Incorporating usability evaluation into iterative development of an online platform to support research participation in Parkinson's disease: a mixed methods protocol.

INTRODUCTION: Many people with Parkinson's (PwP) are not given the opportunity or do not have adequate access to participate in clinical research. To address this, we have codeveloped with users an online platform that connects PwP to clinical studies in their local area. It enables site staff to communicate with potential participants and aims to increase the participation of the Parkinson's community in research. This protocol outlines the mixed methods study protocol for the usability testing of the platform. METHODS AND ANALYSIS: We will seek user input to finalise the platform's design, which will then be deployed in a limited launch for beta testing. The beta version will be used as a recruitment tool for up to three studies with multiple UK sites. Usability data will be collected from the three intended user groups: PwP, care partners acting on their behalf and site study coordinators. Usability questionnaires and website analytics will be used to capture user experience quantitatively, and a purposive sample of users will be invited to provide further feedback via semistructured interviews. Quantitative data will be analysed using descriptive statistics, and a thematic analysis undertaken for interview data. Data from this study will inform future platform iterations. ETHICS AND DISSEMINATION: Ethical approval was obtained from the University of Plymouth (3291; 3 May 2022). We will share our findings via a 'Latest News' section within the platform, presentations, conference meetings and national PwP networks.

The Impact of a Digital Artificial Intelligence System on the Monitoring and Self-management of Nonmotor Symptoms in People With Parkinson Disease: Proposal for a Phase 1 Implementation Study.

BACKGROUND: Nonmotor symptoms of Parkinson disease are a major factor of disease burden but are often underreported in clinical appointments. A digital tool has been developed to support the monitoring and management of nonmotor symptoms. OBJECTIVE: The aim of this study is to establish evidence of the impact of the system on patient confidence, knowledge, and skills for self-management of nonmotor symptoms, symptom burden, and quality of life of people with Parkinson and their care partners. It will also evaluate the usability, acceptability, and potential for adoption of the system for people with Parkinson, care partners, and health care professionals. METHODS: A mixed methods implementation and feasibility study based on the nonadoption, abandonment, scale-up, spread, and sustainability framework will be conducted with 60 person with Parkinson-care partner dyads and their associated health care professionals. Participants will be recruited from outpatient clinics at the University Hospitals Plymouth NHS Trust Parkinson service. The primary outcome, patient activation, will be measured over the 12-month intervention period; secondary outcomes include the system's impact on health and well-being outcomes, safety, usability, acceptability, engagement, and costs. Semistructured interviews with a subset of participants will gather a more in-depth understanding of user perspectives and experiences with the system. Repeated measures analysis of variance will analyze change over time and thematic analysis will be conducted on qualitative data. The study was peer reviewed by the Parkinson's UK Non-Drug Approaches grant board and is pending ethical approval. RESULTS: The study won funding in August 2021; data collection is expected to begin in December 2022. CONCLUSIONS: The study's success criteria will be affirming evidence regarding the system's feasibility, usability and acceptability, no serious safety risks identified, and an observed positive impact on patient activation. Results will be disseminated in academic peer-reviewed journals and in platforms and formats that are accessible to the general public, guided by patient and public collaborators. TRIAL REGISTRATION: ClinicalTrials.gov NCT05414071; https://clinicaltrials.gov/ct2/show/NCT05414071. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/40317.

Water potential affects Coniothyrium minitans growth, germination and parasitism of Sclerotinia sclerotiorum sclerotia.

Water availability is an important environmental factor which has major effects on fungal activity. The effects of osmotic (KCl amended agar) and matric Polyethylene glycol ((PEG) 8000 amended agar) potentials over the range -0.1 to -5.0MPa on mycelial growth and conidial germination of eight isolates of the sclerotial parasite Coniothyrium minitans was assessed. The influence of soil water potential on the ability of three selected isolates (LU112, LU545, and T5R42i) to parasitise sclerotia of the plant pathogen Sclerotinia sclerotiorum was determined. For all eight C. minitans isolates, decreasing osmotic and matric potentials caused a reduction in mycelial growth and conidial germination. Isolates were more sensitive to decreasing matric potential than osmotic potential. Across the isolates, growth at an osmotic potential of -5.0MPa was 30-70% of the growth seen in the control, whereas less than 20% of the control growth was seen at the corresponding matric potential. Across all isolates no conidial germination was seen at matric potential of -5.0MPa. The C. minitans isolates varied in their sensitivity to decreasing water potentials. Mycelial growth and conidial germination of three isolates (LU112, Conio, and CH1) were more tolerant of low osmotic potential and matric potential with respect to mycelial growth. Isolates T5R42i and LU430 were least tolerant. In contrast, conidial germination of isolates Conio, LU545, and T5R42i were less sensitive to decreasing matric potential. Soil water potential was seen to affect infection and viability of sclerotia by the three C. minitans isolates. Isolate LU545 reduced sclerotial viability over a wider water potential range (-0.01 to -1.5MPa) compared with LU112 (-0.01 to -1.0MPa), with isolate T5R42i being intermediate. Indigenous soil fungi (Trichoderma spp. and Clonostachys rosea) were recovered from sclerotia but did not result in reduction in sclerotial viability. The relevance of these results in relation to biocontrol activity of C. minitans in soil is discussed.

Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca Species) phyllosphere.

Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.

Disruption of the Coniothyrium minitans PIF1 DNA helicase gene impairs growth and capacity for sclerotial mycoparasitism.

A non-mycoparasitic restriction enzyme-mediated DNA integration (REMI) mutant of Coniothyrium minitans (R2427) contains two tandem plasmid copies integrated towards the 3' end of an ORF. The predicted polypeptide (845 aa) exhibits high similarity with DNA-helicase proteins from other filamentous fungi and yeasts that play a role in mitochondrial DNA maintenance and repair. Disruption of the C. minitans PIF1 DNA helicase gene results in altered morphology, reduced growth rates and a concomitant loss in ability to mycoparasitize sclerotia of Sclerotinia sclerotiorum. In infection bioassays, R2427 exhibited sparse mycelial growth on the surface of live sclerotia, but no mycelia were detected inside the sclerotia. Conversely, R2427 readily colonized autoclaved sclerotia. Complementation of the mutant with wild-type PIF1 restored normal mycelial growth and mycoparasitic capability, confirming a functional role in the host-pathogen interaction. The C. minitans PIF1 DNA helicase may maintain mitochondrial stability in response to reactive oxygen species, either produced endogenously within the mycoparasite, or exogenously from the sclerotial host.

Analysis of cDNA transcripts from Coniothyrium minitans reveals a diverse array of genes involved in key processes during sclerotial mycoparasitism.

Coniothyrium minitans colonises and destroys the sclerotia of Sclerotinia sclerotiorum in nature exhibiting ecologically obligate mycoparasitism as its spores remain dormant in soil and only grow actively in the presence of the sclerotia. Molecular mechanisms underlying sclerotial mycoparasitism are poorly defined. We identified 251 unisequences representing genes preferentially expressed by C. minitans during sclerotial mycoparasitism, substantially increasing the molecular knowledge of this commercially important biocontrol agent. Genes associated with signalling and cellular communication, degradation of host cell walls and energy reserves, nutrient utilisation, detoxification and stress response were identified suggesting that C. minitans employs a number of key processes during host colonisation. Several of these genes are novel to fungal-fungal interactions (e.g. PTH11-like GPCR and the ETP gene cluster). Secretin receptor-like GPCR and the TGF-beta signalling system have not yet been characterised in filamentous fungi. This study provides the basis for in-depth gene function analysis in sclerotial mycoparasitism.

Forecasting Sclerotinia Disease on Lettuce: A Predictive Model for Carpogenic Germination of Sclerotinia sclerotiorum Sclerotia.

ABSTRACT A predictive model for production of apothecia by carpogenic germination of sclerotia is presented for Sclerotinia sclerotiorum. The model is based on the assumption that a conditioning phase must be completed before a subsequent germination phase can occur. Experiments involving transfer of sclerotia from one temperature regime to another allowed temperature-dependent rates to be derived for conditioning and germination for two S. sclerotiorum isolates. Although the response of each isolate to temperature was slightly different, sclerotia were fully conditioned after 2 to 6 days at 5 degrees C in soil but took up to 80 days at 15 degrees C. Subsequent germination took more than 200 days at 5 degrees C and 33 to 52 days at 20 degrees C. Upper temperature thresholds for conditioning and germination were 20 and 25 degrees C, respectively. A predictive model for production of apothecia derived from these data was successful in simulating the germination of multiple burials of sclerotia in the field when a soil water potential threshold of between -4.0 and -12.25 kilopascals (kPa) was imposed. The use of a germination model as part of a disease forecasting system for Sclerotinia disease in lettuce is discussed.

Differences in microbial activity and microbial populations of peat associated with suppression of damping-off disease caused by Pythium sylvaticum.

