Responding to classroom challenges : report on a blended e-Learning experiment

Articl

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean

Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for . 70 years in the United States and Canada, consisting of 20–50 entries each year at 10–20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement

An efficient miRNA knockout approach using CRISPR-Cas9 in Xenopus

In recent years CRISPR-Cas9 knockouts (KO) have become increasingly ultilised to study gene function. MicroRNAs (miRNAs) are short non-coding RNAs, 20–22 nucleotides long, which affect gene expression through post-transcriptional repression. We previously identified miRNAs-196a and −219 as implicated in the development of Xenopus neural crest (NC). The NC is a multipotent stem-cell population, specified during early neurulation. Following EMT, NC cells migrate to various points in the developing embryo where they give rise to a number of tissues including parts of the peripheral nervous system, pigment cells and craniofacial skeleton. Dysregulation of NC development results in many diseases grouped under the term neurocristopathies. As miRNAs are so small, it is difficult to design CRISPR sgRNAs that reproducibly lead to a KO. We have therefore designed a novel approach using two guide RNAs to effectively ‘drop out’ a miRNA. We have knocked out miR-196a and miR-219 and compared the results to morpholino knockdowns (KD) of the same miRNAs. Validation of efficient CRISPR miRNA KO and phenotype analysis included use of whole-mount in situ hybridization of key NC and neural plate border markers such as Pax3, Xhe2, Sox10 and Snail2, q-RT-PCR and Sanger sequencing. To show specificity we have also rescued the knockout phenotype using miRNA mimics. miRNA-219 and miR-196a KO’s both show loss of NC, altered neural plate and hatching gland phenotypes. Tadpoles show gross craniofacial and pigment phenotypes

Evaluating Visual Acuity in the American Academy of Ophthalmology IRIS® Registry

OBJECTIVE: To describe visual acuity data representation in the American Academy of Ophthalmology Intelligent Research in Sight (IRIS) Registry and present a data-cleaning strategy. DESIGN: Reliability and validity study. PARTICIPANTS: Patients with visual acuity records from 2018 in the IRIS Registry. METHODS: Visual acuity measurements and metadata were identified and characterized from 2018 IRIS Registry records. Metadata, including laterality, assessment method (distance, near, and unspecified), correction (corrected, uncorrected, and unspecified), and flags for refraction or pinhole assessment were compared between Rome (frozen April 20, 2020) and Chicago (frozen December 24, 2021) versions. We developed a data-cleaning strategy to infer patients\u27 corrected distance visual acuity in their better-seeing eye. MAIN OUTCOME MEASURES: Visual acuity data characteristics in the IRIS Registry. RESULTS: The IRIS Registry Chicago data set contains 168 920 049 visual acuity records among 23 001 531 unique patients and 49 968 974 unique patient visit dates in 2018. Visual acuity records were associated with refraction in 5.3% of cases, and with pinhole in 11.0%. Mean (standard deviation) of all measurements was 0.26 (0.41) logarithm of the minimum angle of resolution (logMAR), with a range of - 0.3 to 4.0 A plurality of visual acuity records were labeled corrected (corrected visual acuity [CVA], 39.1%), followed by unspecified (37.6%) and uncorrected (uncorrected visual acuity [UCVA], 23.4%). Corrected visual acuity measurements were paradoxically worse than same day UCVA 15% of the time. In aggregate, mean and median values were similar for CVA and unspecified visual acuity. Most visual acuity measurements were at distance (59.8%, vs. 32.1% unspecified and 8.2% near). Rome contained more duplicate visual acuity records than Chicago (10.8% vs. 1.4%). Near visual acuity was classified with Jaeger notation and (in Chicago only) also assigned logMAR values by Verana Health. LogMAR values for hand motion and light perception visual acuity were lower in Chicago than in Rome. The impact of data entry errors or outliers on analyses may be reduced by filtering and averaging visual acuity per eye over time. CONCLUSIONS: The IRIS Registry includes similar visual acuity metadata in Rome and Chicago. Although fewer duplicate records were found in Chicago, both versions include duplicate and atypical measurements (i.e., CVA worse than UCVA on the same day). Analyses may benefit from using algorithms to filter outliers and average visual acuity measurements over time. FINANCIAL DISCLOSURES: Proprietary or commercial disclosure may be found found in the Footnotes and Disclosures at the end of this article

Interactions among mitochondrial proteins altered in glioblastoma

Mitochondrial dysfunction is putatively central to glioblastoma (GBM) pathophysiology but there has been no systematic analysis in GBM of the proteins which are integral to mitochondrial function. Alterations in proteins in mitochondrial enriched fractions from patients with GBM were defined with label-free liquid chromatography mass spectrometry. 256 mitochondrially-associated proteins were identified in mitochondrial enriched fractions and 117 of these mitochondrial proteins were markedly (fold-change ≥2) and significantly altered in GBM (p ≤ 0.05). Proteins associated with oxidative damage (including catalase, superoxide dismutase 2, peroxiredoxin 1 and peroxiredoxin 4) were increased in GBM. Protein–protein interaction analysis highlighted a reduction in multiple proteins coupled to energy metabolism (in particular respiratory chain proteins, including 23 complex-I proteins). Qualitative ultrastructural analysis in GBM with electron microscopy showed a notably higher prevalence of mitochondria with cristolysis in GBM. This study highlights the complex mitochondrial proteomic adjustments which occur in GBM pathophysiology

