CRISPR-Cas9 Multiplex Editing of the α-Amylase/Trypsin Inhibitor Genes to Reduce Allergen Proteins in Durum Wheat

Wheat and its derived foods are widespread, representing one of the main food sources globally. During the last decades, the incidence of disorders related to wheat has become a global issue for the human population, probably linked to the spread of wheat-derived foods. It has been ascertained that structural and metabolic proteins, like \u3b1-amylase/trypsin inhibitors (ATI), are involved in the onset of wheat allergies (bakers' asthma) and probably Non-Coeliac Wheat Sensitivity (NCWS). The ATI are a group of exogenous protease inhibitors, which are encoded by a multigene family dispersed over several chromosomes in durum and bread wheat. WTAI-CM3 and WTAI-CM16 subunits are considered among the main proteins involved in the onset of bakers' asthma and probably NCWS. A CRISPR-Cas9 multiplexing strategy was used to edit the ATI subunits WTAI-CM3 and WTAI-CM16 in the grain of the Italian durum wheat cultivar Svevo with the aim to produce wheat lines with reduced amount of potential allergens involved in adverse reactions. Using a marker gene-free approach, whereby plants are regenerated without selection agents, homozygous mutant plants without the presence of CRISPR vectors were obtained directly from T0 generation. This study demonstrates the capability of CRISPR technology to knock out immunogenic proteins in a reduced time compared to conventional breeding programmes. The editing of the two target genes was confirmed either at molecular (sequencing and gene expression study) or biochemical (immunologic test) level. Noteworthy, as a pleiotropic effect, is the activation of the ATI 0.28 pseudogene in the edited lines

BioMAJ: a flexible framework for databanks synchronization and processing

Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks

Una herramienta de apoyo a la gestión del proceso de desarrollo de software

En muchos centros de cómputo de la región no se aplican modelos de proceso de desarrollo de software. Esto tiene varios orígenes, principalmente la falta de recursos y capacitación en las mejores prácticas de la industria. En general, no está extendido el conocimiento y el uso de metodologías de gestión de riesgos, la mayoría de las cuales no son estructuradas y requieren de gerentes con experiencia, un recurso siempre escaso. El intercambio de información y experiencia se hace difícil y sólo es posible compararnos con organizaciones de otros contextos sociales, tecnológicos, económicos y culturales. Como resultado, las opiniones están basadas más en percepciones personales que en información objetiva. Esta investigación propone proveer una herramienta de bajo costo junto con un modelo de implantación, que aporte valor a toda la comunidad informática, y permita implantar y controlar un proceso de desarrollo de software, ágil y flexible, orientado a grupos de desarrollo pequeños y medianos, que desarrollan utilizando GeneXus[1], con control de calidad y proceso de mejora continua, que permita la planificación de la capacitación continua del equipo, controlar los costos de calidad y brindar automáticamente indicadores de gestión de proyectos, poniendo énfasis en el seguimiento del riesgo del proyecto.Eje: Ingeniería de Software y Bases de Datos (ISBD)Red de Universidades con Carreras en Informática (RedUNCI

Una herramienta de apoyo a la gestión del proceso de desarrollo de software

En muchos centros de cómputo de la región no se aplican modelos de proceso de desarrollo de software. Esto tiene varios orígenes, principalmente la falta de recursos y capacitación en las mejores prácticas de la industria. En general, no está extendido el conocimiento y el uso de metodologías de gestión de riesgos, la mayoría de las cuales no son estructuradas y requieren de gerentes con experiencia, un recurso siempre escaso. El intercambio de información y experiencia se hace difícil y sólo es posible compararnos con organizaciones de otros contextos sociales, tecnológicos, económicos y culturales. Como resultado, las opiniones están basadas más en percepciones personales que en información objetiva. Esta investigación propone proveer una herramienta de bajo costo junto con un modelo de implantación, que aporte valor a toda la comunidad informática, y permita implantar y controlar un proceso de desarrollo de software, ágil y flexible, orientado a grupos de desarrollo pequeños y medianos, que desarrollan utilizando GeneXus[1], con control de calidad y proceso de mejora continua, que permita la planificación de la capacitación continua del equipo, controlar los costos de calidad y brindar automáticamente indicadores de gestión de proyectos, poniendo énfasis en el seguimiento del riesgo del proyecto.Eje: Ingeniería de Software y Bases de Datos (ISBD)Red de Universidades con Carreras en Informática (RedUNCI

