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Background: The effectiveness of emollients for preventing atopic dermatitis/eczema is controversial. The Barrier Enhancement for Eczema Prevention trial evaluated the effects of daily emollients during the first year of life on atopic dermatitis and atopic conditions to age 5 years.Methods: 1394 term infants with a family history of atopic disease were randomized (1:1) to daily emollient plus standard skin-care advice (693 emollient group) or standard skin-care advice alone (701 controls). Long-term follow-up at ages 3, 4 and 5 years was via parental questionnaires. Main outcomes were parental report of a clinical diagnosis of atopic dermatitis and food allergy.Results: Parents reported more frequent moisturizer application in the emollient group through to 5 years. A clinical diagnosis of atopic dermatitis between 12 and 60 months was reported for 188/608 (31%) in the emollient group and 178/631 (28%) in the control group (adjusted relative risk 1.10, 95% confidence interval 0.93 to 1.30). Although more parents in the emollient group reported food reactions in the previous year at 3 and 4 years, cumulative incidence of doctor-diagnosed food allergy by 5 years was similar between groups (92/609 [15%] emollients and 87/632 [14%] controls, adjusted relative risk 1.11, 95% confidence interval 0.84 to 1.45). Findings were similar for cumulative incidence of asthma and hay fever.Conclusions: Daily emollient application during the first year of life does not prevent atopic dermatitis, food allergy, asthma or hay fever.

Australia’s future energy production will increasingly be focused on developing clean energy resources to achieve the goal of net zero greenhouse gas emissions by 2050. To achieve this, an understanding of Australia’s natural gas resources and greenhouse gas storage potential is needed to facilitate the rapid implementation and expansion of low-emission technologies. While Australia continues to be a net gas exporter, additional volumes are needed to support future domestic manufacturing capabilities. These extra volumes can be produced from existing accumulations that are close to infrastructure or can be unlocked from highly prospective, yet underexplored regions. The coming decade will see a dramatic change in the energy mix that supports the Australian economy. A major driver will be the development of a hydrogen production industry, initially using fossil fuels with carbon capture and storage (CCS) until the cost of hydrogen production from renewable energy becomes more reliable and competitive. The expansion and projected lower costs of renewable energy generation via solar and wind will ultimately replace much of the non-renewable energies for hydrogen production. Geoscience Australia’s energy-related work program is focused on supporting Australia’s energy transformation assessments of untapped resource potential onshore include the evaluation of geologic hydrogen occurrences, the presence and suitability of subsurface salt horizons for hydrogen storage and the distribution of effective reservoir and seal fairways for underground carbon storage. While offshore, new data from Geoscience Australia’s sea-floor mapping project will improve the understanding of suitable areas for offshore wind farms. Results from these research activities are being made publicly available either through Geoscience Australia’s data portal and its data repository.

Geoscience Australia is undertaking a series of basin-scale assessments to identify the ‘yet-to-find’ resource potential for hydrocarbons, as well as for groundwater resources and carbon capture and storage (CCS) opportunities in central Australia under the Exploring for the Future (EFTF) Program. A play-based exploration approach is being used to systematically evaluate the key risk elements for each resource type through the analysis of drilling results and spatial data to map ‘sweet spots’ for exploration. These assessments aim to reduce the risks and uncertainties for explorers by providing spatially enabled assessments of energy resources and CCS potential. The work will also improve the understanding of existing groundwater resources which may be impacted by future energy resource developments or provide feedstock for future green hydrogen projects. A key requirement for undertaking such play-based resource assessments is to apply a common regional chronostratigraphic framework across all the resource types that link different geological unit nomenclatures through defining the assessed reservoir and seal intervals and their associated sequence stratigraphic surfaces (sequence boundaries, transgressive surfaces and maximum flooding surfaces). A Mesozoic chronostratigraphic framework has been developed for the Eromanga Basin, which defines nine regional play intervals that host the known hydrocarbon and groundwater resources, or represent potential CCS targets. The Mesozoic play framework is now being applied to undertake play-based low-carbon energy resource assessments in the western Eromanga Basin, with initial work focussing on the interpretation and correlation of the nine play intervals in wells for post-drill analysis.

