Publications by authors named "Matthew E Smith"

131 Publications

Thaxterogaster revisited: A phylogenetic and taxonomic overview of sequestrate Cortinarius from Patagonia.

Mycologia 2021 Jul 8:1-34. Epub 2021 Jul 8.

Department of Plant Pathology, University of Florida, PO BOX 110680, Gainesville, Florida 32611.

In the Patagonian region, is the most diverse and abundant genus of ectomycorrhizal fungi with at least 250 species. Sequestrate forms were until recently documented within the genus , a genus now known to be polyphyletic, and many were consequently transferred to . Original descriptions were mostly available in German and Spanish and interpretations of morphological structures outdated. Despite recent advances in systematics, the current classification, diversity, and ecology of sequestrate "cortinarioid" fungi in Patagonia remain unclear. The objective of this study was to provide an update on sequestrate of southern South America. We documented each species with morphological descriptions, photographs, basidiospore scanning electron microscopy (SEM) images, and molecular characterization using nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S) sequence data. Original descriptions of taxa were also translated to English and revised based on fresh collections. We documented 24 species from Patagonia based on molecular data and conducted morphological and phylogenetic analysis for 18 previously described species based on type and reference specimens. In addition, we formally described two new species. Four additional taxa were provisionally determined as new but require further study. New ITS sequence data were produced from eight type specimens. We also provide a new name, , nom. nov., for the taxon previously described as . In addition to the species treated in detail, we provided additional reference information and discussion on six described species that remained incompletely known or for which no recent collections were found. Of the 24 taxa documented from Patagonia, 15 species were assigned to 12 current sections in the genus . Analysis of spore ultrastructure showed that sequestrate forms of Patagonian lack a true perisporium.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2021.1894535DOI Listing
July 2021

Multilocus phylogenies reveal three new truffle-like taxa and the traces of interspecific hybridization in Octaviania (Boletaceae, Boletales).

IMA Fungus 2021 Jun 11;12(1):14. Epub 2021 Jun 11.

Department of Plant Pathology, University of Florida, Gainesville, Florida, 32611-0680, USA.

Among many convergently evolved sequestrate fungal genera in Boletaceae (Boletales, Basidiomycota), the genus Octaviania is the most diverse. We recently collected many specimens of Octaviania subg. Octaviania, including several undescribed taxa, from Japan and the Americas. Here we describe two new species in subgenus Octaviania, O. tenuipes and O. tomentosa, from temperate to subtropical evergreen Fagaceae forests in Japan based on morphological observation and robust multilocus phylogenetic analyses (nrDNA ITS and partial large subunit [LSU], translation elongation factor 1-α gene [TEF1] and the largest subunit of RNA polymerase II gene [RPB1]). Based on specimens from the Americas as well as studies of the holotype, we also taxonomically re-evaluate O. asterosperma var. potteri. Our analysis suggests that O. asterosperma var. potteri is a distinct taxon within the subgenus Octaviania so we recognize this as O. potteri stat. nov. We unexpectedly collected O. potteri specimens from geographically widespread sites in the USA, Japan and Colombia. This is the first verified report of Octaviania from the South American continent. Our molecular analyses also revealed that the RPB1 sequence of one O. tenuipes specimen was identical to that of a closely related species, O. japonimontana, and that one O. potteri specimen from Minnesota had an RPB1 sequence of an unknown species of O. subg. Octaviania. Additionally, one O. japonimontana specimen had an unusually divergent TEF1 sequence. Gene-tree comparison and phylogenetic network analysis of the multilocus dataset suggest that these heterogenous sequences are most likely the result of previous inter- and intra-specific hybridization. We hypothesize that frequent hybridization events in Octaviania may have promoted the high genetic and species diversity found within the genus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-021-00066-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8194053PMC
June 2021

Loose Ends in the Phylogeny: Five New Myxotelamonoid Species Indicate a High Diversity of These Ectomycorrhizal Fungi with South American .

Life (Basel) 2021 May 5;11(5). Epub 2021 May 5.

Institute of Microbiology, University Innsbruck, 6020 Innsbruck, Austria.

This paper is a contribution to the current knowledge of taxonomy, ecology and distribution of South American (Pers.) Gray. is among the most widely distributed and species-rich basidiomycete genera occurring with South American and species are found in many distinct habitats, including shrublands and forests. Due to their ectomycorrhizal role, species are critical for nutrient cycling in forests, especially at higher latitudes. Some species have also been reported as edible fungi with high nutritional quality. Our aim is to unravel the taxonomy of selected belonging to phlegmacioid and myxotelamonioid species based on morphological and molecular data. After widely sampling specimens in Patagonian forests and comparing them to reference collections (including holotypes), we propose five new species of in this work. Phylogenetic analyses of concatenated rDNA ITS-LSU and 1 sequences failed to place these new species into known sections or lineages. These findings highlight our knowledge gaps regarding the fungal diversity of South American forests. Due to the high diversity of endemic Patagonian taxa, it is clear that the South American diversity needs to be discovered and described in order to understand the evolutionary history of on a global scale.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/life11050420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148173PMC
May 2021

Effects of Field Fumigation and Inoculation With the Pecan Truffle () on the Fungal Community of Pecan () Seedlings Over 5 Years.

Front Microbiol 2021 13;12:661515. Epub 2021 May 13.

Department of Plant Pathology, University of Florida, Gainesville, FL, United States.

