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1.
Cell ; 185(5): 761-763, 2022 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-35245479

RESUMO

Powdery mildew, a potentially severe crop disease, can be controlled by mlo mutations, which suppress fungal proliferation but typically also reduce yield. Li et al. (2022) demonstrate that productivity can be restored by overexpressing a host sugar transporter, thus offering a new option for economically and environmentally benign disease control.


Assuntos
Ascomicetos , Doenças das Plantas , Ascomicetos/genética , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética
2.
Nature ; 2024 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-38885696

RESUMO

Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security1. Here we examined the genetic and phenotypic diversity of the A.E. Watkins landrace collection2 of bread wheat (Triticum aestivum), a major global cereal, through whole-genome re-sequencing (827 Watkins landraces and 208 modern cultivars) and in-depth field evaluation spanning a decade. We discovered that modern cultivars are derived from just two of the seven ancestral groups of wheat and maintain very long-range haplotype integrity. The remaining five groups represent untapped genetic sources, providing access to landrace-specific alleles and haplotypes for breeding. Linkage disequilibrium (LD) based haplotypes and association genetics analyses link Watkins genomes to the thousands of high-resolution quantitative trait loci (QTL), and significant marker-trait associations identified. Using these structured germplasm, genotyping and informatics resources, we revealed many Watkins-unique beneficial haplotypes that can confer superior traits in modern wheat. Furthermore, we assessed the phenotypic effects of 44,338 Watkins-unique haplotypes, introgressed from 143 prioritised QTL in the context of modern cultivars, bridging the gap between landrace diversity and current breeding. This study establishes a framework for systematically utilising genetic diversity in crop improvement to achieve sustainable food security.

3.
PLoS Biol ; 22(4): e3002232, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38662644

RESUMO

Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.


Assuntos
Genótipo , Hordeum , Microbiota , Raízes de Plantas , Pseudomonas , Rizosfera , Hordeum/microbiologia , Hordeum/genética , Hordeum/metabolismo , Raízes de Plantas/microbiologia , Raízes de Plantas/metabolismo , Microbiota/fisiologia , Microbiota/genética , Pseudomonas/genética , Pseudomonas/metabolismo , Pseudomonas/fisiologia , Microbiologia do Solo , Exsudatos de Plantas/metabolismo
4.
Proc Natl Acad Sci U S A ; 119(16): e2123299119, 2022 04 19.
Artigo em Inglês | MEDLINE | ID: mdl-35412884

RESUMO

Wheat is a widely grown food crop that suffers major yield losses due to attack by pests and pathogens. A better understanding of biotic stress responses in wheat is thus of major importance. The recently assembled bread wheat genome coupled with extensive transcriptomic resources provides unprecedented new opportunities to investigate responses to pathogen challenge. Here, we analyze gene coexpression networks to identify modules showing consistent induction in response to pathogen exposure. Within the top pathogen-induced modules, we identify multiple clusters of physically adjacent genes that correspond to six pathogen-induced biosynthetic pathways that share a common regulatory network. Functional analysis reveals that these pathways, all of which are encoded by biosynthetic gene clusters, produce various different classes of compounds­namely, flavonoids, diterpenes, and triterpenes, including the defense-related compound ellarinacin. Through comparative genomics, we also identify associations with the known rice phytoalexins momilactones, as well as with a defense-related gene cluster in the grass model plant Brachypodium distachyon. Our results significantly advance the understanding of chemical defenses in wheat and open up avenues for enhancing disease resistance in this agriculturally important crop. They also exemplify the power of transcriptional networks to discover the biosynthesis of chemical defenses in plants with large, complex genomes.