Mosquitoes transmit a wide variety of devastating pathogens when they bite vertebrate hosts and feed on their blood. However, three entire mosquito genera and many individual species in other genera have evolved a nonbiting life history in which blood is not required to produce eggs. Our long-term goal is to develop novel interventions that reduce or eliminate the biting behavior in vector mosquitoes. A previous study used biting and nonbiting populations of a nonvector mosquito

Plant-pathogenic fungi are a major threat to food security. Among these are subcuticular pathogens, which often cause latent asymptomatic infections, making them difficult to control.

The principal cultivated potato (Solanum tuberosum) has mainly been vegetatively propagated through its tubers. Potato breeders have therefore made planned artificial hybridizations to generate genetically unique seedlings and their clonal descendants from which to select new cultivars for tuber propagation. After the initial hybridizations, no more sexual reproduction was required to produce a successful new cultivar, which depended on choosing the correct breeding objectives and the ability to recognize a clone that met those objectives. Any impact of the new science of genetics after 1900 needed to be through the production of parental material of known genetic constitution and predictable offspring. This included making use of the many wild tuber-bearing relatives of the potato in Central and South America, as well as the abundance of landraces in South America. This review looks at the history of how potato geneticists: 1) established that the principal cultivated potato is a tetraploid that displays tetrasomic inheritance (2n = 4x = 48); 2) developed progeny tests to determine the dosage of major genes for qualitative traits in potential parents, and also progeny tests for their general combining abilities for quantitative traits; and 3) provided molecular markers for the marker assisted selection of major genes and quantitative trait alleles of large effect, and for the genomic selection of many alleles of small effect. It is argued that the concepts of population genetics are required by breeders, once a number of cycles of hybridization and cultivar production are considered for the genetic improvement of potato crops.

Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F.fulva is a pathogen of tomato, whilst D.septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F.fulva and D.septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F.fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D.septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F.fulva and D.septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F.fulva and D.septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D.septosporum population. In this review, we specifically summarize advances made in our understanding of the F.fulva-tomato and D.septosporum-pine pathosystems over the last 10 years.

BackgroundScab, caused by the biotrophic fungusVenturia inaequalis, is the most economically important disease of apples worldwide. During infection,V. inaequalisoccupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth byV. inaequalis, as well as in activating, suppressing, or circumventing resistance protein-mediated defences in apple, is required.ResultsWe generated the first comprehensive RNA-seq transcriptome ofV. inaequalisduring colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid, or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector fromLeptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi.ConclusionsOur study reveals the transcriptomic profile underpinning subcuticular growth byV. inaequalisand provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins.

Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback – a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.

Scab, caused by the biotrophic fungal pathogen Venturia inaequalis, is the most economically important disease of apples. During infection, V. inaequalis colonizes the subcuticular host environment, where it develops specialized infection structures called runner hyphae and stromata. These structures are thought to be involved in nutrient acquisition and effector (virulence factor) delivery, but also give rise to conidia that further the infection cycle. Despite their importance, very little is known about how these structures are differentiated. Likewise, nothing is known about how these structures are protected from host defences or recognition by the host immune system. To better understand these processes, we first performed a glycosidic linkage analysis of sporulating tubular hyphae from V. inaequalis developed in culture. This analysis revealed that the V. inaequalis cell wall is mostly composed of glucans (44%) and mannans (37%), whereas chitin represents a much smaller proportion (4%). Next, we used transcriptomics and confocal laser scanning microscopy to provide insights into the cell wall carbohydrate composition of runner hyphae and stromata. These analyses revealed that, during subcuticular host colonization, genes of V. inaequalis putatively associated with the biosynthesis of immunogenic carbohydrates, such as chitin and β-1,6-glucan, are down-regulated relative to growth in culture, while on the surface of runner hyphae and stromata, chitin is deacetylated to the less immunogenic carbohydrate, chitosan. These changes are anticipated to enable the subcuticular differentiation of runner hyphae and stromata by V. inaequalis, as well as to protect these structures from host defences and recognition by the host immune system.ImportancePlant-pathogenic fungi are a major threat to food security. Among these are subcuticular pathogens, which often cause latent asymptomatic infections, making them difficult to control. A key feature of these pathogens is their ability to differentiate specialized subcuticular infection structures that, to date, remain largely understudied. This is typified by Venturia inaequalis, which causes scab, the most economically important disease of apples. In this study, we show that, during subcuticular host colonization, V. inaequalis down-regulates genes associated with the biosynthesis of two immunogenic cell wall carbohydrates, chitin and β-1,6-glucan, and coats its infection structures with a less-immunogenic carbohydrate, chitosan. These changes are anticipated to enable subcuticular host colonization by V. inaequalis and provide a foundation for understanding subcuticular host colonization by other plant-pathogenic fungi. Such an understanding is important, as it may inform the development of novel control strategies against subcuticular plant-pathogenic fungi.