Truffle fungi are esteemed for their aromatic qualities and are among the most widely cultivated edible ectomycorrhizal fungi. Here we document a successful method for establishing , the pecan truffle, on pecan () seedlings in a field setting. We assessed the impacts of soil fumigation and varying concentrations of truffle spore inoculum on the ectomycorrhizal fungal and the complete fungal communities as well as the colonization of on pecan roots at three nurseries in Georgia, United States. To identify fungal communities on pecan seedlings, we performed high-throughput amplicon sequencing of the fungal ITS1 rDNA region. Our 5-year long field experiment demonstrates that fumigation and inoculation together resulted in the highest persistence of on pecan roots. While fungal OTU numbers fluctuated over the years of our experiments, there was no statistical support to demonstrate diversification of communities when Shannon diversity metrics were used. However, we did find that older seedlings were less likely to be dominated by compared to younger ones, suggesting successional changes in the fungal community over time. This suggests that transplanting inoculated seedlings after 2 or 3 years post-inoculation is optimal for future truffle propagation efforts. Our results demonstrate that can be established with methods that are compatible with current pecan nursery industry practices and that fungal communities on pecan seedlings vary depending on the experimental treatments used during planting. While the pecan truffle is not yet widely cultivated, our results provide insights for future large-scale cultivation of this and perhaps other species.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2021.661515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155716PMC
May 2021

gen. nov. (Leotiomycetes, Chlorociboriaceae).

MycoKeys 2021 7;80:19-43. Epub 2021 May 7.

Royal Botanic Gardens Victoria, Melbourne, Victoria 3004, Australia Royal Botanic Gardens Victoria Melbourne Australia.

A second genus in Chlorociboriaceae is described here as Macroscopically distinctive, all species have bright yellow apothecia with several apothecial cups held on short branches at the tip of a long stipe. The genus is widely distributed across the Southern Hemisphere; the four new species described here include two from Chile ( , ) and one each from New Zealand ( ) and Australia ( ). They differ from species referred to , the only other genus in Chlorociboriaceae, in their terrestrial habitat and ascomata that are noticeably more hairy than the known species, most of which have apothecia with short, macroscopically indistinct hair-like elements. Based on our analyses, as accepted here is paraphyletic. Additional study is needed to clarify where alternative, monophyletic generic limits should be drawn and how these genera may be recognised morphologically. Also described here are three new spp. from New Zealand ( , , ), distinctive in developing on dead leaves rather than wood and in two of them not forming the green pigmentation characteristic of most species. New Zealand specimens previously incorrectly identified as are provided with a new name,
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3897/mycokeys.80.64435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121775PMC
May 2021

Acute otitis externa: Consensus definition, diagnostic criteria and core outcome set development.

PLoS One 2021 14;16(5):e0251395. Epub 2021 May 14.

Salford Royal Hospital, Salford, United Kingdom.

Objective: Evidence for the management of acute otitis externa (AOE) is limited, with unclear diagnostic criteria and variably reported outcome measures that may not reflect key stakeholder priorities. We aimed to develop 1) a definition, 2) diagnostic criteria and 3) a core outcome set (COS) for AOE.

Study Design: COS development according to Core Outcome Measures in Effectiveness Trials (COMET) methodology and parallel consensus selection of diagnostic criteria/definition.

Setting: Stakeholders from the United Kingdom.

Subjects And Methods: Comprehensive literature review identified candidate items for the COS, definition and diagnostic criteria. Nine individuals with past AOE generated further patient-centred candidate items. Candidate items were rated for importance by patient and professional (ENT doctors, general practitioners, microbiologists, nurses, audiologists) stakeholders in a three-round online Delphi exercise. Consensus items were grouped to form the COS, diagnostic criteria, and definition.

Results: Candidate COS items from patients (n = 28) and literature (n = 25) were deduplicated and amalgamated to a final candidate list (n = 46). Patients emphasised quality-of-life and the impact on daily activities/work. Via the Delphi process, stakeholders agreed on 31 candidate items. The final COS covered six outcomes: pain; disease severity; impact on quality-of-life and daily activities; patient satisfaction; treatment-related outcome; and microbiology. 14 candidate diagnostic criteria were identified, 8 reaching inclusion consensus. The final definition for AOE was 'diffuse inflammation of the ear canal skin of less than 6 weeks duration'.

Conclusion: The development and adoption of a consensus definition, diagnostic criteria and a COS will help to standardise future research in AOE, facilitating meta-analysis. Consulting former patients throughout development highlighted deficiencies in the outcomes adopted previously, in particular concerning the impact of AOE on daily life.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251395PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8121300PMC
May 2021

A single-cell genomics pipeline for environmental microbial eukaryotes.

iScience 2021 Apr 10;24(4):102290. Epub 2021 Mar 10.

US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA.

Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.isci.2021.102290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8042348PMC
April 2021

Four new species of sequestrate from Chilean Nothofagaceae forests.

Mycologia 2021 May-Jun;113(3):629-642. Epub 2021 Mar 2.

Department of Plant Pathology, University of Florida, P.O. Box 110680, Gainesville, Florida 32611.

