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1.
Environ Microbiol ; 26(3): e16616, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38517638

RESUMEN

Nitrification is an important control on the form and distribution of nitrogen in freshwater ecosystems. However, the seasonality of nitrogen pools and the diversity of organisms catalyzing this process have not been well documented in oligotrophic lakes. Here, we show that nitrogen pools and nitrifying organisms in Flathead Lake are temporally and vertically dynamic, with nitrifiers displaying specific preferences depending on the season. While the ammonia-oxidizing bacteria (AOB) Nitrosomonadaceae and nitrite-oxidizing bacteria (NOB) Nitrotoga dominate at depth in the summer, the ammonia-oxidizing archaea (AOA) Nitrososphaerota and NOB Nitrospirota become abundant in the winter. Given clear seasonality in ammonium, with higher concentrations during the summer, we hypothesize that the succession between these two nitrifying groups may be due to nitrogen affinity, with AOB more competitive when ammonia concentrations are higher and AOA when they are lower. Nitrifiers in Flathead Lake share more than 99% average nucleotide identity with those reported in other North American lakes but are distinct from those in Europe and Asia, indicating a role for geographic isolation as a factor controlling speciation among nitrifiers. Our study shows there are seasonal shifts in nitrogen pools and nitrifying populations, highlighting the dynamic spatial and temporal nature of nitrogen cycling in freshwater ecosystems.


Asunto(s)
Lagos , Nitrosomonadaceae , Lagos/microbiología , Estaciones del Año , Ecosistema , Amoníaco , Oxidación-Reducción , Archaea/genética , Nitrificación , Nitritos , Nitrógeno , Dinámica Poblacional , Filogenia
2.
Appl Environ Microbiol ; 89(12): e0109723, 2023 12 21.
Artículo en Inglés | MEDLINE | ID: mdl-38032216

RESUMEN

IMPORTANCE: Methane is an important greenhouse gas that is typically produced under anoxic conditions. We show that methane is supersaturated in a large oligotrophic lake despite the presence of oxygen. Metagenomic sequencing indicates that diverse, widespread microorganisms may contribute to the oxic production of methane through the cleavage of methylphosphonate. We experimentally demonstrate that these organisms, especially members of the genus Acidovorax, can produce methane through this process. However, appreciable rates of methane production only occurred when both methylphosphonate and labile sources of carbon were added, indicating that this process may be limited to specific niches and may not be completely responsible for methane concentrations in Flathead Lake. This work adds to our understanding of methane dynamics by describing the organisms and the rates at which they can produce methane through an oxic pathway in a representative oligotrophic lake.


Asunto(s)
Carbono , Lagos , Compuestos Organofosforados/metabolismo , Metano/metabolismo
3.
Neurogastroenterol Motil ; 35(8): e14584, 2023 08.
Artículo en Inglés | MEDLINE | ID: mdl-36989182

RESUMEN

BACKGROUND: This study seeks to evaluate eating competence and disordered eating likelihood among members of online support groups for irritable bowel syndrome (IBS) and determine whether eating competence and disordered eating likelihood varies according to IBS symptom severity and subtype. METHODS: This cross-sectional study is based on an anonymous survey conducted from August to September 2021. Adults with IBS (N = 225) were recruited from online and social media IBS support forums. IBS symptom severity was assessed using the validated IBS Severity Scoring System (IBS-SSS), likelihood of disordered eating was assessed using the validated Eating Attitudes Test (EAT-26), and eating competence was assessed using the validated Satter Eating Competence Inventory (ecSI 2.0™). Multiple linear regression was used to predict EAT-26 total score from IBS-SSS score, age, and IBS subtype. ANOVAs were used to examine the relationships between IBS severity level, IBS subtype, and ecSI 2.0™ total score. KEY RESULTS: Eating competence among the sample was low at 17% while 27% was classified as likely or very likely disordered eating. IBS severity was positively associated with EAT-26 score (p = 0.011) and ecSI 2.0™ score was significantly lower in the severe IBS group compared to the moderate IBS group (p = 0.016). No relationship was detected between IBS subtype and EAT-26 or ecSI 2.0™ scores. CONCLUSIONS & INFERENCES: IBS severity was positively associated with disordered eating likelihood and negatively associated with eating competence. This sheds light on the importance of assessing eating competence and screening for disordered eating prior to selecting therapies for patients with IBS, particularly in females with severe symptoms.


