Long-read sequencing to resolve the parent of origin of a de novo pathogenic UBE3A variant.

Background The ever-increasing capacity of short-read sequencing instruments is driving the adoption of whole genome sequencing (WGS) as a universal approach to the diagnosis of rare genetic disorders. However, many challenging genomic regions remain, for which alternative technologies must be deployed in order to address the clinical question satisfactorily. Methods Here we report the use of long-read sequencing to resolve ambiguity over a suspected diagnosis of Angelman syndrome. Results Despite a normal chromosomal microarray result and methylation studies at the imprinted 15q11q13 locus, the continued clinical suspicion of Angelman Syndrome prompted trio WGS of the proband and his parents. A de novo heterozygous frameshift variant, c.2370_2373del (NM_130838.2) p.(Asp790Glufs*7), in UBE3A was identified. To determine the parental allele on which this variant arose, long-read sequencing of the flanking genomic region was performed. Comparison of the resulting haplotypes allowed us to determine that the pathogenic frameshift variant arose on the maternal allele, confirming a diagnosis of Angelman syndrome in this case. Conclusion Long-read nanopore sequencing provides significant clinical utility when assessing the parental origin of de novo variants.

Bubble rise in molten glasses and silicate melts during heating and cooling cycles.

The Hadamard-Rybczynski equation describes the steady-state buoyant rise velocity of an unconfined spherical bubble in a viscous liquid. This solution has been experimentally validated for the case where the liquid viscosity is held constant. Here, we extend this result for non-isothermal conditions, by developing a solution for bubble position in which we account for the time-dependent liquid viscosity, liquid and gas densities, and bubble radius. We validate this solution using experiments in which spherical bubbles are created in a molten silicate liquid by cutting gas cavities into glass sheets, which are stacked, then heated through the glass transition interval. The bubble-bearing liquid, which has a strongly temperature-dependent viscosity, is subjected to various heating and cooling programs such that the bubble rise velocity varies through the experiment. We find that our predictions match the final observed position of the bubble measured in blocks of cooled glass to within the experimental uncertainty, even after the application of a complex temperature-time pathway. We explore applications of this solution for industrial, artistic, and natural volcanological applied problems.

Emergency care capacity in Sierra Leone: A multicentre analysis.

Background: The Disease Control Priorities Project estimates that over 50 % of annual mortality in low- and middle-income countries can be addressed by improved emergency care. Sierra Leone's Ministry of Health and Sanitation has highlighted emergency care as a national priority. We conducted the first multicentre analysis of emergency care capacity in Sierra Leone, using the Hospital Emergency Unit Assessment Tool (HEAT) to analyse 14 government hospitals across the country. Methods: HEAT is a standardised assessment that is recommended in the World Health Organisation Emergency Care Toolkit. It has been used comparably elsewhere. To analyse Sierra Leone's emergency care capacity with the HEAT data, we created the HEAT-adjusted Emergency Care Capacity Score. Purposeful sampling was used to select 14 government facilities nationwide. A multidisciplinary team was interviewed over a 2-day in-person visit to each facility. Results: Human Resources was the strongest parameter, scoring 49 %. All hospitals provided emergency cover 24/7. Emergency Diagnostic Services was the most severely limited parameter, scoring 29 %. 3 hospitals had no access to basic radiography. Infrastructure scored 47 %. 2 hospitals had adequate electricity supply; 5 had adequate clean, running water. No hospitals had adequate oxygen supply. Clinical services scored 39 %. 10 hospitals had no designated Emergency Unit, only 2 triaged to stratify severity. Signal functions scored 38 %. No hospitals had reliable access to emergency drugs such as adrenaline. The total HEAT-adjusted Emergency Care Capacity Score across all hospitals was 40 %. Conclusions: These data identify gaps that have already led to local interventions, including focussing emergency resources to a resuscitation area, and training multidisciplinary teams in emergency care skills. This facility-level analysis could feed into wider assessment of Sierra Leone's emergency care systems at every level, which may help prioritise government strategy to target sustainable strengthening of national emergency care.

The efficacy of electroencephalography neurofeedback for enhancing episodic memory in healthy and clinical participants: A systematic qualitative review and meta-analysis.