Sequestrate fungi have enclosed hypogeous, subhypogeous, or epigeous basidiomes and have lost the ability to actively discharge their spores. They can be distinguished as gasteroid (basidiome fully enclosed with a loculated hymenophore) or secotioid (basidiome with some agaricoid or pileate-stipitate features, but the lamellae are misshapen and unexposed or mostly unexposed at maturity). There are only four reports of sequestrate taxa within the ectomycorrhizal family Inocybaceae, three from Australia and one from western North America. Recent field work in Nothofagaceae forests in the Chilean coastal range revealed novel sequestrate forms of . We examined specimens using a combination of morphological and molecular data from nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuc 28S rDNA (28S) and the gene encoding the second largest subunit of RNA polymerase II (). Here, we describe four new sequestrate species, , and . Results of our phylogenetic analysis resolved the four new species as distinct species-level clades with strong support, suggesting that these fungi have convergently evolved sequestrate forms independently. The species described here were all placed along with members of the "smooth-spored temperate austral clade," which includes almost exclusively Australasian and South American species of .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2020.1859324DOI Listing
March 2021

Dissolvable intranasal haemostatic agents for acute epistaxis: A systematic review and meta-analysis.

Clin Otolaryngol 2021 May 27;46(3):485-493. Epub 2021 Jan 27.

Ear, Nose and Throat Department, Addenbrooke's Hospital, Cambridge, UK.

Introduction: Nasal packing is the mainstay of epistaxis management; however, packs cause patient discomfort and can lead to hospital admission. Absorbable haemostats provide clotting factors or act as a substrate to stimulate clotting and represent a potential treatment alternative. A systematic review was performed to evaluate the efficacy of topical haemostats in the management of epistaxis.

Methods: A systematic literature search of 7 databases was performed. Only eligible randomised controlled trials (RCTs) and observational studies were included. The primary outcome was short-term haemostatic success (<7 days). Secondary outcomes included long-term haemostatic control (no rebleeding 7-30 days), patient discomfort and adverse effects. Meta-analysis was performed where possible.

Results: Of 2249 records identified, 12 were included in the qualitative synthesis and 4 RCTs were included in meta-analysis. The following haemostats were reported: gelatin-thrombin matrix (n = 8), aerosolised/gel tranexamic acid (n = 1), cellulose agents (n = 2) and fibrin sealants (n = 1). Studies involving tranexamic acid on removable delivery devices (eg, pledgets) were excluded. There was heterogeneity in outcome measures and inclusion criteria (coagulopathies/anticoagulants were excluded in 3 RCTs and 2 observational studies). The short-term haemostatic success varied between studies (13.9% to 100%). No significant post-procedural complications were reported. The meta-analysis favoured absorbable haemostatic agent versus packing (risk ratio 1.20; 95% confidence interval 1.05 to 1.37; P = .007). The risk of bias across all studies was moderate to high.

Conclusions: The evidence suggests haemostatic agents are effective at managing acute epistaxis when compared with nasal packing. More data are required before recommendations can be made regarding management in patients on anticoagulants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/coa.13717DOI Listing
May 2021

Paediatric tonsillectomy in England: A cohort study of clinical practice and outcomes using Hospital Episode Statistics data (2008-2019).

Clin Otolaryngol 2021 May 19;46(3):552-561. Epub 2021 Jan 19.

The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.

Objectives: To assess the safety of paediatric tonsillectomy procedures conducted in NHS hospitals in England between 2008 and 2019.

Design: Retrospective observational cohort study using Hospital Episode Statistics (HES) data.

Setting: Acute NHS trusts in England conducting paediatric tonsillectomy procedures.

Participants: Children (≤16 years old) undergoing bilateral tonsillectomy.

Main Outcome Measures: Number of tonsillectomies performed per year by procedural method. In-hospital complications including return to theatre for arrest of haemorrhage. Readmission within 28 days, including those for pain, haemorrhage and surgical arrest of haemorrhage. Long-term outcomes: all-cause mortality, revision tonsillectomy.

Results: A total of 318 453 paediatric tonsillectomies were performed from 2008 to 2019:278,772 dissection (87.5%) and 39 681 coblation (12.5%). The proportion of tonsillectomy performed using coblation increased from 7% in 2008/9 to 27% in 2018/9. Five patients died in hospital (including 4 due to respiratory complications). In-hospital complications occurred in 4202 children (1.3%), with the most frequent being haemorrhage. Within 28 days of tonsillectomy, 28 170 patients (8.8%) were readmitted and 7 deaths occurred. Readmission rates for haemorrhage and pain have increased since 2008. The proportion of children undergoing revision tonsillectomy procedures within 5 years following coblation tonsillectomy (1.4%) was approximately double that of dissection (0.6%).

Conclusions: Clinical practice of paediatric tonsillectomy has changed in England over the past 11 years. The overall mortality rate associated with the procedure is 0.0037%. Differences in outcomes have been identified for different procedural methods. However, routine administrative data are limited in differentiating procedural detail (eg we are unable to differentiate intra or extra-capsular techniques from current clinical coding of tonsillectomy procedures). Therefore, prospective national data collection or more granular clinical coding is essential to capture relative outcomes of the different tonsillectomy methods and techniques being used in the NHS.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/coa.13707DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048929PMC
May 2021

Admission avoidance in tonsillitis and peritonsillar abscess: a prospective national audit during the initial peak of the COVID-19 pandemic.

Authors:
Matthew E Smith

Clin Otolaryngol 2020 Dec 2. Epub 2020 Dec 2.

Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.

Objectives: To report changes in practice brought about by COVID-19 and the implementation of new guidelines for the management of tonsillitis and peritonsillar abscess (PTA), and to explore factors relating to unscheduled re-presentations for patients discharged from the emergency department (ED).

Design: Prospective multicentre national audit over 12 weeks from 6th April 2020.

Setting: UK secondary care ENT departments.