Dothistroma septosporum (Ds) and Fulvia fulva (Ff; previously called Cladosporium fulvum) are two closely related Dothideomycete fungal species that cause Dothistroma needle blight in pine and leaf mold in tomato, respectively. During host colonization, these pathogens secrete virulence factors termed effectors to promote infection. In the presence of corresponding host immune receptors, however, these effectors activate plant defenses, including a localized cell death response that halts pathogen growth. We identified two apoplastic effector protein families, Ecp20 and Ecp32, which are conserved between the two pathogens. The Ecp20 family has four paralogues in both species, while the Ecp32 family has four paralogues in D. septosporum and five in F. fulva. Both families have members that are highly expressed during host infection. Members of the Ecp20 family have predicted structural similarity to proteins with a β-barrel fold, including the Alt a 1 allergen from Alternaria alternata, while members of the Ecp32 family have predicted structural similarity to proteins with a β-trefoil fold, such as trypsin inhibitors and lectins. Using Agrobacterium tumefaciens-mediated transient transformation assays, each family member was assessed for its ability to trigger cell death in leaves of the non-host species Nicotiana benthamiana and N. tabacum. Using this approach, FfEcp20-2, DsEcp20-3, and FfEcp20-3 from the Ecp20 family, and all members from the Ecp32 family, except for the Ds/FfEcp32-4 pair, triggered cell death in both species. This cell death was dependent on secretion of the effectors to the apoplast. In line with recognition by an extracellular immune receptor, cell death triggered by Ds/FfEcp20-3 and FfEcp32-3 was compromised in N. benthamiana silenced for BAK1 or SOBIR1, which encode extracellular co-receptors involved in transducing defense response signals following apoplastic effector recognition. We then investigated whether DsEcp20-3 and DsEcp20-4 triggered cell death in the host species Pinus radiata by directly infiltrating purified protein into pine needles. Strikingly, as in the non-host species, DsEcp20-3 triggered cell death, while DsEcp20-4 did not. Collectively, our study describes two new candidate effector families with cell death-eliciting activity from D. septosporum and F. fulva and provides evidence that members of these families are recognized by plant immune receptors.

At present, forage kale cultivars for feeding cattle and sheep are either open-pollinated ones from population-improvement schemes within suitable botanical varieties of Brassica oleracea or triple-cross hybrids from within or between botanical varieties, the only commercialised latter type being between marrow-stem kale and Brussels sprouts. Eight botanical varieties (15 cultivars) and 13 types of hybrids (50 hybrids) between them were produced and assessed for forage traits in SE Scotland in the early 1980s when there was government funding in Great Britain for such work (terminated in 1990). These previously unpublished results may now be of interest to a new generation of commercial forage brassica breeders. In addition to height and dry matter yield and content, quality traits, such as digestibility and antimetabolites, were assessed. The hybrids with marrow-stem kale as one parent varied in height, but combined a high-dry-matter yield with desirable quality traits for a forage crop. None was ideal and none had a superior combination of traits to the hybrids with Brussels sprouts. The hybrids between marrow-stem kale and January King cabbage were the shortest and a possible alternative to dwarf thousand-head kale. The results can be used to justify new forage brassica breeding programmes.

Presented on Tuesday 17 May: Session 1 Geoscience Australia is undertaking a series of basin-scale assessments to identify the ‘yet-to-find’ resource potential for hydrocarbons, as well as for groundwater resources and carbon capture and storage (CCS) opportunities in central Australia under the Exploring for the Future (EFTF) Program. A play-based exploration approach is being used to systematically evaluate the key risk elements for each resource type through the analysis of drilling results and spatial data to map ‘sweet spots’ for exploration. These assessments aim to reduce the risks and uncertainties for explorers by providing spatially enabled assessments of energy resources and CCS potential. The work will also improve the understanding of existing groundwater resources which may be impacted by future energy resource developments or provide feedstock for future green hydrogen projects. A key requirement for undertaking such play-based resource assessments is to apply a common regional chronostratigraphic framework across all the resource types that link different geological unit nomenclatures through defining the assessed reservoir and seal intervals and their associated sequence stratigraphic surfaces (sequence boundaries, transgressive surfaces and maximum flooding surfaces). A Mesozoic chronostratigraphic framework has been developed for the Eromanga Basin, which defines nine regional play intervals that host the known hydrocarbon and groundwater resources, or represent potential CCS targets. The Mesozoic play framework is now being applied to undertake play-based low-carbon energy resource assessments in the western Eromanga Basin, with initial work focussing on the interpretation and correlation of the nine play intervals in wells for post-drill analysis. To access the presentation click the link on the right. To read the full paper click here