Asunto(s)
Trastornos de Alimentación y de la Ingestión de Alimentos , Síndrome del Colon Irritable , Adulto , Femenino , Humanos , Síndrome del Colon Irritable/diagnóstico , Estudios Transversales , Análisis Multivariante , Grupos de Autoayuda , Encuestas y Cuestionarios , Índice de Severidad de la Enfermedad
4.
J Racial Ethn Health Disparities ; 10(2): 761-774, 2023 04.
Artículo en Inglés | MEDLINE | ID: mdl-35175583

RESUMEN

Previous research has demonstrated that undocumented Latinx immigrants in the USA report worse physical health outcomes than documented immigrants. Some studies suggest that immigration-related stress and healthcare related-stress may explain this relationship, but none have tested it empirically. The purpose of this study was to determine if immigration-related stress and healthcare-related stress in the USA explain the relationship between documentation status and physical health among Latinx immigrants in North Carolina. The conceptual model was tested utilizing baseline data from a longitudinal, observational, community-engaged research study of young adult (18-44 years) Latinx immigrants residing in North Carolina (N = 391). Structural equation modeling was used to determine relationships among documentation status, healthcare, and immigration stress in the past six months, and self-rated physical health. Goodness-of-fit measures indicated that data fit the model well (RMSEA = .008; CFI = 1.0; TLI = .999; SRMR = .02; CD = .157). Undocumented individuals were more likely to experience immigration stress than their documented counterparts ([Formula: see text] = - 0.37, p < 0.001). Both immigration stress ([Formula: see text] = - 0.22, p < 0.01) and healthcare stress ([Formula: see text] = - 0.14, p < 0.05) were negatively related to physical health. Additionally, immigration stress was positively related to healthcare stress ([Formula: see text] = 0.72, p < 0.001). Results demonstrate that documentation status is an important social determinant of health. Passage of inclusive immigration and healthcare policies may lessen the stress experienced by Latinx immigrants and subsequently improve physical health.


Asunto(s)
Emigrantes e Inmigrantes , Emigración e Inmigración , Estado de Salud , Hispánicos o Latinos , Humanos , Adulto Joven , Documentación , Accesibilidad a los Servicios de Salud , Adolescente , Adulto , North Carolina
5.
BMC Pregnancy Childbirth ; 22(1): 149, 2022 Feb 22.
Artículo en Inglés | MEDLINE | ID: mdl-35193505

RESUMEN

BACKGROUND: Previous research is inconclusive on the effects of mode of delivery on maternal health-related quality-of-life (HRQoL). We conducted a systematic review and meta-analysis to assess the current evidence for associations between mode of delivery and postpartum health-related quality-of-life. METHODS: Electronic databases MEDLINE ALL (OVID), Web of Science, The Cochrane Library, CINAHL and EMBASE (OVID) were searched for English written articles investigating the relationship between mode of delivery and quality-of-life published form inception to 15th October 2020. Two reviewers independently screened titles and abstracts, assessed full texts, and extracted data. Meta-analysis was conducted where possible. RESULTS: Twenty-one studies, including 19,879 women, met the inclusion criteria. A meta-analysis of 18 studies found HRQoL scores were significantly higher for women after vaginal delivery in comparison to caesarean (emergency and elective combined) (Effect Size (ES) 0.17, 95% CI 0.01-0.25, n = 7665) with highest scores after assisted vaginal delivery (ES 0.21, 95% CI 0.13-0.30, n = 2547). Physical functioning (ES 11.18, 95% CI = 2.29-20.06, n = 1746), physical role (ES 13.10, 95% CI = 1.16-25.05, n = 1471), vitality (ES 6.31, 95% CI = 1.14-10.29, n = 1746) and social functioning (ES 5.69, 95% CI = 1.26-10.11, n = 1746) were significantly higher after vaginal delivery compared to caesarean. CONCLUSIONS: Health-related quality-of-life scores were higher for women after vaginal delivery in comparison to caesarean section. Consequently, women should be encouraged to deliver vaginally where possible. The findings of this research should be available to the relevant population to help support informed choice.


