process by which this can be achieved for any herbal medicine is described, using Hypericum perforatum L. (St John's Wort) and potential adulterant Hypericum species as a case study. A range of practical issues are considered including quality control of DNA sequences from public repositories and the construction of individual curated databases, choice of DNA barcode region(s) and the identification of informative polymorphic nucleotide sequences. A decision tree informs the structure of the manuscript and provides a template to guide the development of future DNA barcode tests for herbals.

Mobile Stroke Unit in the UK Healthcare System: Avoidance of Unnecessary Accident and Emergency Admissions.

BACKGROUND: Acute stroke patients are usually transported to the nearest hospital regardless of their required level of care. This can lead to increased pressure on emergency departments and treatment delay. OBJECTIVE: The aim of the study was to explore the benefit of a mobile stroke unit (MSU) in the UK National Health Service (NHS) for reduction of hospital admissions. METHODS: Prospective cohort audit observation with dispatch of the MSU in the East of England Ambulance Service area in Southend-on-Sea was conducted. Emergency patients categorized as code stroke and headache were included from June 5, 2018, to December 18, 2018. Rate of avoided admission to the accident and emergency (A&E) department, rate of admission directly to target ward, and stroke management metrics were assessed. RESULTS: In 116 MSU-treated patients, the following diagnoses were made: acute stroke, n = 33 (28.4%); transient ischaemic attacks, n = 13 (11.2%); stroke mimics, n = 32 (27.6%); and other conditions, n = 38 (32.8%). Pre-hospital thrombolysis was administered to 8 of 28 (28.6%) ischaemic stroke patients. Pre-hospital diagnosis avoided hospital admission for 29 (25.0%) patients. As hospital treatment was indicated, 35 (30.2%) patients were directly triaged to the stroke unit, 1 patient (0.9%) even directly to the catheter laboratory. Thus, only 50 (43.1%) patients required transfer to the A&E department. Moreover, the MSU enabled thrombolysis with a median dispatch-to-needle time of 42 min (interquartile range, 40-60). CONCLUSION: This first deployment of an MSU in the UK NHS demonstrated improved triage decision-making for or against hospital admission and admission to the appropriate target ward, thereby reducing pressure on strained A&E departments.

No Clinical Predictors of Postconcussion Musculoskeletal Injury in College Athletes.

PURPOSE: This study aimed to identify clinical predictors of postconcussion subsequent musculoskeletal (MSK) injuries. METHODS: We recruited 66 National Collegiate Athletic Association intercollegiate student-athletes with a diagnosed concussion as well as 36 National Collegiate Athletic Association student-athletes without a concussion. All participants completed a multifaceted concussion baseline consisting of 1) 22-item 0-6 self-reported symptom checklist with outcomes including both the number of symptoms endorsed (0-22) and 2) total symptom score (0-132), 3) Standard Assessment of Concussion, 4) Balance Error Scoring System, 5) Immediate Post-Concussion Assessment and Cognitive Testing, 6) clinical reaction time, and 7) the King-Devick as well as demographic and injury characteristics. The concussion participants completed the same examination acutely postconcussion, and binary logistic regression was used to identify predictors of subsequent MSK from the change scores (acute minus baseline). From the 66 concussed student-athletes, a subset 36, matched with the healthy athletes, compared the risk of subsequent MSK in the year before and year after their concussion. RESULTS: The concussion participants were 1.78 times (95% confidence interval, 1.12-2.84; P = 0.015) more likely to suffer a lower extremity MSK in the year after their concussion than the control participants. The participant demographics and injury characteristics (P = 0.318) and concussion clinical outcomes (P = 0.461) did not predict subsequent MSK. CONCLUSION: The concussion participants were 1.78 times more likely to sustain a subsequent MSK; however, no demographic, injury characteristic, or concussion assessments predicted the MSK. Thus, clinicians are not able to utilize common neurological measures or participant demographics to identify those at risk for subsequent lower extremity MSK. Injury prevention strategies should be considered for collegiate student-athletes upon premature return to participation after a concussion to reduce the subsequent MSK.

Health care professionals' personal and professional views of herbal medicines in the United Kingdom.