The family Sclerotiniaceae includes important phytopathogens, such as Botrytis cinerea and Sclerotinia sclerotiorum, that activate plant immune responses to facilitate infection propagation. The mechanisms of plant resistance to these necrotrophic pathogens are still poorly understood. To discover mechanisms of resistance, we used the Ciborinia camelliae (Sclerotiniaceae)–Camellia spp. pathosystem. This fungus induces rapid infection of the blooms of susceptible cultivar Nicky Crisp (Camellia japonica × Camellia pitardii var. pitardii), while Camellia lutchuensis is highly resistant. Genome-wide analysis of gene expression in resistant plants revealed fast modulation of host transcriptional activity 6 h after ascospore inoculation. Ascospores induced the same defense pathways in the susceptible Camellia cultivar but much delayed and coinciding with disease development. We next tested the hypothesis that differences in defense timing influences disease outcome. We induced early defense in the susceptible cultivar using methyl jasmonate and this strongly reduced disease development. Conversely, delaying the response in the resistant species, by infecting it with actively growing fungal mycelium, increased susceptibility. The same plant defense pathways, therefore, contribute to both resistance and susceptibility, suggesting that defense timing is a critical factor in plant health, and resistance against necrotrophic pathogens may occur during the initial biotrophy-like stages.

Fungal effector proteins facilitate host‐plant colonization and have generally been characterized as small secreted proteins (SSPs). We classified and functionally tested SSPs from the secretomes of three closely related necrotrophic phytopathogens: Ciborinia camelliae, Botrytis cinerea, and Sclerotinia sclerotiorum. Alignment of predicted SSPs identified a large protein family that share greater than 41% amino acid identity and that have key characteristics of previously described microbe‐associated molecular patterns (MAMPs). Strikingly, 73 of the 75 SSP family members were predicted within the secretome of the host‐specialist C. camelliae with single‐copy homologs identified in the secretomes of the host generalists S. sclerotiorum and B. cinerea. To explore the potential function of this family of SSPs, 10 of the 73 C. camelliae proteins, together with the single‐copy homologs from S. sclerotiorum (SsSSP3) and B. cinerea (BcSSP2), were cloned and expressed as recombinant proteins. Infiltration of SsSSP3 and BcSSP2 into host tissue induced rapid necrosis. In contrast, only one of the 10 tested C. camelliae SSPs was able to induce a limited amount of necrosis. Analysis of chimeric proteins consisting of domains from both a necrosis‐inducing and a non‐necrosis‐inducing SSP demonstrated that the C‐terminus of the S. sclerotiorum SSP is essential for necrosis‐inducing function. Deletion of the BcSSP2 homolog from B. cinerea did not affect growth or pathogenesis. Thus, this research uncovered a family of highly conserved SSPs present in diverse ascomycetes that exhibit contrasting necrosis‐inducing functions., The C‐terminus of previously uncharacterized small, secreted, cysteine‐rich proteins from three fungal pathogens of the Sclerotiniaceae is responsible for necrosis‐inducing function in plant tissues.

BackgroundScab, caused by the biotrophic fungus Venturia inaequalis, is the most economically important disease of apples worldwide. During infection, V. inaequalis occupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth by V. inaequalis, as well as in activating, suppressing or circumventing resistance protein-mediated defences in apple, is required.ResultsWe generated the first comprehensive RNA-seq transcriptome of V. inaequalis during colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector from Leptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi.ConclusionsOur study reveals the transcriptomic profile underpinning subcuticular growth by V. inaequalis and provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins.