Assuntos
Vias Biossintéticas , Interações Hospedeiro-Patógeno , Doenças das Plantas , Triticum , Vias Biossintéticas/genética , Pão , Resistência à Doença/genética , Família Multigênica/genética , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Triticum/genética , Triticum/metabolismo , Triticum/microbiologia
5.
PLoS Genet ; 17(4): e1009524, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33872310

RESUMO

An important prelude to bacterial infection is the ability of a pathogen to survive independently of the host and to withstand environmental stress. The compatible solute trehalose has previously been connected with diverse abiotic stress tolerances, particularly osmotic shock. In this study, we combine molecular biology and biochemistry to dissect the trehalose metabolic network in the opportunistic human pathogen Pseudomonas aeruginosa PAO1 and define its role in abiotic stress protection. We show that trehalose metabolism in PAO1 is integrated with the biosynthesis of branched α-glucan (glycogen), with mutants in either biosynthetic pathway significantly compromised for survival on abiotic surfaces. While both trehalose and α-glucan are important for abiotic stress tolerance, we show they counter distinct stresses. Trehalose is important for the PAO1 osmotic stress response, with trehalose synthesis mutants displaying severely compromised growth in elevated salt conditions. However, trehalose does not contribute directly to the PAO1 desiccation response. Rather, desiccation tolerance is mediated directly by GlgE-derived α-glucan, with deletion of the glgE synthase gene compromising PAO1 survival in low humidity but having little effect on osmotic sensitivity. Desiccation tolerance is independent of trehalose concentration, marking a clear distinction between the roles of these two molecules in mediating responses to abiotic stress.


Assuntos
Glucanos/genética , Pseudomonas aeruginosa/genética , Estresse Fisiológico/genética , Trealose/genética , Infecções Bacterianas/genética , Infecções Bacterianas/microbiologia , Vias Biossintéticas/genética , Glucanos/biossíntese , Interações Hospedeiro-Patógeno/genética , Humanos , Espectroscopia de Ressonância Magnética , Pressão Osmótica/fisiologia , Pseudomonas aeruginosa/patogenicidade
6.
Plant Cell Environ ; 44(3): 807-820, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33179278

RESUMO

Circadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this circadian variation, we used a delayed fluorescence imaging assay to screen 191 naturally occurring Swedish Arabidopsis accessions for their circadian phenotypes. We demonstrate that the period length co-varies with both geography and population sub-structure. Several candidate loci linked to period, phase and relative amplitude error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution within COR28 is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants. COR28 is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. We demonstrate the effect of the COR28-58S SNP in increasing period length through a co-segregation analysis. Finally, we show that period phenotypic tails remain diverged under lower temperatures and follow a distinctive "arrow-shaped" trend indicative of selection for a cold-biased temperature compensation response.


Assuntos
Arabidopsis/genética , Ritmo Circadiano/genética , Genes de Plantas/genética , Loci Gênicos/genética , Proteínas de Arabidopsis/genética , Variação Genética/genética , Estudo de Associação Genômica Ampla , Geografia , Polimorfismo de Nucleotídeo Único/genética , Proteínas Repressoras/genética , Suécia
7.
Plant Biotechnol J ; 16(1): 63-71, 2018 01.
Artigo em Inglês | MEDLINE | ID: mdl-28436146

RESUMO

Zinc (Zn) is essential for all life forms, including humans. It is estimated that around two billion people are deficient in their Zn intake. Human dietary Zn intake relies heavily on plants, which in many developing countries consists mainly of cereals. The inner part of cereal grain, the endosperm, is the part that is eaten after milling but contains only a quarter of the total grain Zn. Here, we present results demonstrating that endosperm Zn content can be enhanced through expression of a transporter responsible for vacuolar Zn accumulation in cereals. The barley (Hordeum vulgare) vacuolar Zn transporter HvMTP1 was expressed under the control of the endosperm-specific D-hordein promoter. Transformed plants exhibited no significant change in growth but had higher total grain Zn concentration, as measured by ICP-OES, compared to parental controls. Compared with Zn, transformants had smaller increases in concentrations of Cu and Mn but not Fe. Staining grain cross sections with the Zn-specific stain DTZ revealed a significant enhancement of Zn accumulation in the endosperm of two of three transformed lines, a result confirmed by ICP-OES in the endosperm of dissected grain. Synchrotron X-ray fluorescence analysis of longitudinal grain sections demonstrated a redistribution of grain Zn from aleurone to endosperm. We argue that this proof-of-principle study provides the basis of a strategy for biofortification of cereal endosperm with Zn.


