Integration of CRISPR-Cas9, shRNA with other genomic data provides reliable predicions of gene essentiality

Recent genome-wide loss-of-function screening studies have provided an unprecedented amount of information to perform functional analysis of the genome. Two main strategies have been followed to perform these experiments: shRNA and, more recently, CRISPR-Cas9. Both technologies have shown their ability to knock down genes and, in the case of CRISPR-Cas9, the ability to create new cell-line strands with different phenotype

A Hemispherical Contact Model for Simplifying 3D Occlusal Surfaces

Statement of problem Currently, dental articulators can recreate mandibular movements and occlusal contacts. However, whether virtual articulators can also provide information about occluding dental surfaces, functional movements, and the mandibular condyles is unclear. Purpose The purpose of this in vitro study was to evaluate the occluding surfaces on dental casts obtained from a patient and approximate them to a hemispherical contact model. Both models were tested by digitizing the Dentatus ARL dental articulator. Material and methods A combination of photogrammetry and structure from motion methods were used to scan a Dentatus ARL articulator and representative dental casts. Using computer-aided engineering and finite element analysis, contact points and action vectors to the forces on occluding surfaces and condyles were obtained for cast and hemispherical models. This experiment was performed using centric occlusion and 3 different condylar inclinations. The Kruskal-Wallis 1-way analysis of variance on ranks test was used to allow all pairwise comparisons between condylar inclination and mechanical action vector values in each location (α=.05). Results Action vectors from the cast model and each location of the hemispherical model were calculated to show the mechanical consequences and the similarity among models. Overall, no significant differences were observed for action vectors (A20 versus A40 versus A60) at each location (dental cast/hemisphere, right condylar, and left condylar) in the analysis of dental casts and the hemisphere model (.382≤P≤.999). Conclusions This study provided graphical information that may assist the dental professional in determining which occlusal contacts should be modified to attain condylar and balanced centric occlusion

Fast and accurate methodology for direct mercury determination in hair and nails

A solvent-free, easy, fast and waste-free methodology was developed for the determination of total mercury levels in hair and nails. Samples were taken from several volunteers and directly analysed, with levels of mercury in the range between 0.5 and 8 ng/mg. The influence of quantity of hair, as well as the addition of small amount of solvent and the necessity of previous treatment were studied. Also, a history of mercury exposure was provided by the distance of the hair from the scalp of each volunteer, the results of which were correlated with fish consumption. Furthermore, a short study of mercury in nails was carried out and correlated to the results from hair mercury levels. A small quantity of 5 mg of hair with an addition of 50 μL of water to the sample without previous treatment was adequate to get a representative result in less than 10 minutes. The accuracy of the proposed method was confirmed by analysing certified reference materials including Coal Fly Ash-NIST SRM 1633b, Fucus-IAEA 140 and three unpolished Rice Flour NIES-10. The observed results were found to be in good agreement with the certified values

Composición de ácidos grasos de la carne de capones de raza Mos y estirpes comerciales sacrificados a diferentes edades

Se ha estudiado la influencia de la raza [Mos (raza española autóctona), Sasso T-44 y X-44 (estirpes comerciales)] y la edad (5, 6, 7 y 8 meses) de los capones (gallos castrados) en la composición de ácidos grasos de la carne de la pechuga y del muslo. La carne de los capones de raza Mos presentó menor concentración de ácidos grasos monoinsaturados y mayor de poliinsaturados que la carne de las otras razas. Además, dichos capones mostraron mayor contenido de los ácidos margárico (C17:0) y esteárico (C18:0) que las estirpes comerciales; sin embargo, no hubo diferencias significativas entre las distintas razas en el total de ácidos grasos saturados. La carne de los animales más jóvenes mostró menor concentración de ácidos grasos monoinsaturados y mayor de poliinsaturados que la de los animales de mayor edad. Sin embargo, la edad influyó menos que la razaThe influence of the breed [Mos (Spanish indigenous breed), Sasso T-44 and X-44 (commercial strains)] and the age (5, 6, 7 and 8 months) of capons (castrated male cockerels) on the fatty acid compositions of breast and drumstick meat were studied. The meat of the Mos capons showed lower contents of monounsaturated fatty acids and higher concentrations of polyunsaturated fatty acids than those of the other breeds. In addition, the Mos breed showed higher contents of margaric acid (C17:0) and stearic acid (C18:0) as compared to the commercial strains; however, no significant effects of breed were observed in the total contents of saturated fatty acids in the meat. The meat of the youngest animals showed lower contents of monounsaturated fatty acids and higher concentrations of polyunsaturated fatty acids than that of the older ones. Nevertheless, the effect of age was less important than the effect of breedThis study was financially supported by project PGIDIT04RAG012E [Consellería de Innovación, Industria e Comercio da Xunta de Galicia and Asociación de Criadores de Capón de Vilalba]S