The microbiological characteristics associated with disease-suppressive peats are unclear. We used a bioassay for Pythium sylvaticum-induced damping-off of cress seedlings to identify conducive and suppressive peats. Microbial activity in unconditioned peats was negatively correlated with the counts of P. sylvaticum at the end of the bioassay. Denaturing gradient gel electrophoresis (DGGE) profiling and clone library analyses of small-subunit rRNA gene sequences from two suppressive and two conducive peats differed in the bacterial profiles generated and the diversity of sequence populations. There were also significant differences between bacterial sequence populations from suppressive and conducive peats. The frequencies of a number of microbial groups, including the Rhizobium-Agrobacterium group (specifically sequences similar to those for the genera Ochrobactrum and Zoogloea) and the Acidobacteria, increased specifically in the suppressive peats, although no single bacterial group was associated with disease suppression. Fungal DGGE profiles varied little over the course of the bioassay; however, two bands associated specifically with suppressive samples were detected. Sequences from these bands corresponded to Basidiomycete yeast genera. Although the DGGE profiles were similar, fungal sequence diversity also increased during the bioassay. Sequences highly similar to those of Cryptococcus increased in relative abundance during the bioassay, particularly in the suppressive samples. This study highlights the importance of using complementary approaches to molecular profiling of complex populations and provides the first report that basidiomycetous yeasts may be associated with the suppression of Pythium-induced diseases in peats.

Mycorrhization helper bacteria: a case of specificity for altering ectomycorrhiza architecture but not ectomycorrhiza formation.

Mycorrhization helper bacteria (MHB), isolated from phylogenetically distinct ectomycorrhizal symbioses involving Lactarius rufus, Laccaria bicolor or Suillus luteus, were tested for fungus specificity to enhance L. rufus-Pinus sylvestris or L. bicolor-P. sylvestris mycorrhiza formation. As MHB isolated from the L. rufus and S. luteus mycorrhiza were originally characterised using a microcosm system, we assessed their ability to enhance mycorrhiza formation in a glasshouse system in order to determine the extent to which MHB are system-specific. Paenibacillus sp. EJP73, an MHB for L. rufus in the microcosm, significantly enhanced L. bicolor mycorrhiza formation in the glasshouse, demonstrating that the MHB effect of this bacterium is neither fungus-specific nor limited to the original experimental system. Although the five MHB strains studied were unable to significantly enhance L. rufus mycorrhiza formation, two of them did have a significant effect on dichotomous short root branching by L. rufus. The effect was specific to Paenibacillus sp. EJP73 and Burkholderia sp. EJP67, the two strains isolated from L. rufus mycorrhiza, and was not associated with auxin production. Altered mycorrhiza architecture rather than absolute number of mycorrhizal roots may be an important previously overlooked parameter for defining MHB effects.

Importance of mycorrhization helper bacteria cell density and metabolite localization for the Pinus sylvestris-Lactarius rufus symbiosis.

Mycorrhization helper bacteria, Paenibacillus sp. EJP73 and Burkholderia sp. EJP67, were used to study the importance of bacterial inoculum dose and bacterial derived soluble and volatile metabolites localization for enhancing mycorrhiza formation in the Pinus sylvestris-Lactarius rufus symbiosis, using a laboratory based microcosm. EJP73 and EJP67 produced different responses in relation to the inoculum dose; EJP73 significantly enhanced mycorrhiza formation to the same degree at all doses tested (10(5), 10(7), 10(9) and 10(10) CFU mL(-1)), whereas, EJP67 only stimulated mycorrhiza formation within a narrow range of inoculum densities (10(7) and 10(9) CFU mL(-1)). The importance of soluble bacterial metabolites was assessed by applying spent broth derived from exponential and stationary phase bacterial cultures to microcosms. No spent broth enhanced mycorrhiza formation over the control. As EJP73 produced the helper effect over a wide range of inoculum doses, this bacterium was chosen for further study. Physical separation of EJP73 from the fungal and plant symbiosis partners was carried out, in order to determine the contribution of constitutively produced bacterial volatile metabolites to the mycorrhization helper bacteria effect. When EJP73 was physically separated from the symbiosis, it had a significant negative effect on mycorrhiza formation. These results suggest that close proximity, or indeed cell contact, is required for the helper effect. Therefore, fluorescent in situ hybridization in conjunction with cryosectioning was used to determine the localization of EJP73 in mycorrhizal tissue. The cells were found to occur as rows or clusters ( approximately 10 cells) within the mycorrhizal mantle, both at the root tip and along the length of the mycorrhizal short roots.

Use of REMI and Agrobacterium-mediated transformation to identify pathogenicity mutants of the biocontrol fungus, Coniothyrium minitans.