Assuntos
Proteínas de Membrana Transportadoras/metabolismo , Proteínas de Plantas/metabolismo , Zinco/metabolismo , Grão Comestível/genética , Grão Comestível/metabolismo , Endosperma/genética , Endosperma/metabolismo , Hordeum/genética , Hordeum/metabolismo , Proteínas de Membrana Transportadoras/genética , Proteínas de Plantas/genética
8.
Ann Bot ; 121(3): 415-430, 2018 03 05.
Artigo em Inglês | MEDLINE | ID: mdl-29309539

RESUMO

Background and Aims: Ramularia collo-cygni is an ascomycete fungus that colonizes barley primarily as a benign endophyte, although this interaction can become pathogenic, causing the disease Ramularia leaf spot (RLS). Factors, particularly reactive oxygen species, that resulted in the transition of the fungus from endophyte to necrotrophic parasite and the development of disease symptoms were investigated. Methods: Disease development in artificially inoculated seedlings of barley varieties varying in partial resistance to RLS was related to exposure to abiotic stress prior to inoculation. Histochemical and molecular analysis determined the effect of R. collo-cygni colonization on accumulation of reactive oxygen species and antioxidant gene expression. Development of RLS on barley lines defective in antioxidant enzymes and with altered redox status or non-functional chloroplasts was compared with the accumulation of fungal biomass to determine how these factors affect disease symptom expression. Key Results: Exposure to abiotic stress increased symptom development in all susceptible and most partially resistant barley varieties, in association with greater hydrogen peroxide (H2O2) levels in leaves. Decreased activity of the antioxidant enzymes superoxide dismutase and catalase in transgenic and mutant plants had no effect on the disease transition, whereas manipulation of H2O2 levels during asymptomatic growth of the fungus increased disease symptoms in most susceptible varieties but not in partially resistant plants. Barley mutants that undergo rapid loss of green leaf area when infected by R. collo-cygni or albino mutants with non-functional chloroplasts showed reduced development of RLS symptoms. Conclusions: These results imply that in seedlings the pathogenic transition of the normally endophytic fungus R. collo-cygni does not result from senescence as such, but rather is promoted by factors that result in changes to host reactive oxygen species. Barley varieties vary in the extent to which these factors promote RLS disease.


Assuntos
Ascomicetos , Hordeum/microbiologia , Doenças das Plantas/microbiologia , Folhas de Planta/microbiologia , Espécies Reativas de Oxigênio/metabolismo , Plântula/microbiologia , Ascomicetos/crescimento & desenvolvimento , DNA Fúngico/metabolismo , DNA de Plantas/metabolismo , Microscopia , Folhas de Planta/ultraestrutura , Reação em Cadeia da Polimerase Via Transcriptase Reversa
9.
Crop Prot ; 85: 1-8, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-27375312

RESUMO

Crop variety mixtures have the potential to increase yield stability in highly variable and unpredictable environments, yet knowledge of the specific mechanisms underlying enhanced yield stability has been limited. Ecological processes in genetically diverse crops were investigated by conducting field trials with winter barley varieties (Hordeum vulgare), grown as monocultures or as three-way mixtures in fungicide treated and untreated plots at three sites. Mixtures achieved yields comparable to the best performing monocultures whilst enhancing yield stability despite being subject to multiple predicted and unpredicted abiotic and biotic stresses including brown rust (Puccinia hordei) and lodging. There was compensation through competitive release because the most competitive variety overyielded in mixtures thereby compensating for less competitive varieties. Facilitation was also identified as an important ecological process within mixtures by reducing lodging. This study indicates that crop varietal mixtures have the capacity to stabilise productivity even when environmental conditions and stresses are not predicted in advance. Varietal mixtures provide a means of increasing crop genetic diversity without the need for extensive breeding efforts. They may confer enhanced resilience to environmental stresses and thus be a desirable component of future cropping systems for sustainable arable farming.