miRNA/phasiRNA mediated regulation of plant defense response against P. syringae

Gene silencing is a mechanism of regulation of gene expression where the small RNAs (sRNAs) are key components for giving specificity to the system. In plants, two main types of noncoding small RNA molecules have been found: microRNAs (miRNAs) and small interfering RNAs (siRNAs). DCL proteins acting on large RNA precursors produce the mature forms of sRNAs (20-24nt) that can act as negative regulators of gene expression. In recent years, the role of miRNAs in regulation of gene expression in plant responses against bacterial pathogens is becoming clearer. Comparisons carried out in our lab between expression profiles of different Arabidopsis thaliana mutants affected in gene silencing, and plants challenged with Pseudomonas syringae pathovar tomato DC3000, led us to identify a set of uncharacterized R genes, belonging to the TIR-NBS-LRR gene family, as differentially expressed in these conditions. Through the use of bioinformatics tools, we found a miRNA* of 22 nt putatively responsible for down-regulating expression of these R genes. We have validated this regulation, and have also established that the corresponding pri-miRNA is down-regulated upon PAMPs or bacteria perception. Using GUS reporters, we have characterized the expression pattern of both pri-miRNA and its best target R genes. We demonstrate that plants with altered levels of miRNA* (knockdown or overexpression lines) exhibit altered PTI-associated phenotypes, supporting a role for this miRNA* in the defence response against this bacterial pathogen. Finally, we identify phasiRNAs that arise from the transcript of one of the R target genes in a miRNA*-RDR6-DCL4-dependent manner.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Use of synthetic RGB images in train

Ponencia presentada en: 2010 EUMETSAT Meteorological Satellite Conference celebrada del 20-24 de septiembre de 2010 en Córdoba.This paper compares actual and synthetic (calculated) airmass RGB composites, before and after applying different corrections: (a) synthetic airmass RGB calculated with the satellite zenith angle corresponding to the pixel, versus others with fixed zenith angles (0º, 15º, 30º, 45º, 60º and 75º), to observe the blue shift close to the disk boundary due to a longer atmospheric path for the signal in oblique views, (b) Synthetic airmass RGB in areas of sinking tropopause with ozone intrusion for different values in the ozone concentration and humidity. The synthetic RGB for MSG are based on the use of the ECMWF model with RTTOV package and the METEOSAT Second Generation coefficients. Also synthetic MTG-IRS sounder RGBs have been generated. Based on the use of the RTTOV package with the IASI coefficients for one GRIB file of the ECMWF model, synthetic IASI RTTOV radiances are converted to synthetic MTG-IRS RTTOV brightness temperatures (BT). After one selection of the most adequate MTG-IRS brightness temperatures (BTs), two MTG-sounder synthetic RGBs are created. This is a proving ground experiment for the MTG sounder era

Integration of CLIP experiments of RNAbinding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data