Participants: Adult patients with acute tonsillitis or PTA.

Main Outcome Measures: Re-presentation within 10 days for patients discharged from the ED.

Results: 83 centres submitted 765 tonsillitis and 416 PTA cases. 54.4% (n=410) of tonsillitis and 45.3% (187/413) of PTAs were discharged from ED. 9.6% (39/408) of tonsillitis and 10.3% (19/184) of PTA discharges re-presented within 10 days, compared to 9.7% (33/341) and 10.6% (24/224) for those admitted from ED. The subsequent admission rate of those initially discharged from ED was 4.7% for tonsillitis and 3.3% for PTAs. IV steroids and antibiotics increased the percentage of patients able to swallow from 35.8% to 72.5% for tonsillitis (n=270/754 and 441/608) and from 22.3% to 71.0% for PTA (n=92/413 and 265/373). 77.2% of PTAs underwent drainage (n=319/413), with no significant difference in re-presentations in those drained vs not-drained (10.6% vs 9.5%, n=15/142 vs 4/42, p=0.846). Univariable logistic regression showed no significant predictors of re-presentation within 10 days.

Conclusions: Management of tonsillitis and PTA changed during the initial peak of the pandemic, shifting towards outpatient care. Some patients who may previously have been admitted to hospital may be safely discharged from the ED.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/coa.13680DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7753410PMC
December 2020

The Ambrosia Beetle (Scolytinae: Hyorrhynchini) is Associated with the Canker Disease Fungus (Xylariales).

Plant Dis 2020 Dec 2;104(12):3143-3150. Epub 2020 Nov 2.

School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, U.S.A.

Ambrosia beetles in the subtribe Hyorrhynchini are one example of an entire ambrosia beetle lineage whose fungi have never been studied. Here, we identify one dominant fungus associated with a widespread Asian hyorrhynchine beetle . This fungus was consistently isolated from beetle galleries from multiple collections. Phylogenetic analyses of combined ITS rDNA and β-tubulin sequences identified the primary fungal symbiont as Higuchi, Nikaido & Hattori (Diatrypaceae, Xylariales, Sordariomycetes), which was recently described as a pathogen of sycamore ( spp.) in Japan. To assess the invasion potential of this beetle-fungus interaction into the U.S., we have investigated the pathogenicity of two strains on four species of healthy landscape trees native to the southeastern United States. Only Shumard oak () responded with lesions significantly greater than the control inoculations, but there was no observable dieback or tree mortality. Although disease symptoms were not as prominent as in previous studies of the same fungus in Japan, routine reisolation from the inoculation point suggests that this species is capable of colonizing healthy sapwood of several tree species. Our study shows that the geographical area of its distribution is broader in Asia and potentially includes many hosts of its polyphagous vector. We conclude that the - symbiosis has high invasion potential but low damage potential, at least on young trees during the growing season.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PDIS-03-20-0482-REDOI Listing
December 2020

Hysterangium bonobo: A newly described truffle species that is eaten by bonobos in the Democratic Republic of Congo.

Mycologia 2020 Nov-Dec;112(6):1203-1211. Epub 2020 Sep 4.

Department of Plant Pathology, University of Florida , Gainesville, Florida 32611.

Many animals have been shown to eat fungi and most truffle-like fungi depend on animals for spore dispersal via mycophagy. Although these interactions are widespread, they are understudied in many habitats. In this study, we show that bonobos () forage and feed on an undescribed truffle species in the rainforests of the Democratic Republic of Congo. Based on morphological and molecular assessment of collections, we show that the species eaten by bonobos is a previously undescribed taxon described here as . This species is known in the local Bantu language (Bongando) as simbokilo and is used for baiting traps to catch several species of small mammals. Our findings highlight the need for further research into mycophagy and systematics of sequestrate fungi in Africa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2020.1790234DOI Listing
September 2020

Post-Treatment Head and Neck Cancer Care: National Audit and Analysis of Current Practice in the United Kingdom.

Clin Otolaryngol 2020 Jul 30. Epub 2020 Jul 30.

INTEGRATE, (UK ENT Trainee Research Network), Nottingham, UK.

Objectives: We aimed to audit current United Kingdom (UK) practice of Head and Neck Cancer (HNC) post-treatment surveillance against national guidelines, and determine the outcomes of these practices in detecting recurrence.

Design: National cross-sectional study of current HNC surveillance practice.

Setting: UK HNC outpatient departments.

Participants: HNC patients reviewed for post-treatment surveillance.

Main Outcome Measures: Compliance with UK multidisciplinary guidelines, and rates of cancer recurrence detection by time, clinic type and symptoms.

Results: Data were analysed from 5,123 consultations across 89 UK centres. 30% of consultations were in dedicated multidisciplinary clinics, with input from Allied Health Professionals (AHPs) available on the day in 23% of all consultations. Recurrence was suspected in 344 consultations and investigated with MRI in 29.6% (n=102) and PET-CT in 14.2% (n=49). Patient education regarding recurrence symptoms, and smoking and alcohol advice, was provided in 20.4%, 6.2%, and 5.3% of cases, respectively. Rates of recurrence detected were 35% in expedited appointments and 5.2% in planned follow-ups (p=0.0001). Of the expedited appointments, 63% were initiated by patients and 37% by clinicians. Recurrence was higher in those with new symptoms (7.1% versus 2.2%). The strongest predictors of recurrence were dyspnoea (positive predictive value (PPV)=16.2%), neck pain (PPV=10.4%) and mouth/throat pain (PPV=9.2%).