Asunto(s)
Parto Obstétrico/métodos , Parto/psicología , Periodo Posparto/psicología , Calidad de Vida , Adolescente , Adulto , Femenino , Humanos , Persona de Mediana Edad , Adulto Joven
6.
Clin Otolaryngol ; 47(1): 44-51, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34323008

RESUMEN

OBJECTIVES: To report the experience of civilian penetrating neck trauma (PNT) at a UK level I trauma centre, propose an initial management algorithm and assess the degree of correlation between clinical signs of injury, operative findings and radiological reports. DESIGN: Retrospective case note review. SETTING: UK level I trauma centre April 2012-November 2017. PARTICIPANTS: Three hundred ten cases of PNT were drawn from electronic patient records. Data were extracted on hard and soft signs of vascular or aerodigestive tract injury, clinical management, radiological imaging and patient outcomes. MAIN OUTCOME MEASURES: Patient demographics, mechanism of injury, morbidity and mortality. The correlation between clinical signs, and radiological reports to internal injury on surgical exploration. RESULTS: Two hundred seventy-one (87.4%) male and 39 (13.6%) female patients with a mean age of 36 years (16-87) were identified. The most common causes of injury were assault 171 (55.2%) and deliberate self-harm 118 (38%). A knife was the most common instrument 240 (77.4%). Past psychiatric history was noted in 119 (38.4%), and 60 (19.4%) were intoxicated. 50% were definitively managed in theatre with a negative exploration rate of 38%, and 50% were managed in ED. Pre-operative radiological reports correlated with operative reports in 62% of cases with venous injury the most common positive and negative finding. Multivariate correlation was r = 0.89, p = 0.045, between hard signs plus positive radiology findings and internal injury on neck exploration. CONCLUSIONS: Management of PNT by clinical and radiological signs is safe and effective, and can be streamlined by a decision-making algorithm as proposed here.


Asunto(s)
Traumatismos del Cuello/diagnóstico por imagen , Traumatismos del Cuello/cirugía , Centros Traumatológicos , Heridas Penetrantes/diagnóstico por imagen , Heridas Penetrantes/cirugía , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Algoritmos , Femenino , Humanos , Masculino , Persona de Mediana Edad , Traumatismos del Cuello/mortalidad , Estudios Retrospectivos , Tomografía Computarizada por Rayos X , Reino Unido , Heridas Penetrantes/mortalidad , Adulto Joven
7.
Front Plant Sci ; 12: 714325, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34733298

RESUMEN

Washington State University's apple breeding program (WABP) was initiated in 1994 to select new apple cultivars with improved eating quality, appearance, and storability that are suitable for production in the main growing regions of the state. Fruit quality is phenotyped using various instrumental measures, such as penetrometers (texture), titrator (acidity), and refractometer (soluble solids concentration; SSC), as well as sensory assessment. The selection regime of WABP occurs in three sequential phases: phase one (P1)-single, unreplicated seedlings at one site, phase two (P2)-replicated selections at three geographically diverse sites, and phase three (P3)-highly replicated elite selections at one to two grower sites. Most of the data collection of WABP occurs in P2. Knowledge of trends/changes associated with advancing selections is essential for understanding the selection criteria and progress of WABP throughout the changing compositions of advancing and culling selections. For each post-harvest trait, P2 data from harvest years 2005 to 2019 were split across sites, and between selections and reference cultivars (e.g., Cripps Pink, Gala, and Honeycrisp). Means of instrumental crispness (Cn) and inner cortex firmness for the advancing selections increased gradually over this period and were significantly higher than those for cultivars. Means of outer cortex firmness measurements were stable for selections but significantly higher than those for cultivars. The average fruit acidity of selections increased marginally over this period and was higher than that of the cultivars. Meanwhile, the average fruit SSCs of selections and cultivars were statistically indistinguishable. These 15-year trends indicate that WABP has been selecting apples with improved eating quality and storability through increased crispness and inner cortex firmness, respectively.