Several studies have examined whether electroencephalography neurofeedback (EEG-NF), a self-regulatory technique where an individual receives real-time feedback on a pattern of brain activity that is theoretically linked to a target behaviour, can enhance episodic memory. The aim of this research was to i) provide a qualitative overview of the literature, and ii) conduct a meta-analysis of appropriately controlled studies to determine whether EEG-NF can enhance episodic memory. The literature search returned 46 studies, with 21 studies (44 effect sizes) meeting the inclusion criteria for the meta-analysis. The qualitative overview revealed that, across EEG-NF studies on both healthy and clinical populations, procedures and protocols vary considerably and many studies were insufficiently powered with inadequate design features. The meta-analysis, conducted on studies with an active control, revealed a small-size, significant positive effect of EEG-NF on episodic memory performance (g = 0.31, p = 0.003), moderated by memory modality and EEG-NF self-regulation success. These results are discussed with a view towards optimising EEG-NF training and subsequent benefits to episodic memory.

Evaluation of the methodological quality of the Health Protection Agency's 2009 guidance on neuraminidase inhibitors.

BACKGROUND: The Health Protection Agency (HPA) issued guidance advocating the prescription of neuraminidase inhibitors in July 2009 in response to a predicted pandemic of influenza. Although the contents of the guidance have been debated, the methodology has not. METHOD: The guidance was evaluated by two reviewers using a validated and internationally recognised tool for assessing guidelines, the Appraisal of Guidelines Research & Evaluation instrument (AGREE). This tool scores six domains independently of each other. RESULTS: The guidance scored 61% for the domain scope and purpose and 54% for the domain clarity and presentation. By contrast, it scored only 31% for rigour of development due to poor linkage of its recommendations to evidence. CONCLUSION: The HPA should improve its performance in this domain to general practitioners in order to improve the credibility of its future guidance.

Impact of a Novel W2027L Mutation and Non-Target Site Resistance on Acetyl-CoA Carboxylase-Inhibiting Herbicides in a French Lolium multiflorum Population.

Herbicides that inhibit acetyl-CoA carboxylase (ACCase) are among the few remaining options for the post-emergence control of Lolium species in small grain cereal crops. Here, we determined the mechanism of resistance to ACCase herbicides in a Lolium multiflorum population (HGR) from France. A combined biological and molecular approach detected a novel W2027L ACCase mutation that affects aryloxyphenoxypropionate (FOP) but not cyclohexanedione (DIM) or phenylpyraxoline (DEN) subclasses of ACCase herbicides. Both the wild-type tryptophan and mutant leucine 2027-ACCase alleles could be positively detected in a single DNA-based-derived polymorphic amplified cleaved sequence (dPACS) assay that contained the targeted PCR product and a cocktail of two discriminating restriction enzymes. Additionally, we identified three well-characterised I1781L, I2041T, and D2078G ACCase target site resistance mutations as well as non-target site resistance in HGR. The non-target site component endowed high levels of resistance to FOP herbicides whilst partially impacting on the efficacy of pinoxaden and cycloxydim. This study adequately assessed the contribution of the W2027L mutation and non-target site mechanism in conferring resistance to ACCase herbicides in HGR. It also highlights the versatility and robustness of the dPACS method to simultaneously identify different resistance-causing alleles at a single ACCase codon.

A derived Polymorphic Amplified Cleaved Sequence assay for detecting the Δ210 PPX2L codon deletion conferring target-site resistance to protoporphyrinogen oxidase-inhibiting herbicides.

BACKGROUND: Resistance to protoporphyrinogen oxidase (PPO)-inhibiting herbicides in Amaranthus rudis from corn/soybean production systems in the USA appears to be mainly due to a codon deletion at position 210 of the target PPX2L gene. In this study, we have developed a simple and cost-effective derived Polymorphic Amplified Cleaved Sequenced (dPACS) marker for detecting this resistance-causing deletion in A. rudis and other relevant weed species. RESULTS: Ninety-six plants from 16 diverse fomesafen-sensitive and resistant A. rudis populations from Illinois and Iowa were used to establish the dPACS procedure. The assay requires forced mismatches in both the forward and reverse PCR primers and uses the restriction enzyme XcmI for the positive identification of wild type glycine residue at PPX2L codon position 210. The data from the dPACS method, using either leaf tissues or seeds as starting material, were completely correlated with direct Sanger sequencing results for samples that gave readable nucleotide peaks around codon 210 of PPX2L. Furthermore, the assay was directly transferable to all four other Amaranthus species tested, and to Ambrosia artemisiifolia using species-specific primers. CONCLUSION: The proposed assay will allow the rapid detection of the Δ210 codon deletion in the PPX2L gene and the timely development of management strategies for tackling growing resistance to PPO-inhibiting herbicides in A. rudis and other broadleaf weed species. © 2019 Society of Chemical Industry.