This paper reviews the progress and the way ahead in diploid F

During host colonization, plant-associated microbes, including fungi and oomycetes, deliver a collection of glycoside hydrolases (GHs) to their cell surfaces and surrounding extracellular environments. The number and type of GHs secreted by each organism is typically associated with their lifestyle or mode of nutrient acquisition. Secreted GHs of plant-associated fungi and oomycetes serve a number of different functions, with many of them acting as virulence factors (effectors) to promote microbial host colonization. Specific functions involve, for example, nutrient acquisition, the detoxification of antimicrobial compounds, the manipulation of plant microbiota, and the suppression or prevention of plant immune responses. In contrast, secreted GHs of plant-associated fungi and oomycetes can also activate the plant immune system, either by acting as microbe-associated molecular patterns (MAMPs), or through the release of damage-associated molecular patterns (DAMPs) as a consequence of their enzymatic activity. In this review, we highlight the critical roles that secreted GHs from plant-associated fungi and oomycetes play in plant–microbe interactions, provide an overview of existing knowledge gaps and summarize future directions.

Background Patient and public involvement work (PPI) is essential to good research practice. Existing research indicates that PPI offers benefits to research design, conduct, communication, and implementation of findings. Understanding how PPI works and its value helps to provide information about best practice and highlight areas for further development. This study used a values-based approach to reporting PPI at a Research Unit focused on musculoskeletal conditions within a UK medical school. Methods The study was conducted between October 2019 and January 2020 using Gradinger’s value system framework as a theoretical basis. The framework comprises three value systems each containing five clusters. All PPI members and researchers who had attended PPI groups were invited to participate. Participants completed a structured questionnaire based on the value system framework; PPI members also provided further information through telephone interviews. Data were deductively analysed using a framework approach with data mapped onto value systems. Results Twelve PPI members and 17 researchers took part. Views about PPI activity mapped onto all three value systems. PPI members felt empowered to provide their views, and that their opinions were valued by researchers. It was important to PPI members that they were able to ‘give back’ and to do something positive with their experiences. Researchers would have liked the groups to be more representative of the wider population, patients highlighted that groups could include more younger members. Researchers recognised the value of PPI, and the study highlighted areas where researchers members might benefit from further awareness. Conclusions Three areas for development were identified: (i) facilitating researcher engagement in training about the value and importance of PPI in research; (ii) support for researchers to reflect on the role that PPI plays in transparency of healthcare research; (iii) work to further explore and address aspects of diversity and inclusion in PPI.

Background: Italy, France and New York City have reported an increase in out-of-hospital cardiac arrest (OHCA) incidence during the COVID-19 pandemic. The purpose of our study was to assess the effect of COVID-19 on OHCA cases in Chicago. Method: Cardiac Arrest Registry to Enhance Survival (CARES) database was used. Bivariate analysis was conducted to assess changes in demographic and other characteristics. We excluded the cases that occurred in a healthcare facility or a nursing home. We compared the cases reported in 2020 to 2019 (and prior years). ArcGIS was used to geocode incident addresses and to show the temporal distribution by community areas. Bivariate analysis was done using chi-square tests. Results: A total of 3221 OHCA cases were reported in Chicago in 2020, which is 31.5% higher than those reported in 2019 (n=2450 cases). This increase was higher than what has been noticed historically (for instance, the increase from 2018 to 2019 was only 17%). There was an increase in Hispanic OHCA cases (17.3% in 2020 vs. 13.5% in 2019, p Conclusion: A better understanding of the causes of the excess cardiac arrest numbers will be important to help plan and better prepare for future public health interventions. The effect of COVID-19 on OHCA survival needs to be examined further in future studies.

Forests are under threat from pests, pathogens, and changing climate. One of the major forest pathogens worldwide isDothistroma septosporum, which causes dothistroma needle blight (DNB) of pines.D. septosporumis a hemibiotrophic fungus related to well-studied Dothideomycete pathogens, such asCladosporium fulvum. These pathogens use small secreted proteins, termed effectors, to facilitate the infection of their hosts. The same effectors, however, can be recognised by plants carrying corresponding immune receptors, resulting in resistance responses. Hence, effectors are increasingly being exploited to identify and select disease resistance in crop species. In gymnosperms, however, such research is scarce. We predicted and investigated apoplasticD. septosporumcandidate effectors (DsCEs) using bioinformatics and plant-based experiments. We discovered secreted proteins that trigger cell death in the angiospermNicotianaspp., suggesting their recognition by immune receptors in non-host plants. In a first for foliar forest pathogens, we also developed a novel protein infiltration method to show that tissue-cultured pine shoots can respond with a cell death response to one of our DsCEs, as well as to a reference cell death-inducing protein. These results contribute to our understanding of forest pathogens and may ultimately provide clues to disease immunity in both commercial and natural forests.