Restriction enzyme mediated integration (REMI) and Agrobacterium-mediated transformation (ATMT) were used to transform protoplasts or germinated conidia of the mycoparasite Coniothyrium minitans to hygromycin resistance. Using REMI, up to 32 transformants mug DNA(-1) were obtained, while 37.8 transformants 5 x 10(5) germlings(-1) were obtained using ATMT. Single-copy integrations occurred in 8% and 40% of REMI and ATMT transformants, respectively. A novel microtitre plate-based test was developed to expedite screening of 4000 REMI and ATMT C. minitans transformants. Nine pathogenicity mutants that displayed reduced or no pathogenicity on sclerotia of Sclerotinia sclerotiorum were identified.

Forecasting sclerotinia disease on lettuce: toward developing a prediction model for carpogenic germination of sclerotia.

ABSTRACT The feasibility of developing a forecasting system for carpogenic germination of Sclerotinia sclerotiorum sclerotia was investigated in the laboratory by determining key relationships among temperature, soil water potential, and carpogenic germination for sclerotia of two S. sclerotiorum isolates. Germination of multiple burials of sclerotia to produce apothecia also was assessed in the field with concurrent recording of environmental data to examine patterns of germination under different fluctuating conditions. Carpogenic germination of sclerotia occurred between 5 and 25 degrees C but only for soil water potentials of >/=-100 kPa for both S. sclerotiorum isolates. Little or no germination occurred at 26 or 29 degrees C. At optimum temperatures of 15 to 20 degrees C, sclerotia buried in soil and placed in illuminated growth cabinets produced stipes after 20 to 27 days and apothecia after 27 to 34 days. Temperature, therefore, had a significant effect on both the rate of germination of sclerotia and the final number germinated. Rate of germination was correlated positively with temperature and final number of sclerotia germinated was related to temperature according to a probit model. Thermal time analysis of field data with constraints for temperature and water potential showed that the mean degree days to 10% germination of sclerotia in 2000 and 2001 was 285 and 279, respecttively, and generally was a good predictor of the observed appearance of apothecia. Neither thermal time nor relationships established in the laboratory could account for a decline in final percentage of germination for sclerotia buried from mid-May compared with earlier burials. Exposure to high temperatures may explain this effect. This, and other factors, require investigation before relationships derived in the laboratory or thermal time can be incorporated into a forecasting system for carpogenic germination.

Production, survival and efficacy of Coniothyrium minitans conidia produced in shaken liquid culture.

Coniothyrium minitans is a fungal biocontrol agent of the plant pathogen Sclerotinia sclerotiorum. Growth and sporulation of 21 strains of C. minitans were examined on potato dextrose agar (PDA) and compared with that in potato dextrose broth (PDB) in shaken culture after 12 days at 20 degrees C, to identify strains with potential for inoculum production in liquid culture. Four strains that produced high numbers of pycnidia in PDA also formed pycnidia on mycelial strands in PDB and 10(7) conidia ml(-1) broth were produced. The other strains formed pellets during shaking, resulting in production of less than 10(5) conidia ml(-1). Conidia from shaken PDB culture had the same ability to infect and rot sclerotia of S. sclerotiorum as conidia produced routinely on PDA, and survived well in dry kaolin dust for 6 months at temperatures less than 8 degrees C with less than 1 log(10) colony forming units mg(-1) loss. These results suggest that it might be possible to identify useful strains of C. minitans for future commercial conidial production in liquid fermentation systems based on morphological characteristics on agar.

Use of Coniothyrium minitans transformed with the hygromycin B resistance gene to study survival and infection of Sclerotinia sclerotiorum sclerotia in soil.

A Coniothyrium minitans strain (T3) co-transformed with the genes for beta-glucuronidase (uidA) and hygromycin phosphotransferase (hph), the latter providing resistance to the antibiotic hygromycin B, was used to investigate the survival and infection of sclerotia of Sclerotinia sclerotiorum by C. minitans over time in four different soils. Infection of sclerotia was rapid in all cases, with the behaviour of transformant T3 and wild type parent A69 being similar. Differences were seen between the soils in the rate of infection of sclerotia by C. minitans and in their indigenous fungal populations. Amendment of agar with hygromycin B enabled the quantification of C. minitans in soil by dilution plating where there was a high background of other microorganisms. In Lincoln soil from New Zealand, which had a natural but low population of C. minitans, the hygromycin B resistance marker allowed the umambiguous discrimination of the applied transformed isolate from the indigenous hygromycin B sensitive one. In this soil, although the indigenous C. minitans population was detected from sclerotia, none were recovered on the dilution plates, indicating the increased sensitivity of C. minitans detection from soil using sclerotial baiting. C. minitans was a very efficient parasite, being able to infect a large proportion of sclerotia within a relatively short time from an initially low soil population. The addition of hygromycin B to agar also allowed the detection of C. minitans from decaying sclerotia by inhibiting secondary fungal colonisers. This is the first report to show that fungi colonising sclerotia already infected by C. minitans mask the detection of C. minitans from sclerotia rather than displacing the original parasite.