10.
BMC Genomics ; 16: 917, 2015 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-26556056

RESUMO

BACKGROUND: The Avrk1 and Avra10 avirulence (AVR) genes encode effectors that increase the pathogenicity of the fungus Blumeria graminis f.sp. hordei (Bgh), the powdery mildew pathogen, in susceptible barley plants. In resistant barley, MLK1 and MLA10 resistance proteins recognize the presence of AVRK1 and AVRA10, eliciting the hypersensitive response typical of gene for gene interactions. Avrk1 and Avra10 have more than 1350 homologues in Bgh genome, forming the EKA (Effectors homologous to Avr k 1 and Avr a 10) gene family. RESULTS: We tested the hypothesis that the EKA family originated from degenerate copies of Class I LINE retrotransposons by analysing the EKA family in the genome of Bgh isolate DH14 with bioinformatic tools specially developed for the analysis of Transposable Elements (TE) in genomes. The Class I LINE retrotransposon copies homologous to Avrk1 and Avra10 represent 6.5 % of the Bgh annotated genome and, among them, we identified 293 AVR/effector candidate genes. We also experimentally identified peptides that indicated the translation of several predicted proteins from EKA family members, which had higher relative abundance in haustoria than in hyphae. CONCLUSIONS: Our analyses indicate that Avrk1 and Avra10 have evolved from part of the ORF1 gene of Class I LINE retrotransposons. The co-option of Avra10 and Avrk1 as effectors from truncated copies of retrotransposons explains the huge number of homologues in Bgh genome that could act as dynamic reservoirs from which new effector genes may evolve. These data provide further evidence for recruitment of retrotransposons in the evolution of new biological functions.


Assuntos
Ascomicetos/genética , Proteínas Fúngicas/genética , Hordeum/microbiologia , Elementos Nucleotídeos Longos e Dispersos , Família Multigênica , Doenças das Plantas/microbiologia , Ascomicetos/classificação , Ascomicetos/metabolismo , Biologia Computacional , Sequência Consenso , Genoma Fúngico , Fases de Leitura Aberta , Filogenia , Proteômica
11.
Fungal Genet Biol ; 79: 33-41, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-26092788

RESUMO

This paper reviews current knowledge about genes for resistance to Septoria tritici blotch (STB) of wheat, caused by Zymoseptoria tritici (formerly Mycosphaerella graminicola). These genes can be placed into two classes, although a few may have characteristics of both classes. Qualitative resistance is controlled by genes which control large fractions of genetic variation, 21 of which have been discovered and mapped so far. Most of them have been shown to be genotype-specific, being effective against the minority of Z. tritici isolates which are avirulent, and Stb6 has been shown to control a gene-for-gene relationship. Most qualitative resistances are unlikely to be durable and some formerly effective genes have been overcome by the evolution of pathogen virulence. Quantitative resistance is generally controlled by genes with small-to-moderate effects on STB. They have generally weaker specificity than qualitative genes and have provided more durable resistance. 89 genome regions carrying quantitative trait loci (QTL) or meta-QTL have been identified to date. Some QTL have been mapped at or near loci of qualitative genes, especially Stb6, which is present in several sources of resistance. Another gene of particular interest is Stb16q, which has been effective against all Z. tritici isolates tested so far. In addition to resistance, the susceptibility of wheat cultivars to STB can also be reduced by disease escape traits, some of which may be undesirable in breeding. The fundamental requirements for breeding for STB-resistance are genetic diversity for resistance in wheat germplasm and a field trial site at which STB epidemics occur regularly and effective selection can be conducted for resistance combined with other desirable traits. If these are in place, knowledge of resistance genes can be applied to improving control of STB.