Background Operating a motor vehicle involves multiple cognitive and sensorimotor faculties. Neurological conditions pose driving risk, but this has not been examined in patients with primary brain tumors. Methods Sixty-four patients with primary brain tumors (32 left hemisphere; 69% glioblastoma) completed the Cognitive Behavioral Driver’s Inventory (CBDI). A subset also completed broader cognitive testing. Patient characteristics, CBDI measures, and broader neuropsychological test scores were compared between Passing and Nonpassing groups. Follow-up logistic regression analyses identified patient characteristics and CBDI measures predictive of Pass/Nonpass outcome. Point-biserial correlations determined associations between neuropsychological tests and CBDI outcome. Results Sixty-nine percent of patients were classified as passing the CBDI. Nonpassing patients were older and more likely to have WHO grade IV and temporal lobe tumors. Age was the most salient predictor of CBDI performance. CBDI measures of speeded visual search and set-shifting, speeded response inhibition, vigilance and freedom from distractibility, and basic visual scanning speed were predictive of Pass/Nonpass outcome. Neuropsychological tests of memory in particular, but also speeded visual scanning and discrimination, executive function, basic visual attention, visuoconstruction, and manual dexterity (dominant hand), were associated with CBDI outcome. Conclusions A sizeable proportion of patients with primary brain tumors appear at risk of driving difficulty, particularly those with higher-grade tumors and of older age. Memory, visual attention, and executive difficulties appear to contribute most to driving safety risk as determined by the CBDI. These results highlight the importance of driving safety screening in this population.

Summary Dothistroma needle blight is one of the most devastating pine tree diseases worldwide. New and emerging epidemics have been frequent over the last 25 years, particularly in the Northern Hemisphere, where they are in part associated with changing weather patterns. One of the main Dothistroma needle blight pathogens, Dothistroma septosporum, has a global distribution but most molecular plant pathology research has been confined to Southern Hemisphere populations that have limited genetic diversity. Extensive genomic and transcriptomic data are available for a D. septosporum reference strain from New Zealand, where an introduced clonal population of the pathogen predominates. Due to the global importance of this pathogen, we determined whether the genome of this reference strain is representative of the species worldwide by sequencing the genomes of 18 strains sampled globally from different pine hosts. Genomic polymorphism shows substantial variation within the species, clustered into two distinct groups of strains with centres of diversity in Central and South America. A reciprocal chromosome translocation uniquely identifies the New Zealand strains. Globally, strains differ in their production of the virulence factor dothistromin, with extremely high production levels in strain ALP3 from Germany. Comparisons with the New Zealand reference revealed that several strains are aneuploids; for example, ALP3 has duplications of three chromosomes. Increased gene copy numbers therefore appear to contribute to increased production of dothistromin, emphasizing that studies of population structure are a necessary adjunct to functional analyses of genetic polymorphisms to identify the molecular basis of virulence in this important forest pathogen.

Conventional wisdom is that selection decreases genetic variation in populations, variation that should enable and be essential for population persistence in an ever-changing world. Basically, we find the opposite. Response to selection on biting in the pitcher-plant mosquito, Wyeomyia smithii, increases from 20 to 80% in 19 generations, but reverts back to the original 20% after seven generations of relaxed (not reversed) selection. At the same time, biting in the control line remains at the original 20% through 30 generations without blood feeding. Imposition of selection on biting in both lines elicits a rapid response in the previously selected line, but, importantly, not in the control line. Genetic variation for biting has increased, not decreased, as a consequence of long-term directional selection, contrary to expectations. Convergent phenotypes belie the underlying difference in future adaptive potential. Selection events over time in the background of individuals or populations will determine outcomes of applied research, be it in the fields of medicine, agriculture, or conservation. In short, history matters.

