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Timanikova N, Fletcher K, Han JW, van West P, Woodward S, Kim GH, Küpper FC, Wenzel M. Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens. Environ Microbiol 2024; 26:e16656. [PMID: 38818657 DOI: 10.1111/1462-2920.16656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
Seaweeds are important components of marine ecosystems with emerging potential in aquaculture and as sources of biofuel, food products and pharmacological compounds. However, an increasingly recognised threat to natural and industrial seaweed populations is infection with parasitic single-celled eukaryotes from the relatively understudied oomycete lineage. Here we examine the eukaryomes of diverse brown, red and green marine macroalgae collected from polar (Baffin Island), cold-temperate (Falkland Islands) and tropical (Ascension Island) locations, with a focus on oomycete and closely related diatom taxa. Using 18S rRNA gene amplicon sequencing, we show unexpected genetic and taxonomic diversity of the eukaryomes, a strong broad-brush association between eukaryome composition and geographic location, and some evidence of association between eukaryome structure and macroalgal phylogenetic relationships (phylosymbiosis). However, the oomycete fraction of the eukaryome showed disparate patterns of diversity and structure, highlighting much weaker association with geography and no evidence of phylosymbiosis. We present several novel haplotypes of the most common oomycete Eurychasma dicksonii and report for the first time a cosmopolitan distribution and absence of host specificity of this important pathogen. This indicates rich diversity in macroalgal oomycete pathogens and highlights that these pathogens may be generalist and highly adaptable to diverse environmental conditions.
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Fletcher K, Wydera S, Thorpe N, Radford K, das Nair R, Booth V. A rapid realist review of clinical neuropsychology rehabilitation programmes to improve psychological wellbeing and quality of life for people with acquired brain injuries. Neuropsychol Rehabil 2023:1-36. [PMID: 37975854 DOI: 10.1080/09602011.2023.2273580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 10/03/2023] [Indexed: 11/19/2023]
Abstract
Approximately 20% of acquired brain injury (ABI) survivors experience reduced psychological wellbeing (PWB). Neuropsychological rehabilitation (NPR) is one approach supporting people with ABI to participate meaningfully in activities despite challenges. Although literature supports NPR effectiveness, little is known about change mechanisms. This systematic realist review identifies what NPR programmes have been designed, delivered, and evaluated for people with ABI to improve PWB and/or quality of life (QOL), as well as providing a context-relevant understanding of what NPR includes and how NPR might lead to positive outcomes. A rapid realist review was conducted in three phases: (1) structured retrieval and evidence extraction; (2) stakeholder consultation; (3) analysis and synthesis. Searches were completed, and findings from 35 publications and one stakeholder consultation were synthesized into a refined logic model. Six context-mechanism-outcome chains (CMOCs) were identified. Participants' relationships to internal experiences, and feelings of self-worth, mastery, and connection appeared to be mechanisms that led to improved PWB and QOL. Adaptation and individualized programmes were also key mechanisms to explain successful NPR. Embedding CMOCs into NPR could improve PWB and/or QOL for people with ABI. The logic model will inform ongoing development of a new online, group-based, NPR programme.
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Fletcher K, Michelmore R. Genome-Enabled Insights into Downy Mildew Biology and Evolution. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:165-183. [PMID: 37268005 DOI: 10.1146/annurev-phyto-021622-103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Oomycetes that cause downy mildew diseases are highly specialized, obligately biotrophic phytopathogens that can have major impacts on agriculture and natural ecosystems. Deciphering the genome sequence of these organisms provides foundational tools to study and deploy control strategies against downy mildew pathogens (DMPs). The recent telomere-to-telomere genome assembly of the DMP Peronospora effusa revealed high levels of synteny with distantly related DMPs, higher than expected repeat content, and previously undescribed architectures. This provides a road map for generating similar high-quality genome assemblies for other oomycetes. This review discusses biological insights made using this and other assemblies, including ancestral chromosome architecture, modes of sexual and asexual variation, the occurrence of heterokaryosis, candidate gene identification, functional validation, and population dynamics. We also discuss future avenues of research likely to be fruitful in studies of DMPs and highlight resources necessary for advancing our understanding and ability to forecast and control disease outbreaks.