9.
Appl Environ Microbiol ; 87(15): e0046921, 2021 07 13.
Artículo en Inglés | MEDLINE | ID: mdl-34020938

RESUMEN

Apple powdery mildew (APM), caused by Podosphaera leucotricha, is a constant threat to apple production worldwide. Very little is known about the biology and population structure of this pathogen in the United States and other growing regions, which affects APM management. A total of 253 P. leucotricha isolates, sampled from 10 apple orchards in Washington, New York, and Virginia, were genetically characterized with novel single sequence repeat and mating type markers. Eighty-three multilocus genotypes (MLGs) were identified, most of which were unique to a given orchard. Each isolate carried either a MAT1-1 or a MAT1-2 idiomorph at the mating type locus, indicating that P. leucotricha is heterothallic. Virulence tests on detached apple leaves showed that the 10 most frequent P. leucotricha MLGs were avirulent on a line containing a major resistance gene. Analysis of molecular variance showed significant differentiation (P < 0.001) among populations, a result supported by principal coordinate analysis revealing three genetic groups, each represented by nonoverlapping MLGs from Washington, New York, and Virginia. A Bayesian cluster analysis showed genetic heterogeneity between Washington populations, and a relative migration analysis indicated substantial gene flow among neighboring orchards. Random mating tests indicated that APM epidemics during the active cycle were dominated by clonal reproduction. However, the presence of sexual structures in orchards, the likelihood that five repeated MLGs resulted from sexual reproduction, and high genotypic diversity observed in some populations suggest that sexual spores play some role in APM epidemics. IMPORTANCE Understanding the population biology and epidemiology of plant pathogens is essential to develop effective strategies for controlling plant diseases. Herein, we gathered insights into the population biology of P. leucotricha populations from conventional and organic apple orchards in the United States. We showed genetic heterogeneity between P. leucotricha populations in Washington and structure between populations from different U.S. regions, suggesting that short-distance spore dispersal plays an important role in the disease's epidemiology. We presented evidence that P. leucotricha is heterothallic and that populations likely result from a mixed (i.e., sexual and asexual) reproductive system, revealing that the sexual stage contributes to apple powdery mildew epidemics. We showed that the major resistance gene Pl-1 is valuable for apple breeding because virulent isolates have most likely not emerged yet in U.S. commercial orchards. These results will be important to achieve sustainability of disease management strategies and maintenance of plant health in apple orchards.


Asunto(s)
Ascomicetos/genética , Malus/microbiología , Enfermedades de las Plantas/microbiología , Ascomicetos/patogenicidad , ADN de Hongos/análisis , Variación Genética , Genotipo , New York , Virginia , Virulencia , Washingtón
10.
Plants (Basel) ; 10(2)2021 Feb 22.
Artículo en Inglés | MEDLINE | ID: mdl-33671812

RESUMEN

Breeding apple cultivars with durable genetic resistance is a potential long-term solution to fire blight, a devastating bacterial disease caused by Erwinia amylovora. However, phenotyping resistance/susceptibility to fire blight is challenging due to E. amylovora strain virulence, differential host × strain interactions, quantitative host resistance, environmental influences on disease, and impacts of tree vigor on susceptibility. Inheritance of resistance/susceptibility to fire blight is complex and phenotypic information alone is insufficient to guide breeding decisions targeting resistance. Several quantitative trait loci (QTLs) associated with resistance/susceptibility to fire blight have been detected throughout the apple genome. Most resistance alleles at fire blight QTLs have been identified in wild Malus germplasm with poor fruit quality, which limits their breeding utility. Several QTLs have been identified in populations derived from cultivars and reduced-susceptibility alleles have been characterized in multiple important breeding parents. Although resistance to fire blight is an attractive target for DNA-informed breeding, relatively few trait-predictive DNA tests for breeding relevant fire blight QTLs are available. Here we discuss (1) considerations and challenges associated with phenotyping resistance/susceptibility to fire blight; (2) sources of resistance that have been identified for use as parents; and (3) our perspective on short and long-term strategies to breed apple cultivars with durable resistance to fire blight with emphasis on the potential contributions of reduced susceptibility alleles to achieve this goal.

11.
Hortic Res ; 8(1): 28, 2021 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-33518709

RESUMEN

Breeding apple cultivars with resistance offers a potential solution to fire blight, a damaging bacterial disease caused by Erwinia amylovora. Most resistance alleles at quantitative trait loci (QTLs) were previously characterized in diverse Malus germplasm with poor fruit quality, which reduces breeding utility. This study utilized a pedigree-based QTL analysis approach to elucidate the genetic basis of resistance/susceptibility to fire blight from multiple genetic sources in germplasm relevant to U.S. apple breeding programs. Twenty-seven important breeding parents (IBPs) were represented by 314 offspring from 32 full-sib families, with 'Honeycrisp' being the most highly represented IBP. Analyzing resistance/susceptibility data from a two-year replicated field inoculation study and previously curated genome-wide single nucleotide polymorphism data, QTLs were consistently mapped on chromosomes (Chrs.) 6, 7, and 15. These QTLs together explained ~28% of phenotypic variation. The Chr. 6 and Chr. 15 QTLs colocalized with previously reported QTLs, while the Chr. 7 QTL is possibly novel. 'Honeycrisp' inherited a rare reduced-susceptibility allele at the Chr. 6 QTL from its grandparent 'Frostbite'. The highly resistant IBP 'Enterprise' had at least one putative reduced-susceptibility allele at all three QTLs. In general, lower susceptibility was observed for individuals with higher numbers of reduced-susceptibility alleles across QTLs. This study highlighted QTL mapping and allele characterization of resistance/susceptibility to fire blight in complex pedigree-connected apple breeding germplasm. Knowledge gained will enable more informed parental selection and development of trait-predictive DNA tests for pyramiding favorable alleles and selection of superior apple cultivars with resistance to fire blight.