Conclusions: Dedicated multidisciplinary clinics comprise a minority of consultations for HNC surveillance in the UK, with low availability of AHPs. PET-CT and MRI were underutilised for the investigation of suspected recurrence. There may be scope for greater emphasis on patient education and consequent patient-initiated symptom driven follow-up.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/coa.13616DOI Listing
July 2020

Large-spored is a species causing disease on the invasive grass .

Mycologia 2020 Sep-Oct;112(5):921-931. Epub 2020 Jul 23.

Department of Plant Pathology, University of Florida , Gainesville, Florida 32611.

Environmentally damaging invasive plants can also serve as reservoir hosts for agricultural pathogens. is an invasive C4 annual grass that is present throughout the midwestern and eastern United States. It can reach high densities in disturbed areas such as crop-forest interfaces, which creates the potential for pathogen spillover from to agricultural crops and native plants. A previous study that surveyed disease on found a large-spored species that was widespread on and also isolated from co-occurring native grasses. Here, we report that the large-spored fungus isolated from and the native grass is , based on comparison with published descriptions of morphological traits, and establish that is a pathogen of and . We review the phylogenetic placement and taxonomic history of and propose that it be reassigned to the genus as
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2020.1781495DOI Listing
July 2020

Eustachian Tube Function in Patients with Symptoms on Baro-Challenge.

Audiol Neurootol 2020 26;25(5):249-257. Epub 2020 May 26.

Cambridge Ear Institute, University of Cambridge, Cambridge, United Kingdom,

Objectives: To explore the relationship between aural symptoms during baro-challenge and the underlying measured Eustachian tube (ET) function. Two key questions were addressed. (1) In patients who have features of obstructive ET dysfunction, is there a measurable underlying difference in ET function between those who experience severe symptoms on baro-challenge and those that do not? (2) What is the diagnostic value of ET function tests in the identification of patients with severe symptoms on baro-challenge?

Methods: Patients with symptoms of obstructive ET dysfunction were recruited, with the presence of aural symptoms on baro-challenge established via the clinical history and analysis of the Cambridge ET Dysfunction Assessment, a patient-reported outcome measure (PROM). ET function tests were assessed in each patient: 9 objective and semi-objective measures of ET opening, and 2 symptom-based PROMs. The tests' results were grouped by type of ET opening assessed, generating passive and active dysfunction scores. Individual test results were assessed for diagnostic accuracy in reference to features in the history or PROM-based evidence of symptoms on baro-challenge.

Results: Both passive and active opening of the ET was significantly reduced in ears with a history of pain on baro-challenge. Some patients had apparent severe obstructive ET dysfunction without symptoms on baro-challenge, whilst others had symptoms but normal test results. No individual test of ET opening was of diagnostic value in predicting those ears likely to experience pain or exacerbated symptoms on baro-challenge.

Conclusion: The relationship between aural pain during baro-challenge and ET function appears more complex than had been assumed, with pain possibly related to factors other than just ET function.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1159/000505655DOI Listing
May 2021

Taxonomic notes on eight species of obligate mycoparasites in the genus isolated from soil and dung.

Mycologia 2020 May-Jun;112(3):552-569. Epub 2020 Mar 12.

Department of Plant Pathology, 1453 Fifield Hall, P.O. Box 110680, University of Florida , Gainesville, Florida 32611-0680.

Species of (Zoopagomycotina, Piptocephalidaceae) are obligate mycoparasites that grow on common saprobic species of Mortierellomycotina and Mucoromycotina in soil and dung. Despite their ubiquitous occurrence across the globe, fungi in the genus are understudied, and there are few modern taxonomic treatments of these fungi. In order to clarify species concepts in the genus, we provide morphological data and discuss seven classical species: , and . Three of these species are only known as herbarium specimens (). We have isolated co-cultures of the remaining parasites (, and ) on their host fungi both from nature and from culture collections. The remaining taxon () was revived from a lyophilized culture. We provide photos and updated descriptions for all of these species as well as new geographic data and references to documented herbarium specimens for each taxon. In addition, we also describe the new species .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2019.1705126DOI Listing
May 2021

(Boletaceae, Basidiomycota) - a new monotypic sequestrate genus and species from Brazilian Atlantic Forest.

MycoKeys 2020 3;62:53-73. Epub 2020 Feb 3.

Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Campus Universitário, CEP: 59072-970, Natal, RN, Brazil Universidade Federal do Rio Grande do Norte Natal Brazil.

A new monotypic sequestrate genus, is described based on collections from the Neotropical forest of Atlantic forest in Paraíba, Northeast Brazil - an area known for its high degree of endemism. The striking features of this new fungus are the hypogeous habit, the vivid yellow peridium in mature basidiomes, broadly ellipsoid basidiospores with a distinct wall that is ornamented with longitudinal striations and lageniform cystidia with rounded apices. Phylogenetic analysis, based on LSU and regions, showed that the type species, , is phylogenetically sister to the monotypic sequestrate African genus in Boletaceae. Together these two species formed the earliest diverging lineage in the subfamily Zangioideae. is found in nutrient-poor white sand habitats where plants in the genera (Polygonaceae) and (Nyctaginaceae) are the only potential ectomycorrhizal host symbionts.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3897/mycokeys.62.39699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7010843PMC
February 2020

Engineered transient and stable overexpression of translation factors eIF3i and eIF3c in CHOK1 and HEK293 cells gives enhanced cell growth associated with increased c-Myc expression and increased recombinant protein synthesis.