Health care professionals (HCPs) have a pivotal role in optimizing patient care and should be familiar with complementary and alternative medicines. The aim of the study was to explore UK-based HCP personal and professional opinions and experiences of herbal medicines (HMs). An online questionnaire was distributed via social media to recruit (n = 112) a range of HCPs from across the United Kingdom. HCPs from primary and secondary care, the private sector, and academia took part. A large proportion of participants (62%) said they did not personally use any HMs, and 38% did use HMs. HCPs who had personally used HMs had a positive impression of HMs and were more likely to recommend HMs to patients than those who had not used HMs themselves. Participants were given the opportunity to share their perceptions on the safety and efficacy of HMs and their experiences with patients reporting adverse drug reactions to HMs and herb-drug interactions. HCPs identified their lack of knowledge on HMs and insufficient training, which made them unable to advise patients on the safe use of HMs. More education on HMs would help improve HCP knowledge of HMs and help them make better informed decisions when considering patient pharmaceutical care plans.

Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis.

DNA barcoding of herbal medicines has been mainly concerned with authentication of products in trade and has raised awareness of species substitution and adulteration. More recently DNA barcodes have been included in pharmacopoeias, providing tools for regulatory purposes. The commonly used DNA barcoding regions in plants often fail to resolve identification to species level. This can be especially challenging in evolutionarily complex groups where incipient or reticulate speciation is ongoing. In this study, we take a phylogenomic approach, analyzing whole plastid sequences from the evolutionarily complex genus Berberis in order to develop DNA barcodes for the medicinally important species Berberis aristata. The phylogeny reconstructed from an alignment of ∼160 kbp of chloroplast DNA for 57 species reveals that the pharmacopoeial species in question is polyphyletic, complicating development of a species-specific DNA barcode. Instead we propose a DNA barcode that is clade specific, using our phylogeny to define Operational Phylogenetic Units (OPUs). The plastid alignment is then reduced to small, informative DNA regions including nucleotides diagnostic for these OPUs. These DNA barcodes were tested on commercial samples, and shown to discriminate plants in trade and therefore to meet the requirement of a pharmacopoeial standard. The proposed method provides an innovative approach for inferring DNA barcodes for evolutionarily complex groups for regulatory purposes and quality control.

DNA Authentication of St John's Wort (Hypericum perforatum L.) Commercial Products Targeting the ITS Region.

There is considerable potential for the use of DNA barcoding methods to authenticate raw medicinal plant materials, but their application to testing commercial products has been controversial. A simple PCR test targeting species-specific sequences within the nuclear ribosomal internal transcribed spacer (ITS) region was adapted to screen commercial products for the presence of Hypericum perforatum L. material. DNA differing widely in amount and extent of fragmentation was detected in a number of product types. Two assays were designed to further analyse this DNA using a curated database of selected Hypericum ITS sequences: A qPCR assay based on a species-specific primer pair spanning the ITS1 and ITS2 regions, using synthetic DNA reference standards for DNA quantitation and a Next Generation Sequencing (NGS) assay separately targeting the ITS1 and ITS2 regions. The ability of the assays to detect H. perforatum DNA sequences in processed medicines was investigated. Out of twenty different matrices tested, both assays detected H. perforatum DNA in five samples with more than 10³ ITS copies µL-1 DNA extract, whilst the qPCR assay was also able to detect lower levels of DNA in two further samples. The NGS assay confirmed that H. perforatum was the major species in all five positive samples, though trace contaminants were also detected.

Product authenticity versus globalisation-The Tulsi case.

Using the Indian medicinal plant Tulsi (Holy Basil) as a case study, we have tested to what extent the discrepancy between vernacular and scientific nomenclature can be resolved, whether the presumed chemical diversity underlying the medicinal use of Tulsi has a genetic component, and whether it is possible to detect this genetic component using genetic barcoding markers. Based on four plastidic markers, we can define several haplotypes within Ocimum that are consistent across these markers. Haplotype II is congruent with O. tenuiflorum, while haplotype I extends over several members of the genus and cannot be resolved into genetically separate subclades. The vernacular subdivision of Tulsi into three types (Rama, Krishna, Vana) can only be partially linked with genetic differences-whereby Rama and Krishna Tulsi can be assigned to O. tenuiflorum, while Vana Tulsi belongs to haplotype I. This genetic difference is mirrored by differences in the profiles of secondary compounds. While developmental state and light quality modulate the amplitude to which the chemical profile is expressed, the profile itself seems to be linked with genetic differences. We finally develop an authentication assay that makes use of a characteristic single nucleotide polymorphism in one of the barcoding markers, establishing a differential restriction pattern that can be used to discriminate Vana Tulsi.

The Use of Traditional Herbal Medicines Amongst South Asian Diasporic Communities in the UK.