Experimental results are brought together to demonstrate that forage kale population improvement involving full-sib and selfed families can be done on an annual cycle, followed by production of a synthetic cultivar. Furthermore, this new breeding method compares favourably with the two successful methods used to date, namely triple-cross hybrid cultivars from inbreeding and crossbreeding programmes and open-pollinated cultivars from population improvement programmes. The key findings were that natural vernalization of kale in south east Scotland occurred by mid-December so that plants could be pollinated in a glasshouse with heating and lighting by the end of February and seed harvested by the end of May. The resulting full-sib or selfed families could be assessed in a field transplant trial in the same year, from June to November, thus completing an annual cycle. Self-pollination resulted in shorter plants with lower fresh-weight, dry-matter and digestible organic-matter yields, and undesirably higher contents of S-methylcysteine sulphoxide, the haemolytic anaemia factor, and the goitrogenic thiocyanate ion. As a consequence of digestible organic-matter yield being reduced by as much as 22%, the estimated optimum number of selfed parents in a synthetic cultivar was four to eight. Synthetic cultivars are expected to yield as well as triple-cross hybrids as there was no reduction in yield when the latter were open-pollinated.

Apple scab, caused by the fungal pathogen Venturia inaequalis, is the most economically important disease of apple (Malus x domestica) worldwide. To develop durable control strategies against this disease, a better understanding of the genetic mechanisms underlying the growth, reproduction, virulence and pathogenicity of V. inaequalis is required. A major bottleneck for the genetic characterization of V. inaequalis is the inability to easily delete or disrupt genes of interest using homologous recombination. Indeed, no gene deletions or disruptions in V. inaequalis have yet been published. Using the melanin biosynthesis pathway gene trihydroxynaphthalene reductase (THN) as a target for inactivation, which has previously been shown to result in a light-brown colony phenotype when transcriptionally silenced using RNA interference, we show, for the first time, that the CRISPR-Cas9 gene editing system can be successfully applied to the apple scab fungus. More specifically, using a CRISPR-Cas9 single guide RNA (sgRNA) targeted to the THN gene, delivered by a single autonomously replicating Golden Gate-compatible plasmid, we were able to identify six of 36 stable transformants with a light-brown phenotype, indicating an ∼16.7% gene inactivation efficiency. Notably, of the six THN mutants, five had an independent mutation. As part of our pipeline, we also report a high-resolution melting (HRM) curve protocol for the rapid detection of CRISPR-Cas9 gene-edited mutants of V. inaequalis. This protocol identified a single base pair deletion mutation in a sample containing only 5% mutant genomic DNA, indicating high sensitivity for mutant screening. In establishing CRISPR-Cas9 as a tool for gene editing in V. inaequalis, we have provided a strong starting point for studies aiming to decipher gene function in this fungus. The associated HRM curve protocol will enable CRISPR-Cas9 transformants to be screened for gene inactivation in a high-throughput and low-cost manner, which will be particularly powerful in cases where the CRISPR-Cas9-mediated gene inactivation efficiency is low.

BackgroundScab, or black spot, caused by the filamentous fungal pathogenVenturia inaequalis, is the most economically important disease of apple (Malusxdomestica) worldwide. To develop durable control strategies against this disease, a better understanding of the genetic mechanisms underlying the growth, reproduction, virulence and pathogenicity ofV. inaequalisis required. A major bottleneck for the genetic characterization ofV. inaequalisis the inability to easily delete or disrupt genes of interest using homologous recombination. Indeed, no gene deletions or disruptions inV. inaequalishave yet been published. Recently, CRISPR-Cas9 has emerged as an efficient tool for gene editing in filamentous fungi. With this in mind, we set out to establish CRISPR-Cas9 as a gene editing tool inV. inaequalis.ResultsWe showed that CRISPR-Cas9 can be used for gene inactivation in the apple scab fungus. As a proof of concept, we targeted the melanin biosynthesis pathway genetrihydroxynaphthalene reductase(THN), which has previously been shown to result in a light-brown colony phenotype when transcriptionally silenced using RNA interference. Using one of two CRISPR-Cas9 single guide RNAs (sgRNAs) targeted to theTHNgene, delivered by a single autonomously replicating Golden Gate-compatible plasmid, we were able to identify six of 36 stable transformants with a light-brown phenotype, indicating an~16.7% gene inactivation efficiency. Notably, of these sixTHNmutants, five had an independent mutation. As part of our pipeline, we also report a high-resolution melting (HRM) curve protocol for the rapid detection of CRISPR-Cas9 gene-edited mutants ofV. inaequalis. This protocol identified a single base pair deletion mutation in a sample containing only 5% mutant genomic DNA, indicating high sensitivity for mutant screening.ConclusionsIn establishing CRISPR-Cas9 as a tool for gene editing inV. inaequalis, we have provided a strong starting point for studies aiming to decipher the function of genes associated with the growth, reproduction, virulence and pathogenicity of this fungus. The associated HRM curve protocol will enable CRISPR-Cas9 transformants to be screened for gene inactivation in a high-throughput and low-cost manner, which will be particularly powerful in cases where the CRISPR-Cas9-mediated gene inactivation efficiency is low.