Metab Eng 2020 05 13;59:98-105. Epub 2020 Feb 13.

Industrial Biotechnology Centre and School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, UK. Electronic address:

There is a desire to engineer mammalian host cell lines to improve cell growth/biomass accumulation and recombinant biopharmaceutical protein production in industrially relevant cell lines such as the CHOK1 and HEK293 cell lines. The over-expression of individual subunits of the eukaryotic translation factor eIF3 in mammalian cells has previously been shown to result in oncogenic properties being imparted on cells, including increased cell proliferation and growth and enhanced global protein synthesis rates. Here we report on the engineering of CHOK1 and HEK cells to over-express the eIF3i and eIF3c subunits of the eIF3 complex and the resultant impact on cell growth and a reporter of exogenous recombinant protein production. Transient over-expression of eIF3i in HEK293 and CHOK1 cells resulted in a modest increase in total eIF3i amounts (maximum 40% increase above control) and an approximate 10% increase in global protein synthesis rates in CHOK1 cells. Stable over-expression of eIF3i in CHOK1 cells was not achievable, most likely due to the already high levels of eIF3i in CHO cells compared to HEK293 cells, but was achieved in HEK293 cells. HEK293 cells engineered to over-express eIF3i had faster growth that was associated with increased c-Myc expression, achieved higher cell biomass and gave enhanced yields of a reporter of recombinant protein production. Whilst CHOK1 cells could not be engineered to over-express eIF3i directly, they could be engineered to over-express eIF3c, which resulted in a subsequent increase in eIF3i amounts and c-Myc expression. The CHOK1 eIF3c engineered cells grew to higher cell numbers and had enhanced cap- and IRES-dependent recombinant protein synthesis. Collectively these data show that engineering of subunits of the eIF3 complex can enhance cell growth and recombinant protein synthesis in mammalian cells in a cell specific manner that has implications for the engineering or selection of fast growing or high producing cells for production of recombinant proteins.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymben.2020.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118365PMC
May 2020

The mechanism of balloon Eustachian tuboplasty: a biomechanical study.

Med Biol Eng Comput 2020 Apr 17;58(4):689-699. Epub 2020 Jan 17.

Engineering Department, University of Cambridge, Trumpington Street, Cambridge, CB2 1PZ, UK.

Obstructive Eustachian tube dysfunction (OETD) is a common condition resulting from inadequate opening of the Eustachian tube (ET). A new surgical treatment involves high-pressure inflation of a balloon within the ET, with the aim of dilating the soft tissue structure. However, the mechanical effects of this intervention have not been established, nor the impact of changing device size or other technical parameters. A novel experimental technique allowed quantification of plastic and elastic tissue deformation in model materials and then human cadaver ETs during balloon dilation, based on the measured balloon inflation pressure-volume relationship. Plastic tissue deformation was found to be greater using larger balloons and deeper device insertion, but increasing the inflation pressure had a more limited effect, with most deformation occurring well below the clinically used pressures. Histological assessment of ET tissue suggested that mucosal tearing and cartilage cracking were in part responsible for the mechanical changes. Balloon dilation of the ET has huge potential if found to be clinically effective, but currently there is a need to understand and develop the technique further. The novel methods employed in this study will be valuable in future laboratory and in vivo studies of ET balloon dilation. Pressures are reported in Bar as this unit is used for medical balloon dilation procedures in clinical practice. 1 Bar = 100,000 Pa. Graphical abstract caption Dilation of the Eustachian tube for obstructive dysfunction is performed clinically with 3- and 6-mm-diameter balloons of approximately the same overall length. Our data suggest that dilation with a 6-mm balloon causes greater deformation of the soft tissue structure than dilation with a 3-mm balloon. This difference has yet to be demonstrated clinically. Plastic deformation was measured in terms of energy (J) dissipated during balloon inflation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11517-020-02121-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7156363PMC
April 2020

section in South American Nothofagaceae forests.

Mycologia 2020 Mar-Apr;112(2):329-341. Epub 2020 Jan 7.

Department of Plant Pathology, University of Florida, P.O. Box 110680, Gainesville, Florida 32611.

We studied the South American species of section based on morphological and molecular data. Members of this group can easily be identified in the field because the basidiomata are small and -like with a bulbous stipe and the universal veil in most species forms a distinct volva at the base of the stipe. The phylogenetic delimitation of the clade was mostly in concordance with the earlier, morphology-based grouping of the South American taxa except that was resolved outside of the clade. Altogether nine species were recognized in the section. Four species, , and , were previously described by other authors, whereas three species, , and , are described here as new. We were able to identify two remaining taxa, but we do not have sufficient morphological data to allow for a formal description. All of the species in . section form ectomycorrhizal associations with Nothofagaceae. They have been documented from South America and New Zealand. The Patagonian species are considered endemic to the region. A key to the described species is provided.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2019.1689763DOI Listing
March 2021

Patulous Eustachian tube (PET), a practical overview.

World J Otorhinolaryngol Head Neck Surg 2019 Sep 11;5(3):137-142. Epub 2019 Oct 11.

Cambridge Ear Institute, Cambridge University Hospitals Trust, Cambridge UK.

Symptoms of patulous Eustachian tube (ET), particularly autophony, can overlap with other conditions, and can arise from a variety of causes. We review the pathophysiology of "speech hyper-resonance syndromes", and possible mechanisms, including resonances in the tympanic membrane, Eustachian tube and nasopharynx. Treatment can be directed at the eardrum or the ET depending on site of pathology. We review typical presentations, examination findings, and useful clinical tests to distinguish PET from other disorders, and our philosophy of management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.wjorl.2019.08.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849362PMC
September 2019

Advances in Eustachian tube function testing.