Migrant South Asian communities in the UK have brought with them their own traditional forms of medicine, yet little is known about their current use of herbal medicines (HMs) in the UK. The aim of the study was to explore the origins, use and transmission of knowledge of traditional HMs used by diasporic South Asian communities in the UK. A researcher-administered questionnaire was used for data collection (n = 192). An opportunity sampling technique was used to recruit participants across several locations in Birmingham and Leicester. Two thirds of participants (n = 126) stated they used HMs to maintain their health and to treat various health conditions such as digestive problems, skin conditions and diabetes. Almost 2000 actively used HMs were documented including 123 plant species that were identified. Participants imported HMs from abroad as well as sourcing them locally and even growing some of their own plants. Up to 82% (n = 87) of participants who took prescription medicines did not tell their healthcare professionals about any HMs they consumed; this raises concerns about people's knowledge of herb-drug interactions, compliance and effect on prescribed medicine regimens. Similar studies to explore the use of HMs by other ethnic groups are imperative to help optimise pharmaceutical care of patients. Copyright © 2017 John Wiley & Sons, Ltd.

DNA Barcoding for Industrial Quality Assurance.

DNA barcoding methods originally developed for the identification of plant specimens have been applied to the authentication of herbal drug materials for industrial quality assurance. These methods are intended to be complementary to current morphological and chemical methods of identification. The adoption of these methods by industry will be accelerated by the introduction of DNA-based identification techniques into regulatory standards and monographs. The introduction of DNA methods into the British Pharmacopoeia is described, along with a reference standard for use as a positive control for DNA extraction and polymerase chain reaction (PCR). A general troubleshooting chart is provided to guide the user through the problems that may be encountered during this process. Nevertheless, the nature of the plant materials and the demands of industrial quality control procedures mean that conventional DNA barcoding is not the method of choice for industrial quality control. The design of DNA barcode-targeted quantitative PCR and high resolution melt curve tests is one strategy for developing rapid, robust, and reliable protocols for high-throughput screening of raw materials. The development of authentication tests for wild-harvested Rhodiola rosea L. is used as a case study to exemplify these relatively simple tests. By way of contrast, the application of next-generation sequencing to create a complete profile of all the biological entities in a mixed herbal drug is described and its potential for industrial quality assurance discussed.

Prescribing pharmacists in the ambulatory care setting: Experience at the University of North Carolina Medical Center.

PURPOSE: The prescribing authorities, clinical activities, and productivity documentation strategies of ambulatory care clinic-based pharmacists practicing within a large academic health system are described. SUMMARY: North Carolina law encourages progressive pharmacy practice through acquisition of the clinical pharmacist practitioner (CPP) designation. Qualified CPPs are authorized to provide collaborative drug therapy management services, including medication prescribing and ordering of laboratory tests, according to defined protocols and under physician supervision. The University of North Carolina Medical Center has approximately 30 CPPs deployed across a wide range of ambulatory care clinical practice sites. This article describes (1) the pharmacy department's implementation of an ambulatory care practice model, (2) the credentialing and privileging process leading to granting of prescribing privileges, (3) metrics used to demonstrate the impact of CPP activities, (4) recommended general criteria for ambulatory care practice site identification, and (5) strategies for overcoming barriers to successful implementation of ambulatory care-focused clinical pharmacist services. Aggregated intervention-tracking data compiled by seven of the medical center's CPP ambulatory care practice sites indicate extensive CPP involvement in direct patient care encounters and patient or provider consultations, with large numbers of medication-related interventions to support institutional cost-avoidance and revenue goals. CONCLUSION: CPPs deployed at the medical center's ambulatory care clinics have had a positive impact on clinical and cost outcomes, improving patient care through interventions, contributing to readmission reduction efforts, generating indirect revenue through cost avoidance, and generating new revenue through billing for patient visits.

The application of a DNA-based identification technique to over-the-counter herbal medicines.

Reliable methods to identify medicinal plant material are becoming more important in an increasingly regulated market place. DNA-based methods have been recognised as a valuable tool in this area with benefits such as being unaffected by the age of the plant material, growth conditions and harvesting techniques. It is possible that the methods of production used for medicinal plant products will degrade or remove DNA. So how applicable are these techniques to processed medicinal plant products? A simple PCR-based identification technique has been developed for St. John's Wort, Hypericum perforatum L. Thirteen St. John's Wort products were purchased including capsules, tablets and tinctures. DNA was extracted from each product, and the species specific PCR test conducted. DNA was successfully extracted from all thirteen products, using a fast and efficient modified method for extracting DNA from tinctures. Only four products yielded the full length ITS region (850 bp) due to the quality of the DNA. All of the products tested positive for H. perforatum DNA. DNA-based identification methods can complement existing methods of authentication. This paper shows that these methods are applicable to a wide range of processed products, provided that they are designed to account for the possibility of DNA degradation.