Characterization of individuals at high risk of developing melanoma in Latin America: bases for genetic counseling in melanoma

PURPOSE: CDKN2A is the main high-risk melanoma-susceptibility gene, but it has been poorly assessed in Latin America. We sought to analyze CDKN2A and MC1R in patients from Latin America with familial and sporadic multiple primary melanoma (SMP) and compare the data with those for patients from Spain to establish bases for melanoma genetic counseling in Latin America. METHODS: CDKN2A and MC1R were sequenced in 186 Latin American patients from Argentina, Brazil, Chile, Mexico, and Uruguay, and in 904 Spanish patients. Clinical and phenotypic data were obtained. RESULTS: Overall, 24 and 14% of melanoma-prone families in Latin America and Spain, respectively, had mutations in CDKN2A. Latin American families had CDKN2A mutations more frequently (P = 0.014) than Spanish ones. Of patients with SMP, 10% of those from Latin America and 8.5% of those from Spain had mutations in CDKN2A (P = 0.623). The most recurrent CDKN2A mutations were c.-34G>T and p.G101W. Latin American patients had fairer hair (P = 0.016) and skin (P < 0.001) and a higher prevalence of MC1R variants (P = 0.003) compared with Spanish patients. CONCLUSION: The inclusion criteria for genetic counseling of melanoma in Latin America may be the same criteria used in Spain, as suggested in areas with low to medium incidence, SMP with at least two melanomas, or families with at least two cases among first- or second-degree relatives.Genet Med 18 7, 727-736

A comprehensive overview of grain development in Brachypodium distachyon variety Bd21

A detailed and comprehensive understanding of seed reserve accumulation is of great importance for agriculture and crop improvement strategies. This work is part of a research programme aimed at using Brachypodium distachyon as a model plant for cereal grain development and filling. The focus was on the Bd21-3 accession, gathering morphological, cytological, and biochemical data, including protein, lipid, sugars, starch, and cell-wall analyses during grain development. This study highlighted the existence of three main developmental phases in Brachypodium caryopsis and provided an extensive description of Brachypodium grain development. In the first phase, namely morphogenesis, the embryo developed rapidly reaching its final morphology about 18 d after fertilization (DAF). Over the same period the endosperm enlarged, finally to occupy 80% of the grain volume. During the maturation phase, carbohydrates were continuously stored, mainly in the endosperm, switching from sucrose to starch accumulation. Large quantities of β-glucans accumulated in the endosperm with local variations in the deposition pattern. Interestingly, new β-glucans were found in Brachypodium compared with other cereals. Proteins (i.e. globulins and prolamins) were found in large quantities from 15 DAF onwards. These proteins were stored in two different sub-cellular structures which are also found in rice, but are unusual for the Pooideae. During the late stage of development, the grain desiccated while the dry matter remained fairly constant. Brachypodium exhibits some significant differences with domesticated cereals. Beta-glucan accumulates during grain development and this cell wall polysaccharide is the main storage carbohydrate at the expense of starch

Estimating CDKN2A mutation carrier probability among global familial melanoma cases using GenoMELPREDICT

Background: Although rare in the general population, highly penetrant germline mutations in CDKN2A are responsible for 5%-40% of melanoma cases reported in melanoma-prone families. We sought to determine whether MELPREDICT was generalizable to a global series of families with melanoma and whether performance improvements can be achieved. Methods: In total, 2116 familial melanoma cases were ascertained by the international GenoMEL Consortium. We recapitulated the MELPREDICT model within our data (GenoMELPREDICT) to assess performance improvements by adding phenotypic risk factors and history of pancreatic cancer. We report areas under the curve (AUC) with 95% confidence intervals (CIs) along with net reclassification indices (NRIs) as performance metrics. Results: MELPREDICT performed well (AUC 0.752, 95% CI 0.730-0.775), and GenoMELPREDICT performance was similar (AUC 0.748, 95% CI 0.726-0.771). Adding a reported history of pancreatic cancer yielded discriminatory improvement (P &lt; .0001) in GenoMELPREDICT (AUC 0.772, 95% CI 0.750-0.793, NRI 0.40). Including phenotypic risk factors did not improve performance. Conclusion: The MELPREDICT model functioned well in a global data set of familial melanoma cases. Adding pancreatic cancer history improved model prediction. GenoMELPREDICT is a simple tool for predicting CDKN2A mutational status among melanoma patients from melanoma-prone families and can aid in directing these patients to receive genetic testing or cancer risk counseling