Risk Assessment of Food Allergens. Part 1: Review and Validation of Codex Alimetarius Priority Allergen list Through Risk Assessment

The labelling of food allergens in pre-packaged foods plays a key role in protecting food allergic individuals, as no preventative clinical treatment is currently available. The list of major foods and ingredients known to cause hypersensitivity was included into the Codex General Standard for the Labelling of Packaged Foods (GSLPF) in 1999. There have been many scientific developments in the understanding of food allergens and their management since the original drafting of the GSLPF. Thus, in response to the request from Codex for scientific advice, including current evidence of consumer understanding of allergens, FAO and WHO convened a series of three expert meetings to provide scientific advice on this subject. The purpose of the first meeting of the Ad hoc Joint FAO/WHO Expert Consultation on Risk Assessment of Food Allergens was to review and validate the Codex priority allergen list through risk assessment. This report focuses on the deliberations and conclusions of this meeting. Resumen: El etiquetado de los alérgenos alimentarios en los alimentos preenvasados ​​juega un papel clave en la protección personas alérgicas a los alimentos, ya que actualmente no se dispone de un tratamiento clínico preventivo. Se incluyó la lista de los principales alimentos e ingredientes que causan hipersensibilidad en la Norma General del Codex para el Etiquetado de Alimentos Envasados ​​(GSLPF) en 1999. Ha habido muchos avances científicos en la comprensión de alérgenos alimentarios y su gestión desde la redacción original de la GSLPF. Por lo tanto, en respuesta a la solicitud del Codex de asesoramiento científico, incluida la actual evidencia de la comprensión del consumidor de los alérgenos, la FAO y la OMS convocaron una serie de tres reuniones de expertos para proporcionar asesoramiento científico sobre este tema. El propósito de la primera reunión de la Consulta Conjunta Especial de Expertos FAO/OMS sobre evaluación de riesgos de los alérgenos alimentarios fue revisar y validar la prioridad del Codex lista de alérgenos a través de la evaluación de riesgos. Este informe se centra en las deliberaciones y conclusiones de esta reunión.Instituto de Investigación de Tecnología de Alimentos (ITA)Fil: Baumert, Joseph. Universidad de Nebraska-Lincoln. Departamento de Ciencia y Tecnología de Alimentos; Estados UnidosFil: Brooke-Taylor, Simon. Imperial College London. Instituto Nacional del Corazón y los Pulmones; Reino Unido.Fil: Che, Huilian. Universidad de Agricultura de China. Facultad de Ciencias de la Alimentación e Ingeniería Nutricional; China.Fil: Chen, Hongbing. Nanchang Universidad. Instituto Conjunto de Investigación Chino-Alemán; China.Fil: Crevel, René W.R. René Crevel Consulting Limited; Reino Unido.Fil: Houben, Geert F. Alergia alimentaria e inmunotoxicología. Científico principal de TNO; Países Bajos.Fil: Jackson, Lauren. Administración de Alimentos y Medicamentos. División de Ciencia y Tecnología del Procesamiento de Alimentos. Ingeniería de Procesos; Estados UnidosFil: Kyriakidis, Symeon. Autoridad Independiente de Ingresos Públicos. Laboratorio Estatal de Química General; Grecia.Fil: La Vieille, Sébastien. Salud Canadá. Dirección de Alimentos; Canadá.Fil: Lee, N Alice. Universidad de Nueva Gales del Sur. Escuela de Química e Ingeniería. Ciencia e ingeniería de los alimentos; Australia.Fil: López, María Cristina. Universidad Nacional de San Martín. Ingeniería de Alimentos; Argentina.Fil: Luccioli, Stefano. Administración de Alimentos y Medicamentos. Centro de Seguridad Alimentaria y Nutrición Aplicada; Estados UnidosFil: O’Mahony, Patrick. Autoridad de Seguridad Alimentaria de Irlanda . Ciencia y Tecnología de los Alimentos; Irlanda.Fil: Polenta, Gustavo Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Investigación Tecnología de Alimentos; Argentina.Fil: Pöpping, Bert. Food Consulting Strategically (FOCO); Alemania.Fil: Remington, Benjamin C. Grupo BV. Consultoría Remington; Holanda.Fil: Södergren, Eva. Agencia Sueca de Alimentos. Equipo de Encuestas Dietéticas y Departamento de Nutrición para Beneficio de Riesgo Evaluación; Suecia.Fil: Srikulnath, Sirinrat. Universidad de Kasetsart (UKaset). Instituto de Investigación y Desarrollo de Productos Alimentarios. Centro de Servicio de Aseguramiento de la Calidad de los Alimentos. Unidad de Alérgenos Alimentarios; Tailandia.Fil: Taylor, Stephen L. Universidad de Nebraska-Lincoln. Departamento de Ciencia y Tecnología de Alimentos; Estados UnidosFil: Turner, Paul J. Colegio Imperial de Ciencia, Tecnología y Medicina. Alergia e Inmunología Pediátricas; Inglaterra