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Fletcher K, Martin F, Isakeit T, Cavanaugh K, Magill C, Michelmore R. The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes. G3 (BETHESDA, MD.) 2023; 13:jkac340. [PMID: 36592124 PMCID: PMC9997571 DOI: 10.1093/g3journal/jkac340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/14/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023]
Abstract
Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.
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Abstract
BACKGROUND Systemic racism and inequity are embedded in higher education, especially in nursing. By disregarding health disparities and inequities, a hidden curriculum is endorsed, implicitly letting both instructors and students know that not addressing these subjects is acceptable. METHOD Needs assessments were performed to assess faculty and student attitudes about the needs for justice, equity, diversity, and inclusion (JEDI) concepts. Using the Plan-Do-Study-Act model, the School of Nursing leadership, faculty, and students created taskforces to implement anti-oppression curricula throughout prelicensure courses. RESULTS Anti-oppression curricula and workshops were piloted successfully in the first semester of prelicensure nursing. Student feedback was positive with constructive suggestions. JEDI curriculum mapping was completed across the prelicensure nursing curriculum. CONCLUSION JEDI concepts must be integrated across nursing curricula to identify gaps. Forming a collaboration between leadership, faculty, and students is an optimal way to proceed as they all are invested and accountable for change. [J Nurs Educ. 2022;61(8):447-454.].
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Fletcher K, Shin OH, Clark KJ, Feng C, Putman AI, Correll JC, Klosterman SJ, Van Deynze A, Michelmore RW. Ancestral Chromosomes for Family Peronosporaceae Inferred from a Telomere-to-Telomere Genome Assembly of Peronospora effusa. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:450-463. [PMID: 35226812 DOI: 10.1094/mpmi-09-21-0227-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Downy mildew disease of spinach, caused by the oomycete Peronospora effusa, causes major losses to spinach production. In this study, the 17 chromosomes of P. effusa were assembled telomere-to-telomere, using Pacific Biosciences high-fidelity reads. Of these, 16 chromosomes are complete and gapless; chromosome 15 contains one gap bridging the nucleolus organizer region. This is the first telomere-to-telomere genome assembly for an oomycete. Putative centromeric regions were identified on all chromosomes. This new assembly enables a reevaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora species. Genome fragments consistently underrepresented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. Putative effectors were annotated on 16 of the 17 chromosomes. The intergenic distances between annotated genes were consistent with compartmentalization of the genome into gene-dense and gene-sparse regions. Genes encoding putative effectors were enriched in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae; high levels of synteny were also detected with Phytophthora sojae. Extensive synteny between phylogenetically distant species suggests that many other oomycete species may have similar chromosome organization. Therefore, this assembly provides the foundation for genomic analyses of diverse oomycetes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Fletcher K, Han R, Smilde D, Michelmore R. Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state. BMC Bioinformatics 2022; 23:150. [PMID: 35468720 PMCID: PMC9040317 DOI: 10.1186/s12859-022-04685-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to infer polyploidy and heterokaryosis in diverse organisms using read sets sequenced to greater than 50× whole-genome coverage. However, sequencing to adequate depth is costly if applied to multiple individuals or large genomes. Results We developed VCFvariance.pl to utilize the variance of allele balance to infer polyploidy and/or heterokaryosis at low sequence coverage. This analysis requires as little as 10× whole-genome coverage and reduces the allele balance profile down to a single value, which can be used to determine if an individual has two or more haplotypes. This approach was validated using simulated, synthetic, and authentic read sets from the oomycete species Bremia lactucae and Phytophthora infestans, the fungal species Saccharomyces cerevisiae, and the plant species Arabidopsis arenosa. This approach was deployed to determine that nine of 21 genotyped European race-type isolates of Bremia lactucae were inconsistent with diploidy and therefore likely heterokaryotic. Conclusions Variance of allele balance is a reliable metric to detect departures from a diploid state, including polyploidy, heterokaryosis, a mixed sample, or chromosomal copy number variation. Deploying this strategy is computationally inexpensive, can reduce the cost of sequencing by up to 80%, and used to test any organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04685-z.
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Fletcher K, Zhang L, Gil J, Han R, Cavanaugh K, Michelmore R. AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data. Genome Biol 2021; 22:115. [PMID: 33883006 PMCID: PMC8061198 DOI: 10.1186/s13059-021-02326-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/25/2021] [Indexed: 11/20/2022] Open
Abstract
Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.
