Capillary electrophoresis as a tool for genotyping SH3 mediated coffee leaf rust resistance

Coffee is an important agricultural commodity in the world. However, it is susceptible to Hemileia vastatrix (Hv), an obligatory biotrophic fungus that causes coffee leaf rust (CLR). Natural resistance to rust has been identified in the wild species Coffea canephora and Coffea liberica. These species have been used in breeding programs where interspecific resistant hybrids have been generated. The SH3 gene, derived from C. liberica, has been shown to confer extreme and long-lasting resistance to Hv. A total of 167 accessions of the INIA’s Coffee Germplasm Collection of Peru (INIA-CGC) were screened with 4 markers linked to the SH3 gene. As positive controls, EA67 (C. liberica) and the hybrid S.288 (C. arabica x C. liberica) were used. Separation of PCR products was done by capillary electrophoresis, which allow to discriminate the alleles of each marker. For three markers, specific alleles for either C. arabica or C. liberica species were found. In all cases, S.288 exhibited specific alleles for both species; whereas the INIA-CGC accessions had exclusively C. arabica alleles and EA67 had C. liberica alleles. The BA-48-21O-f marker did not produce PCR fragments for any of the positive controls, suggesting that this marker is not as predictive as the other three to determine the presence of SH3. This work reports the existence of multiple alleles for the Sat244 marker; however, the collection does not have the SH3 mediated-resistance gene. Finally, the utility of capillary electrophoresis as a tool to identify alleles linked to SH3 was demonstrated

Detection of rat brain activation using statistical parametric mapping analysis in FDG-PET studies

[Abstract] AMI International Conference 2003, September 21 - 27, Madrid, Spain: High Resolution Molecular Imaging: from Basic Science to Clinical ApplicationsStatistical parametric mapping (SPM) is an analysis technique long been used in clinical research to detect subtle activity changes in brain; it is an excellent exploratory tool as it does not require a priori assumptions about the expected brain region activations. Research in animal imaging may also take benefit from this technique, if properly adapted to the new scenario. This is the case of brain activation studies in murine models using PET tracers and dedicated imaging devices. This work proposes the use of an SPM methodology adapted to the analysis of 2-deoxy-2-[18F] fluoro-D-Glucose (FDG) positron emission tomography (PET) scans of rat brains. Advantages over conventional region of interest (ROI) based analysis were assessed in an experiment addressing the detection of brain activation in of rats which underwent three different visual stimulation paradigmsPublicad

Detection of visual activation in the rat brain using 2-deoxy-2-[18F]fluoro-D-glucose and statistical parametric mapping (SPM)

Purpose: This study was designed to assess changes in brain glucose metabolism in rats after visual stimulation. Materials and methods: We sought to determine whether visual activation in the rat brain could be detected using a small-animal positron emission tomography (PET) scanner and 2-deoxy-2- [18F]fluoro-D-glucose (FDG). Eleven rats were divided into two groups: (a) five animals exposed to ambient light and (b) six animals stimulated by stroboscopic light (10 Hz) with one eye covered. Rats were injected with FDG and, after 45 min of visual stimulation, were sacrificed and scanned for 90 min in a dedicated PET tomograph. Images were reconstructed by a threedimensional ordered subset expectation maximization algorithm (1.8 mm full width at half maximum). A region-of-interest (ROI) analysis was performed on 14 brain structures drawn on coronal sections. Statistical parametric mapping (SPM) adapted for small animals was also carried out. Additionally, the brains of three rats were sliced into 20-μm sections for autoradiography. Results: Analysis of ROI data revealed significant differences between groups in the right superior colliculus, right thalamus, and brainstem (p≤0.05). SPM detected the same areas as the ROI approach. Autoradiographs confirmed the existence of hyperactivation in the left superior colliculus and auditory cortex. Conclusions: To our knowledge, this is the first report that uses FDG-PET and SPM analysis to show changes in rat brain glucose metabolism after a visual stimulusThis work was supported by grants from the Ministerio de Ciencia y Tecnología (TEC2004-07052), Ministerio de Sanidad y Consumo (CIBERsam CB07/09/0031 and Plan Nacional sobre Drogas 2007/043), Ministerio de Industria (CDTEAM Project), and Fundación de Investigación Médica Mutua Madrileña. We thank Alexandra de Francisco for her assistance with the PET studies, the Atomic, Molecular, and Nuclear Physics Department of the Universidad Complutense in Madrid for reconstructing the PET images, and the National Institute of Health for facilitating the piPET system.Publicad

