Insights on conducting digital patient and public involvement in dementia research during the COVID-19 pandemic: supporting the development of an “E-nabling digital co-production” framework

BackgroundThe rapid transition to digital working, accelerated due to the response to the COVID-19 pandemic, has impacted the involvement of patients and public in research. This paper presents experiences of engaging in digital Patient and Public Involvement (e-PPI) in dementia research since the lockdowns, offering recommendations regarding future digital and hybrid working. Furthermore, it introduces a co-produced framework for researchers, PPI coordinators and public contributors to identify and discuss challenges and opportunities provided by e-PPI.MethodsTwo online workshops and one individual interview were performed with a group of researchers and PPI coordinators with experience in PPI in dementia research, and with an existing dementia PPI group having some experience of working online during the pandemic. The project was constructed as a PPI activity, with the MindTech Involvement Team (PPI group) involved in the entire process, and a collaborative data analysis process was adopted.ResultsAfter refinement of the coding structure, the MindTech Involvement Team and Project Leaders identified four main themes, resulting in the ‘E-nabling Digital Co-production' Framework. During this framework development, different positions were expressed, associated with the transition to digital working. Two main themes were shared by the participating groups regarding e-PPI: wider potential reach without geographical constraints, and the perception of more business-like sessions with reduced opportunities for social interactions and communication. Specifically for dementia research, whilst e-PPI may allow public contributors to attend more meetings, potentially mutually supportive environments provided by face-to-face meetings could be diminished, with carers experiencing a possible reduction in informal respite opportunities.ConclusionsThrough involving public contributors, researchers, and PPI coordinators with a focus on digital PPI in dementia research, we were able to further refine and co-produce the ‘E-nabling Digital Co-production' Framework. Demonstrating potential for analysis of benefits and limitations within e-PPI, it was possible to identify both general insights and those specific to dementia research. However, the most significant contribution of the framework is the potential to support local journeys of co-production in ongoing digital and hybrid public involvement activities

Clinical profile of patients with ATP1A3 mutations in Alternating Hemiplegia of Childhood\u2014a study of 155 patients

Background: Mutations in the gene ATP1A3 have recently been identified to be prevalent in patients with alternating hemiplegia of childhood (AHC2). Based on a large series of patients with AHC, we set out to identify the spectrum of different mutations within the ATP1A3 gene and further establish any correlation with phenotype. Methods: Clinical data from an international cohort of 155 AHC patients (84 females, 71 males; between 3 months and 52 years) were gathered using a specifically formulated questionnaire and analysed relative to the mutational ATP1A3 gene data for each patient. Results: In total, 34 different ATP1A3 mutations were detected in 85 % (132/155) patients, seven of which were novel. In general, mutations were found to cluster into five different regions. The most frequent mutations included: p.Asp801Asn (43 %; 57/132), p.Glu815Lys (16 %; 22/132), and p.Gly947Arg (11 %; 15/132). Of these, p.Glu815Lys was associated with a severe phenotype, with more severe intellectual and motor disability. p.Asp801Asn appeared to confer a milder phenotypic expression, and p.Gly947Arg appeared to correlate with the most favourable prognosis, compared to the other two frequent mutations. Overall, the comparison of the clinical profiles suggested a gradient of severity between the three major mutations with differences in intellectual (p = 0.029) and motor (p = 0.039) disabilities being statistically significant. For patients with epilepsy, age at onset of seizures was earlier for patients with either p.Glu815Lys or p.Gly947Arg mutation, compared to those with p.Asp801Asn mutation (p < 0.001). With regards to the five mutation clusters, some clusters appeared to correlate with certain clinical phenotypes. No statistically significant clinical correlations were found between patients with and without ATP1A3 mutations. Conclusions: Our results, demonstrate a highly variable clinical phenotype in patients with AHC2 that correlates with certain mutations and possibly clusters within the ATP1A3 gene. Our description of the clinical profile of patients with the most frequent mutations and the clinical picture of those with less common mutations confirms the results from previous studies, and further expands the spectrum of genotype-phenotype correlations. Our results may be useful to confirm diagnosis and may influence decisions to ensure appropriate early medical intervention in patients with AHC. They provide a stronger basis for the constitution of more homogeneous groups to be included in clinical trial

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

BackgroundTrunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.ResultsThe integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.ConclusionsThis study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management