World J Otorhinolaryngol Head Neck Surg 2019 Sep 11;5(3):131-136. Epub 2019 Oct 11.

Cambridge Ear Institute, University of Cambridge, Cambridge, UK.

Obstructive and patulous Eustachian tube dysfunction provide a significant diagnostic and management challenge. The development of new treatments such as balloon Eustachian tuboplasty has generated renewed interest in measuring Eustachian tube function, as a method of selecting appropriate patients for intervention, and measuring their treatment outcomes. This review summarises recent findings relating to Eustachian tube function assessment. Increasingly it is recognised that patient reported outcome measures based on symptoms are highly non-specific and non-diagnostic, and clinical assessment alone may not permit the selection of individuals with abnormal Eustachian tube opening. Tests of Eustachian tube opening therefore may represent a practical and objective addition to patient assessment in clinic, allowing the identification of individuals with abnormal (patulous or obstructive) Eustachian tube function. A diagnostic pathway is described on this basis. More work is required to validate the described Eustachian tube function tests, and there remain individuals, such as those with dysfunction limited to pressure challenges, in whom function tests have yet to fully characterise the disorder.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.wjorl.2019.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6849358PMC
September 2019

The role of allied healthcare professionals in head and neck cancer surveillance: A systematic review.

Clin Otolaryngol 2020 01 22;45(1):83-98. Epub 2019 Nov 22.

Derriford Hospital, Plymouth, UK.

Objectives: The roles of Allied Health Care Professionals (AHPs) in Head and Neck Cancer (HNC) are wide ranging but not clearly defined. Inter-regional variability in practice results from a lack of standardisation in approaches to the Multidisciplinary Team (MDT) make-up and structure. Traditionally, the follow-up of HNC patients is clinician led with multiple scheduled follow-up appointments. The increasing population of HNC patients provides logistical, monetary and efficiency challenges. This systematic review presents the roles of the multiple AHP sub-groups in HNC with the aim of presenting how their differing skill sets can be integrated to modernise our approach in follow-up.

Design: We searched MEDLINE, Embase, the Cochrane Library, NIHR Dissemination Centre, The Kings Fund Library, Clinical Evidence, National Health Service Evidence and the National Institute of Clinical Excellence to identify multiple subgroups of AHPs (Dentists, Speech and Language Therapists, Dieticians, Physiotherapists, Psychologists, Clinical Nurse Specialists) and evidence of their role in HNC follow-up. Evidence not directly relating to HNC follow-up was excluded.

Setting And Participants: This Systematic Review was undertaken online by the Integrate (UK ENT Trainee National Collaborative) Head and Neck Subcommittee.

Main Outcome Measures: Most evidence was of low-quality, and the broad nature of the protocol provided a wide variety of study models. Two authors screened the articles for relevance to the topic before final analysis.

Results: The main role identified was improvement in Quality of Life and symptom control rather than detecting recurrence. We also demonstrate that it is possible to stratify HNC follow-up patients using their received treatment modality and Distress Thermometers to identify groups who will require more intensive AHP input.

Conclusions: HNC follow-up covers a broad group of patients with differing needs. As such, a blanket approach to this phase of treatment is likely to be less effective than a patient-led model where the group of AHPs are employed on a needs basis rather than at set time points. This will likely lead to greater patient satisfaction, earlier detection of recurrence and efficiency savings.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/coa.13471DOI Listing
January 2020

Two new species of from temperate Himalayan Oak forests of Pakistan.

MycoKeys 2019 10;56:33-47. Epub 2019 Jul 10.

Department of Plant Pathology, University of Florida, Gainesville, FL, USA.

The genus is poorly studied from Asia. From Pakistan, only one species has been reported so far. Two new species in the genus have been collected from Himalayan oak forests of Pakistan. (section Pudorini, subgenus Colorati) is characterised by its pure white, centrally depressed pileus, occurrence of white stipe with yellow patches at lower half and broader (4.98 μm) basidiospores. (section Hygrophorus, subgenus Hygrophorus) is characterised by its yellowish-green stipe with white apex that has fine scales on the entire stipe, an off-white pileus with dark green and greyish fibrils, ovoid to ellipsoid basidiospores and clavate 4-spored basidia. Macro- and micromorphological descriptions have revealed that both these taxa are not yet described. Phylogenetic estimation based on DNA sequences from the internal transcribed spacer (ITS) region and large subunit (LSU) of the nuclear ribosomal DNA (rDNA) genes, is congruent with the morphological characters that help to delimit these as new species of . Allied taxa are also compared.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3897/mycokeys.56.30280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637032PMC
July 2019

James William Kimbrough, 1934-2017.

Mycologia 2019 May-Jun;111(3):517-524. Epub 2019 Apr 23.

a Department of Plant Pathology , University of Florida , 2527 Fifield Hall, Gainesville , Florida 32611-0680.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2019.1598768DOI Listing
April 2019

Systematic study of truffles in the genus , with the description of two new species from Patagonia.