Assuntos
Ascomicetos/patogenicidade , Cruzamento/métodos , Resistência à Doença , Doenças das Plantas/imunologia , Doenças das Plantas/microbiologia , Triticum/imunologia , Triticum/microbiologia , Ascomicetos/imunologia , Genes de Plantas , Herança Multifatorial , Característica Quantitativa Herdável
12.
J Exp Bot ; 66(11): 3417-28, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25873675

RESUMO

Lesion mimic mutants display spontaneous necrotic spots and chlorotic leaves as a result of mis-regulated cell death programmes. Typically these mutants have increased resistance to biotrophic pathogens but their response to facultative fungi that cause necrotrophic diseases is less well studied. The effect of altered cell death regulation on the development of disease caused by Ramularia collo-cygni, Fusarium culmorum and Oculimacula yallundae was explored using a collection of barley necrotic (nec) lesion mimic mutants. nec8 mutants displayed lower levels of all three diseases compared to nec9 mutants, which had increased R. collo-cygni but decreased F. culmorum disease symptoms. nec1 mutants reduced disease development caused by both R. collo-cygni and F. culmorum. The severity of the nec1-induced lesion mimic phenotype and F. culmorum symptom development was reduced by mutation of the negative cell death regulator MLO. The significant reduction in R. collo-cygni symptoms caused by nec1 was completely abolished in the presence of the mlo-5 allele and both symptoms and fungal biomass were greater than in the wild-type. These results indicate that physiological pathways involved in regulation of cell death interact with one another in their effects on different fungal pathogens.


Assuntos
Ascomicetos/fisiologia , Resistência à Doença , Hordeum/imunologia , Doenças das Plantas/imunologia , Proteínas de Plantas/metabolismo , Alelos , Morte Celular , Fusarium/fisiologia , Hordeum/genética , Hordeum/microbiologia , Hordeum/fisiologia , Mutação , Folhas de Planta/genética , Folhas de Planta/imunologia , Folhas de Planta/microbiologia , Folhas de Planta/fisiologia , Proteínas de Plantas/genética
13.
Phytopathology ; 105(7): 895-904, 2015 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-25626073

RESUMO

Ramularia collo-cygni is the biotic factor responsible for the disease Ramularia leaf spot (RLS) of barley (Hordeum vulgare). Despite having been described over 100 years ago and being considered a minor disease in some countries, the fungus is attracting interest in the scientific community as a result of the increasing number of recorded economically damaging disease epidemics. New reports of disease spread and fungal identification using molecular diagnostics have helped redefine RLS as a global disease. This review describes recent developments in our understanding of the biology and epidemiology of the fungus, outlines advances made in the field of the genetics of both the fungus and host, and summarizes the control strategies currently available.


Assuntos
Ascomicetos/fisiologia , Hordeum/microbiologia , Hordeum/genética , Interações Hospedeiro-Patógeno , Controle de Pragas , Doenças das Plantas
14.
J Exp Bot ; 65(4): 1025-37, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24399175

RESUMO

Ramularia leaf spot (RLS), caused by the fungus Ramularia collo-cygni, is a serious, recently emerged disease of barley in Europe and other temperate regions. This study investigated the trade off between strong resistance to powdery mildew conferred by mlo mutant alleles and increased susceptibility to RLS. In field trials and seedling tests, the presence of mlo alleles increased severity of RLS. Genetic analysis of a doubled-haploid population identified one quantitative trait locus for susceptibility to RLS, colocalizing with the mlo-11 allele for mildew resistance. The effect of mlo-11 on RLS severity was environmentally sensitive. Analysis of near-isogenic lines of different mlo mutations in various genetic backgrounds confirmed that mlo alleles increased RLS severity in seedlings and adult plants. For mlo resistance to mildew to be fully effective, the genes ROR1 and ROR2 are required. RLS symptoms were significantly reduced on mlo-5 ror double mutants but fungal DNA levels remained as high as in mlo-5 single mutants, implying that ror alleles modify the transition of the fungus from endophytism to necrotrophy. These results indicate that the widespread use of mlo resistance to control mildew may have inadvertently stimulated the emergence of RLS as a major disease of barley.