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Wood KJ, Nur M, Gil J, Fletcher K, Lakeman K, Gann D, Gothberg A, Khuu T, Kopetzky J, Naqvi S, Pandya A, Zhang C, Maisonneuve B, Pel M, Michelmore R. Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif. PLoS Pathog 2020; 16:e1009012. [PMID: 33104763 PMCID: PMC7644090 DOI: 10.1371/journal.ppat.1009012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/05/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors that has been implicated in immune suppression as well as effector recognition by host resistance proteins. We predicted 55 WY domain containing proteins in the genome of B. lactucae and found substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis of 21 effectors containing WY domains revealed 11 that elicited cell death on wild accessions and domesticated lettuce lines containing resistance genes, indicative of recognition of these effectors by the host immune system. Only two of the 11 recognized effectors contained the canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.
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Zhang Y, Fletcher K, Han R, Michelmore R, Yang R. Genome-Wide Analysis of Cyclophilin Proteins in 21 Oomycetes. Pathogens 2019; 9:E24. [PMID: 31888032 PMCID: PMC7168621 DOI: 10.3390/pathogens9010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/20/2022] Open
Abstract
Cyclophilins (CYPs), a highly-conserved family of proteins, belong to a subgroup of immunophilins. Ubiquitous in eukaryotes and prokaryotes, CYPs have peptidyl-prolyl cis-trans isomerase (PPIase) activity and have been implicated as virulence factors in plant pathogenesis by oomycetes. We identified 16 CYP orthogroups from 21 diverse oomycetes. Each species was found to encode 15 to 35 CYP genes. Three of these orthogroups contained proteins with signal peptides at the N-terminal end, suggesting a role in secretion. Multidomain analysis revealed five conserved motifs of the CYP domain of oomycetes shared with other eukaryotic PPIases. Expression analysis of CYP proteins in different asexual life stages of the hemibiotrophic Phytophthora infestans and the biotrophic Plasmopara halstedii demonstrated distinct expression profiles between life stages. In addition to providing detailed comparative information on the CYPs in multiple oomycetes, this study identified candidate CYP effectors that could be the foundation for future studies of virulence.
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Fletcher K, Gil J, Bertier LD, Kenefick A, Wood KJ, Zhang L, Reyes-Chin-Wo S, Cavanaugh K, Tsuchida C, Wong J, Michelmore R. Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae. Nat Commun 2019; 10:2645. [PMID: 31201315 PMCID: PMC6570648 DOI: 10.1038/s41467-019-10550-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.
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Fletcher K, Klosterman SJ, Derevnina L, Martin F, Bertier LD, Koike S, Reyes-Chin-Wo S, Mou B, Michelmore R. Comparative genomics of downy mildews reveals potential adaptations to biotrophy. BMC Genomics 2018; 19:851. [PMID: 30486780 PMCID: PMC6264045 DOI: 10.1186/s12864-018-5214-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/31/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. RESULTS We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. CONCLUSIONS We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
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Fletcher K, Baines D. The effects of acaricide treatment of sheep on red grouse Lagopus lagopus scotica tick burdens and productivity in a multi-host system. MEDICAL AND VETERINARY ENTOMOLOGY 2018; 32:235-243. [PMID: 29194726 DOI: 10.1111/mve.12282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/14/2017] [Accepted: 10/07/2017] [Indexed: 06/07/2023]
Abstract
Ixodes ricinus (Ixodida: Ixodidae) ticks are of economic and pathogenic importance across Europe. Within the uplands of the U.K., management to reduce ticks is undertaken to benefit red grouse Lagopus lagopus scotica (Galliformes: Phasianidae). Management strategies focus on the acaricide treatment of domestic sheep Ovis aries (Artiodactyla: Bovidae), but the effectiveness of this is less certain in the presence of wild hosts, particularly red deer Cervus elaphus (Artiodactyla: Cervidae) and mountain hare Lepus timidus (Lagomorpha: Leporidae). This study examines the effects of sheep management on grouse tick burdens and productivity using sites with a range of wild host densities. Sites at which applications of acaricide were more frequent had lower tick burdens; this relationship was similar on sites with a range of deer densities. However, no direct link was detected between acaricide treatment interval and grouse productivity. Sites with higher deer densities had higher grouse tick burdens and lower productivity [mean ± standard error (SE) young : adult ratio: 1.2 ± 0.2] compared with sites with lower deer densities (mean ± SE young : adult ratio: 1.8 ± 0.1). Sites with higher grouse brood sizes and higher proportions of hens with broods were also those with higher mountain hare abundance indices. This study highlights the importance of the frequent treatment of sheep with acaricide to reduce tick burdens on grouse, even in the presence of wild hosts.