Background: Splicing is a genetic process that has important implications in several diseases including cancer. Deciphering the complex rules of splicing regulation is crucial to understand and treat splicing-related diseases. Splicing factors and other RNA-binding proteins (RBPs) play a key role in the regulation of splicing. The specific binding sites of an RBP can be measured using CLIP experiments. However, to unveil which RBPs regulate a condition, it is necessary to have a priori hypotheses, as a single CLIP experiment targets a single protein. Results: In this work, we present a novel methodology to predict context-specific splicing factors from transcriptomic data. For this, we systematically collect, integrate and analyze more than 900 CLIP experiments stored in four CLIP databases: POSTAR2, CLIPdb, DoRiNA and StarBase. The analysis of these experiments shows the strong coherence between the binding sites of RBPs of similar families. Augmenting this information with expression changes, we are able to correctly predict the splicing factors that regulate splicing in two gold-standard experiments in which specific splicing factors are knocked-down. Conclusions: The methodology presented in this study allows the prediction of active splicing factors in either cancer or any other condition by only using the information of transcript expression. This approach opens a wide range of possible studies to understand the splicing regulation of different conditions. A tutorial with the source code and databases is available at https://gitlab.com/fcarazo.m/sfprediction

Integrative Oncogenomic Analysis of Microarray Data in Hematologic Malignancies

During the last decade, gene expression microarrays and array-based comparative genomic hybridization (array-CGH) have unraveled the complexity of human tumor genomes more precisely and comprehensively than ever before. More recently, the simultaneous assessment of global changes in messenger RNA (mRNA) expression and in DNA copy number through "integrative oncogenomic" analyses has allowed researchers the access to results uncovered through the analysis of one-dimensional data sets, thus accelerating cancer gene discovery. In this chapter, we discuss the major contributions of DNA microarrays to the study of hematological malignancies, focusing on the integrative oncogenomic approaches that correlate genomic and transcriptomic data. We also present the basic aspects of these methodologies and their present and future application in clinical oncology

Author Correction: Infuence of the surface viscous stress on the pinch‑of of free surfaces loaded with nearly‑inviscid surfactants [Corrección]

Correction to: Scientifc Reports https://doi.org/10.1038/s41598-020-73007-1, published online 30 September 2020. The original version of this Article contained errors

Rendimiento de terneros alimentados con silo de maíz o láctico con un promotor de la fermentación ruminal

Se efectuó el engorde de 120 bovinos (296 &plusmn; 6,9 kg) machos cruzados de Cebú durante 120 días divididos en tres tratamientos. Tratamiento 1: 40 animales alimentados con ensilaje normal de maíz (EN). Tratamiento 2: n= 40 animales alimentados con ensilaje inoculado con probiótico láctico enriquecido en N no proteico (NNP) (EP). Tratamiento 3 (EPS): 40 bovinos alimentados con EP más un suplemento nitrogenado de lento consumo (SNLC). Se emplearon tres toros canulados para estudiar la cinética ruminal y la digestibilidad in vivo. La concentración de NH3 en el fluido ruminal fue significativamente menor en EN (15 mg/100 ml) que en EP y EPS (18 y 22 mg/100 ml, respectivamente). La degradabilidad in situ de la FND fue 28% en EN, 38% para EP y 48% en EPS (p<0,05). El coeficiente de digestibilidad aparente de la MS fue significativamente menor en EN (57%) comparado con 68% en EP y 70% en EPS. El consumo voluntario fue menor (p<0,05) en EN (90 g/kg0,75/d) comparado con 120 y 140 g/kg0,75/d para EP y EPS respectivamente. Se observó un aumento en la ingestión de N de 72 g/d (EN) a 218 g/d (EP) y 277 g/d en EPS, aunque no se observan diferencias en la eficiencia de utilización entre los tratamientos EP y EPS. La digestibilidad aparente del N aumentó de un 73% para EN a un 76% para EP y EPS. Las cuentas de lactobacilos fueron de 1,6 millones/ml en EN, 10,5 en EP, a 12,5 millones/ml en el EPS. La excreción de derivados púricos aumentó en las dos dietas con el probiótico (p<0,05). Las ganancias diarias de peso fueron diferentes (p<0,05) para las 3 dietas (0,874 kg/d para EN, 1,172 para EP y 1,250 para EPS). La oferta de ensilaje de maíz enriquecido con probióticos con o sin suplemento nitrogenado de lento consumo incrementó la ganancia de peso en bovinos en engorde mejorando el proceso de fermentación ruminal e incrementando la producción de proteína microbiana