Purpose Faecal incontinence (FI) is estimated to affect around 7.7% of people. There is a lack of uniformity in outcome definitions, measurement and reporting in FI studies. Until now, there is no general consensus on which outcomes should be assessed and reported in FI research. This complicates comparison between studies and evidence synthesis, potentially leading to recommendations not evidence-based enough to guide physicians in selecting an FI therapy. A solution for this lack of uniformity in reporting of outcomes is the development of a Core Outcome Set (COS) for FI. This paper describes the protocol for the development of a European COS for FI. Methods Patient interviews and a systematic review of the literature will be performed to identify patient-, physician- and researcher-oriented outcomes. The outcomes will be categorised using the COMET taxonomy and put forward to a group of patients, physicians (i.e. colorectal surgeons, gastroenterologists and general practitioners) and researchers in a Delphi consensus exercise. This exercise will consist of up to three web-based rounds in which participants will prioritise and condense the list of outcomes, which is expected to result in consensus. A consensus meeting with participants from all stakeholder groups will take place to reach a final agreement on the COS. Discussion This study protocol describes the development of a European COS to improve reliability and consistency of outcome reporting in FI studies, thereby improving evidence synthesis and patient care. Trial registration This project has been registered in the COMET database on the 1st of April 2020, available at http://www.comet-initiative.org/Studies/Details/1554. The systematic review has been registered on the PROSPERO database on the 31st of August 2020, available at https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=202020&VersionID=1381336.

The intended end uses of new cultivars determine the quality criteria that need to be added as breeding objectives to yield in the production environments. Nutritional value will be important for the potato as a staple food; cooking quality, texture, taste and flavour will be important for the potato as a vegetable sold for cash; processing quality will be defined by the manufacturers of French fries, chips (crisps) and other processed products and the composition of the potato starch will determine its value for different uses in the starch industry. This chapter considers the challenges of translating these breeding objectives into selection criteria and methods of measurement for use on the tubers from assessment plots and yield trials, both immediately after harvest and after storage. Tuber appearance and freedom from internal defects are also selection criteria. Mineral and vitamin biofortification, beneficial phytochemicals, steroidal glycoalkaloids and acrylamide formation are also considered.

Better parents for use in the breeding of new cultivars are provided by the introgression of desirable genes from the landraces and wild relatives of cultivated potatoes, the use of landraces in a more general broadening (incorporation) of the genetic base of breeding, and the intercrossing of the resulting clones in population improvement schemes for long-term crop improvement. The germplasm is conserved in situ and ex situ in genebanks such as the one at the International Potato Centre (CIP). The crossability of wild to cultivated species is discussed in terms of the Endosperm Balance Number (EBN) concept and examples given of introgression from 1EBN, 2EBN and 4EBN species. Base broadening examples presented are Neotuberosum, CIP’s B and LTVR populations and diploid populations of Groups Phureja and Stenotomum. The theory and practice of marker-assisted introgression and selection and genomic selection are presented along with examples of the use of molecular markers.

Gene editing and genetic transformation are alternatives to sexual hybridization for potato improvement. Engineered nucleases catalyse a double-stranded DNA break at a specific location in the genome so that desired DNA modifications can occur at the break site rather than at random. TALENS and CRISPR-Cas9 can be designed to target all four alleles of a gene in tetraploid potato and hence achieve a knock-out mutation, but more research is required to create and fix novel alleles. Agrobacterium-mediated transformation is now free of selectable markers, and currently up to eight transgenes are being stacked. Potatoes have been transformed for improved disease and pest resistance, processing quality and nutritional value. Transgene-mediated post-transcriptional gene silencing through RNA interference has provided a number of desirable phenotypes by inactivating one or several specific genes. The reluctance to accept genetically modified potatoes is considered along with the GM regulations in the European Union and the USA.