Assuntos
Ascomicetos/fisiologia , Resistência à Doença/genética , Hordeum/genética , Interações Hospedeiro-Patógeno , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Alelos , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Europa (Continente) , Hordeum/imunologia , Hordeum/microbiologia , Hordeum/fisiologia , Mutação , Folhas de Planta/genética , Folhas de Planta/imunologia , Folhas de Planta/microbiologia , Folhas de Planta/fisiologia , Proteínas de Plantas/metabolismo , Locos de Características Quantitativas , Plântula/genética , Plântula/imunologia , Plântula/microbiologia , Plântula/fisiologia
15.
Ann Bot ; 112(7): 1439-47, 2013 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-24047715

RESUMO

BACKGROUND AND AIMS: Plant genotypic mixtures have the potential to increase yield stability in variable, often unpredictable environments, yet knowledge of the specific mechanisms underlying enhanced yield stability remains limited. Field studies are constrained by environmental conditions which cannot be fully controlled and thus reproduced. A suitable model system would allow reproducible experiments on processes operating within crop genetic mixtures. METHODS: Phenotypically dissimilar genotypes of Arabidopsis thaliana were grown in monocultures and mixtures under high levels of competition for abiotic resources. Seed production, flowering time and rosette size were recorded. KEY RESULTS: Mixtures achieved high yield stability across environments through compensatory interactions. Compensation was greatest when plants were under high levels of heat and nutrient stress. Competitive ability and mixture performance were predictable from above-ground phenotypic traits even though below-ground competition appeared to be more intense. CONCLUSIONS: This study indicates that the mixing ability of plant genotypes can be predicted from their phenotypes expressed in a range of relevant environments, and implies that a phenotypic screen of genotypes could improve the selection of suitable components of genotypic mixtures in agriculture intended to be resilient to environmental stress.


Assuntos
Arabidopsis/crescimento & desenvolvimento , Arabidopsis/genética , Teste de Complementação Genética , Bioensaio , Biomassa , Genótipo , Raízes de Plantas/crescimento & desenvolvimento , Característica Quantitativa Herdável , Sementes/genética , Sementes/crescimento & desenvolvimento
16.
Plant Pathol ; 72(3): 536-547, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38516179

RESUMO

Crop diseases can cause major yield losses, so the ability to detect and identify them in their early stages is important for disease control. Deep learning methods have shown promise in classifying multiple diseases; however, many studies do not use datasets that represent real field conditions, necessitating either further image processing or reducing their applicability. In this paper, we present a dataset of wheat images taken in real growth situations, including both field and glasshouse conditions, with five categories: healthy plants and four foliar diseases, yellow rust, brown rust, powdery mildew and Septoria leaf blotch. This dataset was used to train a deep learning model. The resulting model, named CerealConv, reached a 97.05% classification accuracy. When tested against trained pathologists on a subset of images from the larger dataset, the model delivered an accuracy score 2% higher than the best-performing pathologist. Image masks were used to show that the model was using the correct information to drive its classifications. These results show that deep learning networks are a viable tool for disease detection and classification in the field, and disease quantification is a logical next step.

17.
AJPM Focus ; 2(2): 100084, 2023 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-37790642

RESUMO

Introduction: Veterans are at high risk for lung cancer and are an important group for lung cancer screening. Previous research suggests that lung cancer screening may not be reaching healthier and/or non-White individuals, who stand to benefit most from lung cancer screening. We sought to test whether lung cancer screening is associated with poor health and/or race and ethnicity among veterans. Methods: This cross-sectional, population-based study included veterans eligible for lung cancer screening (aged 55-79 years, ≥30 pack-year smoking history, current smokers or quit within 15 years, no previous lung cancer) in the 2017-2020 Behavioral Risk Factor Surveillance System surveys. Exposures were (1) poor health, defined as fair/poor health status and difficulty walking or climbing stairs, aligning with eligibility criteria for a pivotal lung cancer screening trial, and (2) race/ethnicity. The outcome was a receipt of lung cancer screening. All variables were self-reported. Results: Of 3,376 lung cancer screening-eligible veterans representing an underlying population of 866,000 individuals, 20.3% (95% CI=17.3, 23.6) had poor health, and 13.7% (95% CI=10.6, 17.5) identified as non-White. Poor health was strongly associated with lung cancer screening (adjusted RR=1.64, 95% CI=1.06, 2.27); one third of veterans screened for lung cancer would not qualify for a pivotal lung cancer screening trial in terms of health. Marked racial disparities were observed among veterans: after adjustment, non-White veterans were 67% less likely to report lung cancer screening than White veterans (adjusted RR=0.33, 95% CI=0.11, 0.66). Conclusions: Lung cancer screening is correlated with poorer health and White race/ethnicity among veterans, which may undermine its population-level effectiveness. These results highlight the need to promote lung cancer screening, especially for healthier and/or non-White veterans, an important group of Americans for lung cancer screening.