Ascospore release and survival in Sclerotinia sclerotiorum.

The release and survival of ascospores of a UK Sclerotinia sclerotiorum isolate were studied. Apothecia placed in a spore clock apparatus with different lighting regimes at 15 degrees C released ascospores continuously with an increasing rate for the duration of experiments (72-84 h). Spore release was not confined to light or dark periods in alternating regimes and occurred in continuous dark or light. Ascospores were released in both saturated air (90-95% rh) and at 65-75% rh. High temperature and rh were detrimental to ascospore survival but spore viability was maintained for longer periods than previously reported. The significance of these results in relation to disease control is discussed.

Spatial and temporal analysis of the microbial community in slow sand filters used for treating horticultural irrigation water.

An experimental slow sand filter (SSF) was constructed to study the spatial and temporal structure of a bacterial community suppressive to an oomycete plant pathogen, Phytophthora cryptogea. Passage of water through the mature sand column resulted in complete removal of zoospores of the plant pathogen. To monitor global changes in the microbial community, bacterial and fungal numbers were estimated on selective media, direct viable counts of fungal spores were made, and the ATP content was measured. PCR amplification of 16S rRNA genes and denaturing gradient gel electrophoresis (DGGE) were used to study the dynamics of the bacterial community in detail. The top layer (1 cm) of the SSF column was dominated by a variable and active microbial population, whereas the middle (50 cm) and bottom (80 cm) layers were dominated by less active and diverse bacterial populations. The major changes in the microbial populations occurred during the first week of filter operation, and these populations then remained to the end of the study. Spatial and temporal nonlinear mapping of the DGGE bands provided a useful visual representation of the similarities between SSF samples. According to the DGGE profile, less than 2% of the dominating bands present in the SSF column were represented in the culturable population. Sequence analysis of DGGE bands from all depths of the SSF column indicated that a range of bacteria were present, with 16S rRNA gene sequences similar to groups such as Bacillus megaterium, Cytophaga, Desulfovibrio, Legionella, Rhodococcus rhodochrous, Sphingomonas, and an uncharacterized environmental clone. This study describes the characterization of the performance, and microbial composition, of SSFs used for the treatment of water for use in the horticultural industry. Utilization of naturally suppressive population of microorganisms either directly or by manipulation of the environment in an SSF may provide a more reproducible control method for the future.

Production of macrosphelide A by the mycoparasite Coniothyrium minitans.

Coniothyrium minitans, a mycoparasite of sclerotia of Sclerotinia sclerotiorum and Sclerotium cepivorum, produced four closely related metabolites inhibitory to fungal growth. The major metabolite, identified as macrosphelide A, had IG(50) values (the concentration of metabolite to inhibit growth by 50%) of 46.6 and 2.9 microgram ml(-1) against S. sclerotiorum and S. cepivorum, respectively. This is the first report of both antifungal activity due to macrosphelide A as well as isolation of macrosphelide A from C. minitans.

Molecular characterization of Legionella populations present within slow sand filters used for fungal plant pathogen suppression in horticultural crops.

The total bacterial community of an experimental slow sand filter (SSF) was analyzed by denaturing gradient gel electrophoresis (DGGE) of partial 16S rRNA gene PCR products. One dominant band had sequence homology to Legionella species, indicating that these bacteria were a large component of the SSF bacterial community. Populations within experimental and commercial SSF units were studied by using Legionella-specific PCR primers, and products were studied by DGGE and quantitative PCR analyses. In the experimental SSF unit, the DGGE profiles for sand column, reservoir, storage tank, and headwater tank samples each contained at least one intense band, indicating that a single Legionella strain was predominant in each sample. Greater numbers of DGGE bands of equal intensity were detected in the outflow water sample. Sequence analysis of these PCR products showed that several Legionella species were present and that the organisms exhibited similarity to strains isolated from environmental and clinical samples. Quantitative PCR analysis of the SSF samples showed that from the headwater sample through the sand column, the number of Legionella cells decreased, resulting in a lower number of cells in the outflow water. In the commercial SSF, legionellae were also detected in the sand column samples. Storing prefilter water or locating SSF units within greenhouses, which are often maintained at temperatures that are higher than the ambient temperature, increases the risk of growth of Legionella and should be avoided. Care should also be taken when used filter sand is handled or replaced, and regular monitoring of outflow water would be useful, especially if the water is used for misting or overhead irrigation.