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Abstract
A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
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Roper DR, De la Salle B, Soni V, Fletcher K, Green JA. Abrogation of red blood cell G6PD enzyme activity through Heat treatment: development of survey material for the UK NEQAS G6PD scheme. Int J Lab Hematol 2017; 39:308-316. [PMID: 28318100 DOI: 10.1111/ijlh.12627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 12/28/2016] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Participation in external quality assessment (EQA) is central to the maintenance of high-quality laboratory results in patient diagnosis and clinical trials. Laboratories in the TAF112582 DETECTIVE study (ClinicalTrials.gov identifier: NCT01376167) are enrolled in the United Kingdom National Quality Assessment Scheme (UK NEQAS) for glucose-6-phosphate dehydrogenase (G6PD) quantitative assay, which utilizes ovine (sheep) blood as a readily available source of apparently G6PD-deficient survey material. A substitute for sheep blood was sought because some non-UK sites in the study encountered participation difficulties due to the strict regulations on the import of sheep blood into their countries. METHODS G6PD activity in normal human donor blood was abrogated by the action of heat under controlled conditions. Residual G6PD activity in the heated samples was measured by UK NEQAS using the Trinity Biotech 345 kit (Trinity Biotech) and a Jenway 6715 UV/Vis spectrophotometer with external temperature control to monitor enzyme kinetics and linearity over a set time. Heat-treated material was also assayed for G6PD activity and assessed for its acceptability as EQA survey material by selected UK laboratories. RESULTS Blood heated at 45 °C for 15 h showed a reduction in G6PD activity of 76.3 ± 4.6% (n = 6) and was considered acceptable as EQA material in terms of appearance and behaviour by the majority of UK sites in the trial. CONCLUSIONS We have developed a simple heat-treatment procedure to produce EQA survey material with low/intermediate G6PD activity, similar to that found in females heterozygous for G6PD deficiency.
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Salih Z, Conway A, Papaxoinis G, Patrao A, Fletcher K, Noble R, Owen-Holt V, Mansoor W. Prognostic significance of neutrophil to lymphocyte ratio (NLR) in patients (pts) with resectable gastric/gastroesophageal junction (GOJ) adenocarcinoma undergoing perioperative chemotherapy. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw371.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bayes AJ, McClure G, Fletcher K, Román Ruiz Del Moral YE, Hadzi-Pavlovic D, Stevenson JL, Manicavasagar VL, Parker GB. Differentiating the bipolar disorders from borderline personality disorder. Acta Psychiatr Scand 2016; 133:187-95. [PMID: 26432099 DOI: 10.1111/acps.12509] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/08/2015] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To identify features differentiating bipolar disorder (BP) from borderline personality disorder (BPD) and with each condition variably defined. METHOD Participants were assigned a BP or BPD diagnosis on the basis of DSM criteria and, separately, by clinical judgment, and undertook a diagnostic interview and completed self-report measures. RESULTS Predictors of BPD status varied according to diagnostic decisions, but with the most consistent items being childhood sexual abuse, childhood depersonalization, personality variables relating to relationship difficulties and sensitivity to criticism, and the absence of any BP family history. Across diagnostic groups, personality measure items alone predicted diagnostic allocation with an accuracy of 81-84%, the refined study variables other than hypo/manic features improved the classification rates to 88%, and when the presence or absence of hypo/manic features was added, classification rates increased to 92-95%. CONCLUSION Study findings indicate that BPD can be differentiated from BP with a high degree of accuracy.