12.
Surgeon ; 19(5): e276-e280, 2021 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-33558142

RESUMEN

The impact on the provision of care within the NHS due to COVID-19 can not be understated. It has created various challenges for Oral and Maxillofacial Surgeons due to the high-risk nature of working within this specialty. The aims of this study were to identify the ongoing clinical activities at the height of pandemic, the guidance issued to staff regarding the use of personal protective equipment and the changes to maxillofacial practice. A prospective analysis was commenced within six Oral and Maxillofacial Surgery units in the East Midlands, UK with data being collected by means of a 10-item questionnaire relating to changes in patient care during this time. The responses were analysed to identify compliance with the national guidance produced by the British Association of Oral and Maxillofacial Surgeons. An 87% response rate was obtained (26 respondents from 30 invitations). 73.1% of participants confirmed all surgical members of staff were offered fit tests for FFP3 masks. All units reported a continuation of Head and Neck cancer and emergency operations with a complete reduction in TMJ and orthognathic surgery. FFP3 masks were the most popular masks used for theatre activity whilst FFP2 and surgical masks were more widely used for examining patients and performing procedures in the emergency department. Changes in maxillofacial practice included the use of local flaps compared to free flaps, use of intermaxillary fixation (IMF) where appropriate for craniofacial trauma and routine COVID-19 testing for all inpatients.


Asunto(s)
COVID-19/epidemiología , Control de Infecciones/organización & administración , Procedimientos Quirúrgicos Orales/estadística & datos numéricos , Pautas de la Práctica en Medicina/estadística & datos numéricos , Cirugía Bucal/organización & administración , COVID-19/prevención & control , COVID-19/transmisión , Humanos , Equipo de Protección Personal , Encuestas y Cuestionarios , Reino Unido
13.
Mol Breed ; 41(9): 57, 2021 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-37309399

RESUMEN

The 'Honeycrisp' apple, an economically important cultivar and breeding parent, is prone to soft scald and soggy breakdown postharvest physiological disorders. Phenotypic evaluation of soft scald is time consuming and costly, making it an excellent target for DNA-informed breeding. The objective of this study was to develop a DNA test for a soft scald and soggy breakdown quantitative trait locus (QTL) on linkage group two (LG2) that was characterized in a previous study. 'Honeycrisp' is homozygous for the undesirable high disorder incidence haplotype (HDI) at this QTL. In this study, sixteen single nucleotide polymorphism markers were evaluated for their associations with the HDI haplotype in a set of 132 unique cultivars and important breeding parents. A DNA test was successfully developed utilizing KASP™ (Kompetitive Allele Specific PCR) chemistry to identify the number of HDI haplotypes in individuals. This test had a 100% accuracy for detecting homozygous unfavorable HDI individuals and has an expected 88% accuracy over all three haplotype copy groups across the evaluated germplasm. This DNA test is a promising tool for minimizing the chances of selecting individuals that exhibit high incidence of soft scald postharvest disorder in 'Honeycrisp'-related germplasm. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01245-w.

15.
Clin Med (Lond) ; 19(5): 396-398, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31530688

RESUMEN

Diabetic ketoacidosis (DKA) is not a rare presentation to hospital, despite being an entirely preventable condition. A concerning number of people also develop DKA while already in hospital. Management of DKA has changed in the last decade, and national guidelines introduced, to help standardise care, spread best practice, and reduce mortality and morbidity.