18.
Chest ; 163(4): 966-976, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36368616

RESUMO

BACKGROUND: Deficiencies in risk assessment for patients with pulmonary nodules (PNs) contribute to unnecessary invasive testing and delays in diagnosis. RESEARCH QUESTION: What is the accuracy of a novel PN risk model that includes plasma proteins and clinical factors? How does the accuracy compare with that of an established risk model? STUDY DESIGN AND METHODS: Based on technology using magnetic nanosensors, assays were developed with seven plasma proteins. In a training cohort (n = 429), machine learning approaches were used to identify an optimal algorithm that subsequently was evaluated in a validation cohort (n = 489), and its performance was compared with the Mayo Clinic model. RESULTS: In the training set, we identified a support vector machine algorithm that included the seven plasma proteins and six clinical factors that demonstrated an area under the receiver operating characteristic curve of 0.87 and met other selection criteria. The resulting risk reclassification model (RRM) was used to recategorize patients with a pretest risk of between 10% and 84%, and its performance was assessed across five risk strata (low, ≤ 10%; moderate, 10%-34%; intermediate, 35%-70%; high, 71%-84%; very high, > 85%). Stratification by the RRM decreased the proportion of intermediate-risk patients from 26.7% to 10.8% (P < .001) and increased the low-risk and high-risk strata from 16.8% to 21.9% (P < .001) and from 3.7% to 12.1% (P < .001), respectively. Among patients classified as low risk by the RRM and Mayo Clinic model, the corresponding true-negative to false-negative ratios were 16.8 and 19.5, respectively. Among patients classified as very high risk by the RRM and Mayo Clinic model, the corresponding true-positive to false-positive ratios were 28.5 and 17.0, respectively. Compared with the Mayo Clinic model, the RRM provided higher specificity at the low-risk threshold and higher sensitivity at the very high-risk threshold. INTERPRETATION: The RRM accurately reclassified some patients into low-risk and very high-risk categories, suggesting the potential to improve PN risk assessment.


Assuntos
Nódulos Pulmonares Múltiplos , Humanos , Medição de Risco , Algoritmos , Instituições de Assistência Ambulatorial , Proteínas Sanguíneas
19.
Am J Prev Med ; 65(5): 901-905, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37169315

RESUMO

INTRODUCTION: Lung cancer screening can save lives through the early detection of lung cancer, and professional societies recommend key lung cancer screening program components to ensure high-quality screening. Yet, little is known about the key components that comprise the various screening program models in routine clinical settings. The objective was to compare the utilization of these key components across centralized, hybrid, and decentralized lung cancer screening programs. METHODS: The survey was designed to identify current structures and processes of lung cancer screening programs. It was administered electronically to Veterans Health Administration facilities nationally (N=122) between August and December 2021. Results were analyzed between March and August 2022 and stratified by self-identified lung cancer screening program type, and we tested the hypothesis that centralized screening programs would be more likely to have implemented practices that support lung cancer screening, followed by hybrid and decentralized programs, using the Cochran-Armitage trend test. RESULTS: Overall, 69 (56.6%) facilities completed the survey, and respondents were lung cancer screening coordinators (39.1%), pulmonologists (33.3%), and oncologists (10.1%). Facilities most frequently self-identified as having a centralized (37.7%) program model, followed by identifying as having hybrid (30.4%) and decentralized (20.3%) programs. There was varying implementation of practices to support lung cancer screening, with hybrid and decentralized programs less likely to have lung cancer screening registries, lung cancer screening steering committees, or dedicated lung cancer screening coordinators. CONCLUSIONS: Although there is overlap between the components of various lung cancer screening program types, centralized programs more frequently implemented practices before the initial screening to support lung cancer screening. This work provides a path for future investigations to identify which lung cancer screening practices are effective to improve lung cancer screening outcomes, which could help inform implementation in settings with limited resources.