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Fletcher K, Uljević A, Tsirigoti A, Antolić B, Katsaros C, Nikolić V, van West P, Küpper FC. New record and phylogenetic affinities of the oomycete Olpidiopsis feldmanni infecting Asparagopsis sp. (Rhodophyta). DISEASES OF AQUATIC ORGANISMS 2015; 117:45-57. [PMID: 26575155 DOI: 10.3354/dao02930] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new geographic record of the oomycete Olpidiopsis feldmanni infecting the tetrasporophytic stage of the red alga Asparagopsis sp. from the Adriatic Sea, confirmed through morphological identification, allowed us to expand previous observations of this organism. Ultrastructural investigations of environmental material showed a large central vacuole and a cell wall thicker than previously reported from other basal oomycete pathogens of algae. Phylogenetic analysis closely associates O. feldmanni to O. bostrychiae concurrent with structural observations. This constitutes the first genetic characterisation of an Olpidiopsis species that was initially described before 1960, adding to the genetic data of 3 other marine Olpidiopsis species established and genetically characterised in the last 2 decades. The paper discusses concurrences of the ultrastructural observations made here and in previous studies of the marine Olpidiopsis species with those made on the freshwater species.
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Fletcher K. Very Low Cost Intensive Therapeutic Support and Long Term Monitoring for Patients with Alcohol Dependence Using New Technology. Eur Psychiatry 2015. [DOI: 10.1016/s0924-9338(15)31902-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Fletcher K, Stone E. New Technology to Support Abstinence From Alcohol, Predict Relapse and Reduce Out-patient Costs. Eur Psychiatry 2015. [DOI: 10.1016/s0924-9338(15)30855-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Parker G, Fletcher K, Blanch B, Greenfield L. The 'real world' utility of a web-based bipolar disorder screening measure. Acta Psychiatr Scand 2013; 127:373-80. [PMID: 23039131 DOI: 10.1111/acps.12017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/03/2012] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To determine whether those completing a self-report bipolar self-test measure and identified as having a likely bipolar disorder judged the self-test as useful and had a subsequent superior illness course. METHOD We invited those completing the web-based Mood Swings Questionnaire (or MSQ) to provide contact details and contribute to a 3-month study evaluating their responses to being identified as having a likely bipolar disorder, any subsequent action taken and the impact of such actions on their illness trajectory. RESULTS We analysed data received from 665 participants screening 'positive' on the MSQ and completing baseline and 3-month follow-up data. High rates of satisfaction with the MSQ were quantified, with respondents viewing the measure as informative, validating and/or motivating. Of those receiving a confirmed bipolar diagnosis, such clarification occurred on average 12 years after their first depressive episode. Most implemented self-management strategies irrespective of whether seeking formal diagnostic clarification or not. Participants improved on depressive, quality of life and overall functioning measures over the study period, but with results indicating (via analysis of three sample subsets differing by the degree of 'actions taken') that those who took assertive action and had the diagnosis confirmed had the most superior outcome. CONCLUSION This is the first study to formally evaluate the clinical impact of a self-report bipolar disorder screening measure. High acceptance and superior outcomes quantified for those acting assertively in response to such a new diagnosis argue for its 'real world' utility.
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Casey DT, Frenje JA, Johnson MG, Séguin FH, Li CK, Petrasso RD, Glebov VY, Katz J, Magoon J, Meyerhofer DD, Sangster TC, Shoup M, Ulreich J, Ashabranner RC, Bionta RM, Carpenter AC, Felker B, Khater HY, LePape S, MacKinnon A, McKernan MA, Moran M, Rygg JR, Yeoman MF, Zacharias R, Leeper RJ, Fletcher K, Farrell M, Jasion D, Kilkenny J, Paguio R. The magnetic recoil spectrometer for measurements of the absolute neutron spectrum at OMEGA and the NIF. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:043506. [PMID: 23635195 DOI: 10.1063/1.4796042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The neutron spectrum produced by deuterium-tritium (DT) inertial confinement fusion implosions contains a wealth of information about implosion performance including the DT yield, ion-temperature, and areal-density. The Magnetic Recoil Spectrometer (MRS) has been used at both the OMEGA laser facility and the National Ignition Facility (NIF) to measure the absolute neutron spectrum from 3 to 30 MeV at OMEGA and 3 to 36 MeV at the NIF. These measurements have been used to diagnose the performance of cryogenic target implosions to unprecedented accuracy. Interpretation of MRS data requires a detailed understanding of the MRS response and background. This paper describes ab initio characterization of the system involving Monte Carlo simulations of the MRS response in addition to the commission experiments for in situ calibration of the systems on OMEGA and the NIF.