Asunto(s)
Cetoacidosis Diabética , Diabetes Mellitus Tipo 1/complicaciones , Cetoacidosis Diabética/diagnóstico , Cetoacidosis Diabética/etiología , Cetoacidosis Diabética/prevención & control , Cetoacidosis Diabética/terapia , Humanos , Guías de Práctica Clínica como Asunto
16.
FEBS J ; 286(21): 4261-4277, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31243889

RESUMEN

Bacteriophytochrome proteins (BphPs) are molecular light switches that enable organisms to adapt to changing light conditions through the control of gene expression. Canonical type 1 BphPs have histidine kinase output domains, but type 3 RpBphP1, in the bacterium Rhodopseudomonas palustris (Rps. palustris), has a C terminal PAS9 domain and a two-helix output sensor (HOS) domain. Type 1 BphPs form head-to-head parallel dimers; however, the crystal structure of RpBphP1ΔHOS, which does not contain the HOS domain, revealed pseudo anti-parallel dimers. HOS domains are homologs of Dhp dimerization domains in type 1 BphPs. We show, by applying the small angle X-ray scattering (SAXS) technique on full-length RpBphP1, that HOS domains fulfill a similar role in the formation of parallel dimers. On illumination with far-red light, RpBphP1 forms a complex with gene repressor RpPpsR2 through light-induced structural changes in its HOS domains. An RpBphP1:RpPpsR2 complex is formed in the molecular ratio of 2 : 1 such that one RpBphP1 dimer binds one RpPpsR2 monomer. Molecular dimers have been modeled with Pfr and Pr SAXS data, suggesting that, in the Pfr state, stable dimeric four α-helix bundles are formed between HOS domains, rendering RpBphP1functionally inert. On illumination with light of 760 nm wavelength, four α-helix bundles formed by HOS dimers are disrupted, rendering helices available for binding with RpPpsR2.


Asunto(s)
Proteínas Bacterianas/química , Fitocromo/química , Rhodopseudomonas/genética , Proteínas Bacterianas/genética , Cristalografía por Rayos X , Dimerización , Regulación Bacteriana de la Expresión Génica/genética , Luz , Fitocromo/genética , Fitocromo/efectos de la radiación , Rhodopseudomonas/efectos de la radiación , Dispersión del Ángulo Pequeño , Difracción de Rayos X
17.
BMC Genomics ; 20(1): 331, 2019 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-31046664

RESUMEN

BACKGROUND: Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behind other fruit and nut crops in terms of employment of available genetic resources for new cultivar development. To address this gap, we designed a high-density, high-efficiency and robust single nucleotide polymorphism (SNP) array for pear, with the main objectives of conducting genetic diversity and genome-wide association studies. RESULTS: By applying a two-step design process, which consisted of the construction of a first 'draft' array for the screening of a small subset of samples, we were able to identify the most robust and informative SNPs to include in the Applied Biosystems™ Axiom™ Pear 70 K Genotyping Array, currently the densest SNP array for pear. Preliminary evaluation of this 70 K array in 1416 diverse pear accessions from the USDA National Clonal Germplasm Repository (NCGR) in Corvallis, OR identified 66,616 SNPs (93% of all the tiled SNPs) as high quality and polymorphic (PolyHighResolution). We further used the Axiom Pear 70 K Genotyping Array to construct high-density linkage maps in a bi-parental population, and to make a direct comparison with available genotyping-by-sequencing (GBS) data, which suggested that the SNP array is a more robust method of screening for SNPs than restriction enzyme reduced representation sequence-based genotyping. CONCLUSIONS: The Axiom Pear 70 K Genotyping Array, with its high efficiency in a widely diverse panel of Pyrus species and cultivars, represents a valuable resource for a multitude of molecular studies in pear. The characterization of the USDA-NCGR collection with this array will provide important information for pear geneticists and breeders, as well as for the optimization of conservation strategies for Pyrus.


Asunto(s)
Mapeo Cromosómico/métodos , Ligamiento Genético , Marcadores Genéticos , Genoma de Planta , Polimorfismo de Nucleótido Simple , Pyrus/genética , Semillas/genética , Cromosomas de las Plantas , Estudio de Asociación del Genoma Completo , Técnicas de Genotipaje
18.
Front Plant Sci ; 10: 576, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31134116