Assuntos
Neoplasias Pulmonares , Humanos , Neoplasias Pulmonares/diagnóstico , Saúde dos Veteranos , Detecção Precoce de Câncer/métodos , Inquéritos e Questionários
20.
J Asthma ; 49(1): 36-44, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-22176690

RESUMO

BACKGROUND: Few studies have examined the ethnic differences in symptom reporting and airway hyperresponsiveness (AHR) for women with mild asthma during a methacholine (McH) challenge. OBJECTIVE: The purpose of this sub-analysis was to determine: (1) whether AHR to McH varied by the ethnicity of women with mild asthma and (2) whether ethnic word descriptors (EWDs) varied by the ethnicity during induced bronchoconstriction. METHODS: Specific inclusion criteria included the following: FEV(1) (forced expiratory volume in 1 second) ≥ 70% predicted normal, PC(30) ≤ 8 mg/McH, ß(2) inhaler only, and self-reported ethnicity of African American (AFAM), Mexican American-Hispanic-Latino (MexAMLat), Asian-Pacific Islander (Asian PI), or white. Serial pulmonary function testing (PFT) and Borg, visual analogue scale (VAS), and EWDs were collected. RESULTS: A total of 44 women, mean age of 31.3 years old, with a mean baseline FEV(1) of 2.85 L comprised this sub-analysis. Ethnic-racial diversity included: 12 AFAMs, 5 MexAMLat, 13 Asian-PIs, and 14 whites. All had atopy ≥ 2 pinprick responses of 3 mm. At PC(30), Asian-PI women required a significantly (p < .05) smaller mean dose of McH 1.9 mg/mL. MexAMLat women required an McH dose of 1.6 mg/mL. At PC(30), McH dose was 2.9 mg/mL for AFAMs and 3.0 mg/mL for whites, respectively. Asian-PIs who used only upper airway EWDs at PC(30) vere itchy throat, itchy chin, and constricted throat (p < .001). AFAMs significant EWDs were itchy throat, itchy chin/face, and tight throat (p < .01). Lower airway EWD was used by both MexAMLat and whites. Significant EWD for Whites were tight chest (p < .01) and hard to inhale/lungs tight (p < .001). CONCLUSION: Asian-PI women required a significantly smaller dose (p < .05) of McH to induce a PC(30). AFAM and whites required a comparable dose of Mch at PC(30). Asian-PI and AFAM women used only upper airway EWD. Asian-PI women may be at a greater risk for acute asthma episodes that are not recognized or treated due to their upper airway symptom reporting.


Assuntos
Asma/diagnóstico , Asma/etnologia , Hiper-Reatividade Brônquica/diagnóstico , Hiper-Reatividade Brônquica/etnologia , Cloreto de Metacolina , Adolescente , Adulto , Negro ou Afro-Americano/estatística & dados numéricos , Análise de Variância , Povo Asiático/estatística & dados numéricos , Asma/imunologia , Hiper-Reatividade Brônquica/imunologia , Testes de Provocação Brônquica , Broncoconstritores , Estudos de Coortes , Feminino , Volume Expiratório Forçado , Hispânico ou Latino/estatística & dados numéricos , Humanos , Pessoa de Meia-Idade , Prognóstico , Estudos Prospectivos , Medição de Risco , Índice de Gravidade de Doença , Testes Cutâneos , População Branca/estatística & dados numéricos , Adulto Jovem
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