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Casey DT, Frenje JA, Gatu Johnson M, Séguin FH, Li CK, Petrasso RD, Glebov VY, Katz J, Knauer JP, Meyerhofer DD, Sangster TC, Bionta RM, Bleuel DL, Döppner T, Glenzer S, Hartouni E, Hatchett SP, Le Pape S, Ma T, MacKinnon A, McKernan MA, Moran M, Moses E, Park HS, Ralph J, Remington BA, Smalyuk V, Yeamans CB, Kline J, Kyrala G, Chandler GA, Leeper RJ, Ruiz CL, Cooper GW, Nelson AJ, Fletcher K, Kilkenny J, Farrell M, Jasion D, Paguio R. Measuring the absolute deuterium-tritium neutron yield using the magnetic recoil spectrometer at OMEGA and the NIF. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2012; 83:10D912. [PMID: 23126915 DOI: 10.1063/1.4738657] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A magnetic recoil spectrometer (MRS) has been installed and extensively used on OMEGA and the National Ignition Facility (NIF) for measurements of the absolute neutron spectrum from inertial confinement fusion implosions. From the neutron spectrum measured with the MRS, many critical implosion parameters are determined including the primary DT neutron yield, the ion temperature, and the down-scattered neutron yield. As the MRS detection efficiency is determined from first principles, the absolute DT neutron yield is obtained without cross-calibration to other techniques. The MRS primary DT neutron measurements at OMEGA and the NIF are shown to be in excellent agreement with previously established yield diagnostics on OMEGA, and with the newly commissioned nuclear activation diagnostics on the NIF.
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Sheppard JP, Singh S, Fletcher K, McManus RJ, Mant J. Impact of age and sex on primary preventive treatment for cardiovascular disease in the West Midlands, UK: cross sectional study. BMJ 2012; 345:e4535. [PMID: 22791787 PMCID: PMC3395734 DOI: 10.1136/bmj.e4535] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/23/2012] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To establish the impact of age and sex on primary preventive treatment for cardiovascular disease in a typical primary care population. DESIGN Cross sectional study of anonymised patient records. PARTICIPANTS All 41,250 records of patients aged ≥ 40 registered at 19 general practices in the West Midlands, United Kingdom, were extracted and analysed. MAIN OUTCOME MEASURES Patients' demographics, risk factors for cardiovascular disease (blood pressure, total cholesterol concentration), and prescriptions for primary preventive drugs were extracted from patients' records. Patients were subdivided into five year age bands up to 85 (patients aged ≥ 85 were analysed as one group) and prescribing trends across the population were assessed by estimating the proportion of patients prescribed with antihypertensive drug or statin drug, or both, in each group. RESULTS Of the 41,250 records screened in this study, 36,679 (89%) patients did not have a history of cardiovascular disease and therefore could be considered for primary preventive treatment. The proportion receiving antihypertensive drugs increased with age (from 5% (378/6978) aged 40-44 to 57% (621/1092) aged ≥ 85) as did the proportion taking statins up to the age of 74 (from 3% (201/6978) aged 40-44 to 29% (675/2367) aged 70-74). In those aged 75 and above, the odds of a receiving prescription for a statin (relative to the 40-44 age group) decreased with every five year increment in age (odds ratio 12.9 (95% confidence interval 10.8 to 15.3) at age 75-79 to 5.7 (4.6 to 7.2) at age ≥ 85; P<0.001). There were no consistent differences in prescribing trends by sex. CONCLUSIONS Previously described undertreatment of women in secondary prevention of cardiovascular disease was not observed for primary prevention. Low use of statins in older people highlights the need for a stronger evidence base and clearer guidelines for people aged over 75.
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Roalfe AK, Bryant TL, Davies MH, Hackett TG, Saba S, Fletcher K, Lip GYH, Hobbs FDR, Mant J. A cross-sectional study of quality of life in an elderly population (75 years and over) with atrial fibrillation: secondary analysis of data from the Birmingham Atrial Fibrillation Treatment of the Aged study. Europace 2012; 14:1420-7. [DOI: 10.1093/europace/eus102] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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