A holistic approach in herbicide resistance research and management: from resistance detection to sustainable weed control.

Agricultural weeds can adapt rapidly to human activities as exemplified by the evolution of resistance to herbicides. Despite its multi-faceted nature, herbicide resistance has rarely been researched in a holistic manner. A novel approach combining timely resistance confirmation, investigation of resistance mechanisms, alternative control solutions and population modelling was adopted for the sustainable management of the Amaranthus palmeri weed in soybean production systems in Argentina. Here, we show that resistance to glyphosate in the studied population from Cordoba province was mainly due to a P106S target-site mutation in the 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) gene, with minor contributions from EPSPS gene duplication/overexpression. Alternative herbicides, such as fomesafen, effectively controlled the glyphosate-resistant plants. Model simulations revealed the tendency of a solo herbicidal input to primarily select for a single resistance mechanism and suggested that residual herbicides, alongside chemical diversity, were important for the sustainable use of these herbicides. We also discuss the value of an interdisciplinary approach for improved understanding of evolving weeds.

Evolution of Target-Site Resistance to Glyphosate in an Amaranthus palmeri Population from Argentina and Its Expression at Different Plant Growth Temperatures.

The mechanism and expression of resistance to glyphosate at different plant growing temperatures was investigated in an Amaranthus palmeri population (VM1) from a soybean field in Vicuña Mackenna, Cordoba, Argentina. Resistance was not due to reduced glyphosate translocation to the meristem or to EPSPS duplication, as reported for most US samples. In contrast, a proline 106 to serine target-site mutation acting additively with EPSPS over-expression (1.8-fold increase) was respectively a major and minor contributor to glyphosate resistance in VM1. Resistance indices based on LD50 values generated using progenies from a cross between 52 PS106 VM1 individuals were estimated at 7.1 for homozygous SS106 and 4.3 for heterozygous PS106 compared with homozygous wild PP106 plants grown at a medium temperature of 24 °C day/18 °C night. A larger proportion of wild and mutant progenies survived a single commonly employed glyphosate rate when maintained at 30 °C day/26 °C night compared with 20 °C day/16 night in a subsequent experiment. Interestingly, the P106S mutation was not identified in any of the 920 plants analysed from 115 US populations, thereby potentially reflecting the difference in A. palmeri control practices in Argentina and USA.

Comparative genomic hybridization using DNA from laser capture microdissected tissue.

Comparative genomic hybridization (CGH) is a powerful screening technique that can identify regions of gain and loss within the whole genome in a single experiment. The combination of laser capture microdissection, whole-genome amplification, and CGH permits genomic screening with high specificity and sensitivity. This complement of techniques has enabled analysis of focal regions and subpopulations of cells within a tissue, which has previously been difficult, providing insight into disease progression and heterogeneity. This chapter outlines the techniques involved in producing labeled probes from DNA extracted from laser capture microdissected material and the methods for hybridization of these probes to metaphase chromosomes. This protocol can also be applied to the preparation of probes for CGH arrays.

Identification and validation of prognostic markers in breast cancer with the complementary use of array-CGH and tissue microarrays.

Gene amplification, an important mechanism of oncogene activation in breast cancer, can have both prognostic and therapeutic implications. In this work, an attempt is made to identify amplified genes that can be used to improve prognostication in breast cancer. A series of 52 node-negative tumours was screened for genomic gains at 57 loci by array-CGH. A subset of these genes was identified that could divide the series into two divergent outcome groups of either long-term survivors or early disease-related deaths (p = 0.01) using a combination of k-means clustering and statistical analysis. The prognostic significance of amplification of four of the genes (EMS1, TOP2A, CCNE1, and ERBB2) was then evaluated, using fluorescent in situ hybridization on a tissue microarray, in a second larger 'validation' series of 232 tumours with a median follow-up of 4.8 years. Adverse disease-related outcome was associated with amplification of TOP2A (p = 0.004); ERBB2 (p = 0.002); and with the combined amplification of TOP2A, ERBB2, and EMS1 (p = 0.01). EMS1 amplification was more common (26% of cases) than previously reported but, in isolation, had no prognostic significance. Amplification of CCNE1, seen in only 6% of cases, had no prognostic role. These results indicate that the complementary use of array-CGH and tissue microarrays has the potential to help in the identification and validation of molecular markers that can be used to classify breast cancers into different prognostic groups.