RESUMEN

Washington State produces about 70% of total fresh market apples in the United States. One of the primary goals of apple breeding programs is the development of new cultivars resistant to devastating diseases such as fire blight. The overall objective of this study was to investigate high-throughput phenotyping techniques to evaluate fire blight disease symptoms in apple trees. In this regard, normalized stomatal conductance data acquired using a portable photosynthetic system, image data collected using RGB and multispectral cameras, and visible-near infrared spectral reflectance acquired using a hyperspectral sensing system, were independently evaluated to estimate the progression of fire blight infection in young apple trees. Sensors with ranging complexity - from simple RGB to multispectral imaging to hyperspectral system - were evaluated to select the most accurate technique for the assessment of fire blight disease symptoms. The proximal multispectral images and visible-near infrared spectral reflectance data were collected in two field seasons (2016, 2017); while, proximal side-view RGB images and multispectral images using unmanned aerial systems were collected in 2017. The normalized stomatal conductance data was correlated with disease severity rating (r = 0.51, P < 0.05). The features extracted from RGB images (e.g., maximum length of senesced leaves, area of senesced leaves, ratio between senesced and healthy leaf area) and multispectral images (e.g., vegetation indices) also demonstrated potential in evaluation of disease rating (|r| > 0.35, P < 0.05). The average classification accuracy achieved using visible-near infrared spectral reflectance data during the classification of susceptible from symptomless groups ranged between 71 and 93% using partial least square regression and quadratic support vector machine. In addition, fire blight disease ratings were compared with normalized difference spectral indices (NDSIs) that were generated from visible-near infrared reflectance spectra. The selected spectral bands in the range 710-2,340 nm used for computing NDSIs showed consistently higher correlation with disease severity rating than data acquired from RGB and multispectral imaging sensors across multiple seasons. In summary, these specific spectral bands can be used for evaluating fire blight disease severity in apple breeding programs and potentially as early fire blight disease detection tool to assist in production systems.

19.
Nucleic Acids Res ; 47(D1): D1137-D1145, 2019 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-30357347

RESUMEN

The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology. Annotated and searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well as EST datasets, are newly available for major crop species. Significantly more quantitative trait loci, genetic maps and markers are available in MapViewer, a new visualization tool that better integrates with other pages in GDR. Pathways can be accessed through the new GDR Cyc Pathways databases, and synteny among the newest genome assemblies from eight species can be viewed through the new synteny browser, SynView. Collated single-nucleotide polymorphism diversity data and phenotypic data from publicly available breeding datasets are integrated with other relevant data. Also, the new Breeding Information Management System allows breeders to upload, manage and analyze their private breeding data within the secure GDR server with an option to release data publicly.


Asunto(s)
Biología Computacional/métodos , Bases de Datos Genéticas , Genoma de Planta/genética , Genómica/métodos , Rosaceae/genética , Biología Computacional/estadística & datos numéricos , Perfilación de la Expresión Génica/métodos , Genes de Plantas/genética , Almacenamiento y Recuperación de la Información/métodos , Internet , Fitomejoramiento/métodos , Sitios de Carácter Cuantitativo/genética , Rosaceae/clasificación , Especificidad de la Especie , Sintenía , Factores de Tiempo , Interfaz Usuario-Computador
20.
J Appl Ecol ; 55(4): 1976-1986, 2018 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-30008482

RESUMEN

Transmission of parasites between host species affects host population dynamics, interspecific competition, and ecosystem structure and function. In areas where wild and domestic herbivores share grazing land, management of parasites in livestock may affect or be affected by sympatric wildlife due to cross-species transmission.We develop a novel method for simulating transmission potential based on both biotic and abiotic factors in a semi-arid system in Botswana. Optimal timing of antiparasitic treatment in livestock is then compared under a variety of alternative host scenarios, including seasonally migrating wild hosts.In this region, rainfall is the primary driver of seasonality of transmission, but wildlife migration leads to spatial differences in the effectiveness of treatment in domestic animals. Additionally, competent migratory wildlife hosts move parasites across the landscape.Simulated transmission potential matches observed patterns of clinical disease in livestock in the study area. Increased wildlife contact is correlated with a decrease in disease, suggesting that non-competent wild hosts may attenuate transmission by removing infective parasite larvae from livestock pasture.Optimising the timing of treatment according to within-year rainfall patterns was considerably more effective than treating at a standard time of year. By targeting treatment in this way, efficient control can be achieved, mitigating parasite spillover from wildlife where it does occur. Synthesis and applications. This model of parasite transmission potential enables evidence-based management of parasite spillover between wild and domestic species in a spatio-temporally dynamic system. It can be applied in other mixed-use systems to mitigate parasite transmission under altered climate scenarios or changes in host ranges.

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