The genome of the emerging barley pathogen Ramularia collo-cygni

Background Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and hence grain yield and quality. Results The R. collo-cygni genome was sequenced using a combination of Illumina and Roche 454 technologies. The draft assembly of 30.3 Mb contained 11,617 predicted gene models. Our phylogenomic analysis confirmed the classification of this ascomycete fungus within the family Mycosphaerellaceae, order Capnodiales of the class Dothideomycetes. A predicted secretome comprising 1053 proteins included redox-related enzymes and carbohydrate-modifying enzymes and proteases. The relative paucity of plant cell wall degrading enzyme genes may be associated with the stealth pathogenesis characteristic of plant pathogens from the Mycosphaerellaceae. A large number of genes associated with secondary metabolite production, including homologs of toxin biosynthesis genes found in other Dothideomycete plant pathogens, were identified. Conclusions The genome sequence of R. collo-cygni provides a framework for understanding the genetic basis of pathogenesis in this important emerging pathogen. The reduced complement of carbohydrate-degrading enzyme genes is likely to reflect a strategy to avoid detection by host defences during its prolonged asymptomatic growth. Of particular interest will be the analysis of R. collo-cygni gene expression during interactions with the host barley, to understand what triggers this fungus to switch from being a benign endophyte to an aggressive necrotroph

Histopathological Findings in Brain Tissue Obtained during Epilepsy Surgery

BACKGROUND: Detailed neuropathological information on the structural brain lesions underlying seizures is valuable for understanding drug-resistant focal epilepsy. / METHODS: We report the diagnoses made on the basis of resected brain specimens from 9523 patients who underwent epilepsy surgery for drug-resistant seizures in 36 centers from 12 European countries over 25 years. Histopathological diagnoses were determined through examination of the specimens in local hospitals (41%) or at the German Neuropathology Reference Center for Epilepsy Surgery (59%). / RESULTS: The onset of seizures occurred before 18 years of age in 75.9% of patients overall, and 72.5% of the patients underwent surgery as adults. The mean duration of epilepsy before surgical resection was 20.1 years among adults and 5.3 years among children. The temporal lobe was involved in 71.9% of operations. There were 36 histopathological diagnoses in seven major disease categories. The most common categories were hippocampal sclerosis, found in 36.4% of the patients (88.7% of cases were in adults), tumors (mainly ganglioglioma) in 23.6%, and malformations of cortical development in 19.8% (focal cortical dysplasia was the most common type, 52.7% of cases of which were in children). No histopathological diagnosis could be established for 7.7% of the patients. / CONCLUSIONS: In patients with drug-resistant focal epilepsy requiring surgery, hippocampal sclerosis was the most common histopathological diagnosis among adults, and focal cortical dysplasia was the most common diagnosis among children. Tumors were the second most common lesion in both groups. (Funded by the European Union and others.

A comparison of the molecular mechanisms underpinning high-intensity, pulsed polychromatic light and low-intensity UV-C hormesis in tomato fruit

Postharvest treatment of tomato fruit with high-intensity, pulsed polychromatic light (HIPPL) has previously been shown to induce delayed ripening and disease resistance comparable to that of low-intensity UV-C (LIUV). Little, however, is known of the mechanisms underpinning postharvest HIPPL hormesis in tomato fruit. Expression of genes involved in plant hormone biosynthesis, defence, secondary metabolism and ripening were monitored 24 h post treatment (24 HPT), 10 d post treatment (10 DPT) and 12 h post inoculation with Botrytis cinerea (12 HPI). All genes monitored were constitutively expressed and changes in expression profiles following treatment were highly similar for both HIPPL and LIUV treatments. Expression of pathogenesis-related proteins P4, β-1,3,-Glucanase and Chitinase 9 and a jasmonate biosynthesis enzyme (OPR3), were significantly upregulated at 10 DPT and 12 HPI. Both treatments significantly downregulated the expression of polygalacturonase and flavonol synthase at 10 DPT and 12 HPI. Ethylene biosynthesis enzyme ACO1 and β-carotene hydroxylase were significantly upregulated at 24 HPT, and phenylalanine ammonia-lyase (PAL) was significantly upregulated at 12 HPI. Both HIPPL and LIUV treatments stimulate defence responses that are mediated by salicylic acid, jasmonic acid and ethylene. This may lead to broad range resistance against both necrotrophic and biotrophic pathogens as well as abiotic stresses and herbivorous pests. Following inoculation with B. cinerea only PAL showed indication of a gene priming response for HIPPL- and LIUV-treated fruit

RNA-seq analysis in plant–fungus interactions

Many fungi are pathogens that infect important food and plantation crops, reducing both yield and quality of food products. Understanding plant–fungus interactions is crucial as knowledge in this area is required to formulate sustainable strategies to improve plant health and crop productivity. High-throughput RNA-sequencing (RNA-seq) enables researchers to gain insights of the mixed and multispecies transcriptomes in plant–fungus interactions. Interpretation of huge data generated by RNA-seq has led to new insights in this area, facilitating a system approach in unraveling interactions between plant hosts and fungal pathogens. In this review, the application and challenges of RNA-seq analysis in plant–fungus interactions will be discussed

Food consumption and nutritional status of rural families in the semidry tropics of Central America

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