Mycologia 2019 May-Jun;111(3):477-492. Epub 2019 Apr 1.

a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611.

is a genus of exothecial, ectomycorrhizal fungi in the order Pezizales. Ascomata of exothecial fungi typically lack a peridium and are covered with a hymenial layer instead. species have nonoperculate asci and highly ornamented ascospores. The genus was first described by Hennings in 1903 to include the single species, . Since then, mycologists have uncovered species in many locations around the globe, including Australia, Spain, Italy, and the USA. Currently, there are four recognized species: , and . All were found near or trees of Australasian origin. Recently, we discovered two new species of in Nothofagaceae forests in South America. They regularly form mitotic spore mats directly on soil in the forests of Patagonia. Here, we formally describe these new species and construct the phylogeny of and related genera using a multilocus phylogenetic analysis. We also revise the taxonomy of and provide an identification key to accepted species of .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2019.1574490DOI Listing
April 2020

The Cedrus-associated truffle Trappeindia himalayensis is a morphologically unique and phylogenetically divergent species of Rhizopogon.

Mycologia 2019 Mar-Apr;111(2):225-234. Epub 2019 Feb 12.

a Department of Plant Pathology , University of Florida , Gainesville , Florida 32611.

In the northwestern Himalayan mountains of India, the hypogeous sequestrate fungus Trappeindia himalayensis is harvested from forests dominated by the ectomycorrhizal tree Cedrus deodara (Himalayan cedar). This truffle has basidiospores that are ornamented with raised reticulation. The original description of Trappeindia himalayensis suggested that the gleba of this species is similar to young specimens of Scleroderma (Boletales), whereas its basidiospores are ornamented with raised reticulation, suggesting a morphological affinity to Leucogaster (Russulales) or Strobilomyces (Boletales). Given this systematic ambiguity, we have generated DNA sequence data from type material and other herbarium specimens and present the first molecular phylogenetic analysis of this unusual Cedrus-associated truffle. Despite the irregular ornamented basidiospore morphology, T. himalayensis is resolved within the genus Rhizopogon (Suillineae, Boletales) and represents a unique lineage that has not been previously detected. All known Rhizopogon species possess an ectomycorrhizal trophic mode, and because of its placement in this lineage, it is likely that Trappeindia himalayensis is an ectomycorrhizal partner of Cedrus deodara. This study highlights the importance of generating sequence data from herbarium specimens in order to identify fungal biodiversity and clarify the systematic relationships of poorly documented fungi.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2018.1542864DOI Listing
June 2019

An Assessment of the Change in Compliance of Observational Otology and Audiology Studies With the STROBE Statement Guidelines: A Systematic Review.

Otol Neurotol 2019 03;40(3):284-291

Addenbrooke's Hospital, Cambridge.

Objectives: Observational studies often represent the best available evidence for surgical practice. Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) recommendations were generated in 2007 with the aim of improving the quality of reporting. This study was designed to assess whether publication of STROBE guidelines has improved the quality of reporting in observational otology and audiology studies.

Data Sources: EMBASE and MEDLINE were searched using a comprehensive keyword search developed in conjunction with a scientific librarian.

Study Selection: English language papers from six Otorhinolaryngology journals during two 6-month periods (2005 and 2016) were evaluated.

Data Extraction: Two reviewers independently analyzed papers according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

Data Synthesis: Percentage scores for the two periods were compared using Mann-Whitney U test.

Conclusions: Forty and 42 studies were returned for the 2005 and 2016 periods, respectively. The mean percentage of STROBE items that were met improved between 2005 and 2016 (58, 76%, respectively; p < 0.0001). Analysis indicated that improvements were greater in journals that endorsed STROBE guidelines (p = 0.02). This data suggests that STROBE has increased the reporting quality of observational studies; however, there are still significant further improvements to be met.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1097/MAO.0000000000002139DOI Listing
March 2019

Phylogenetic and morphological analyses of the mycoparasitic genus  Piptocephalis.

Mycologia 2019 Jan-Feb;111(1):54-68. Epub 2019 Feb 4.

a Department of Plant Pathology, University of Florida , Gainesville , Florida 32611.

The Piptocephalidaceae (Zoopagales, Zoopagomycota) contains three genera of mycoparasitic, haustoria-forming fungi: Kuzuhaea, Piptocephalis, and Syncephalis. Although the species in this family are diverse and ubiquitous in soil and dung, they are among the least studied fungi. Co-cultures of Piptocephalis and their hosts are relatively easy to isolate from soil and dung samples across the globe, making them a good model taxon for the order Zoopagales. This study focuses on the systematics of the genus Piptocephalis. Despite the fact that there are approximately 40 described Piptocephalis species, there are no modern taxonomic or molecular phylogenetic treatments of this group. Minimal sequence data are available, and relatively little is known about the true diversity or biogeography of the genus. Our study addresses two aspects: Piptocephalis systematics and analyses of the length and inter- and infraspecific variation of the nuc rDNA internal transcribed spacer (ITS1-5.8S-ITS2 = ITS) region. First, we generated a large subunit (28S) nuc rDNA phylogeny and evaluated several morphological characters by testing their correlation with the phylogeny using Bayesian Tip-association Significance testing (BaTS). We found monophyly of Piptocephalis species identified based on morphological traits, but morphological character states were not conserved across clades, suggesting that there have been multiple gains and losses of morphological characters. We also found that Kuzhuaea is nested within Piptocephalis. Second, we amplified the ITS from many Piptocephalis isolates, created a sequence alignment, and measured the lengths using the software ITSx. Piptocephalis species had ITS regions that were longer than the average for most Dikarya but were similar in length to those of the related genus Syncephalis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1080/00275514.2018.1538439DOI Listing
May 2019