Influence of metal organic chemical vapour deposition growth conditions on vibrational and luminescent properties of ZnO nanorods

Producción CientíficaA detailed optical characterization by means of micro Raman and cathodoluminescence spectroscopy of catalyst-free ZnO nanorods grown by atmospheric-metal organic chemical vapour deposition has been carried out. This characterization has allowed correlating the growth conditions, in particular the precursors partial-pressures and growth time, with the optical properties of nanorods. It has been shown that a high Zn supersaturation can favor the incorporation of nonradiative recombination centers, which can tentatively be associated with ZnI-related defects. Characterization of individual nanorods has evidenced that ZnI-related defects have a tendency to accumulate in the tip part of the nanorods, which present dark cathodoluminescence contrast with respect to the nanorods bottom. The effect of a ZnO buffer layer on the properties of the nanorods has been also investigated, showing that the buffer layer improves the luminescence efficiency of the ZnO nanorods, revealing a significant reduction of the concentration of nonradiative recombination centers.Ministerio de Ciencia e Innovación (Projects MAT2007-66129, MAT-2010-20441-C02, MAT-2010-16116, and TEC2011-28076-C02-02)Generalitat Valenciana (Prometeo/2011-035 and ISIC/2012/008, Institute of Nanotechnologies for Clean Energies

WALLABY Pilot Survey: H i gas disc truncation and star formation of galaxies falling into the Hydra I cluster

We present results from our analysis of the Hydra I cluster observed in neutral atomic hydrogen (HI) as part of the Widefield ASKAP L-band Legacy All-sky Blind Survey (WALLABY). These WALLABY observations cover a 60-square-degree field of view with uniform sensitivity and a spatial resolution of 30 arcsec. We use these wide-field observations to investigate the effect of galaxy environment on HI gas removal and star formation quenching by comparing the properties of cluster, infall and field galaxies extending up to ∼5R200 from the cluster centre. We find a sharp decrease in the HI-detected fraction of infalling galaxies at a projected distance of ∼1.5R200 from the cluster centre from ∼0.85% to ∼0.35%. We see evidence for the environment removing gas from the outskirts of HI-detected cluster and infall galaxies through the decrease in the HI to r-band optical disc diameter ratio. These galaxies lie on the star forming main sequence, indicating that gas removal is not yet affecting the inner star-forming discs and is limited to the galaxy outskirts. Although we do not detect galaxies undergoing galaxy-wide quenching, we do observe a reduction in recent star formation in the outer disc of cluster galaxies, which is likely due to the smaller gas reservoirs present beyond the optical radius in these galaxies. Stacking of HI non-detections with HI masses below MHI≲108.4M⊙ will be required to probe the HI of galaxies undergoing quenching at distances ≳60 Mpc with WALLABY

Small-animal PET registration method with intrinsic validation designed for large datasets

Proceeding of: 2007 IEEE Nuclear Science Symposium Conference Record (NSS'07), Honolulu, Hawaii, USA, Oct. 27 - Nov. 3, 2007We present a procedure to validate the results of small animal Positron Emission Tomography (PET) image registration by means of consistency measures. Small animal 2-Deoxy-2-[F-18]fluoro-D-glucose (FDG) PET studies do not show the same intensity distribution even for images acquired in similar conditions, as the resulting image is influenced by several variables which are not always completely under control. Because of these difficulties, the results from automatic registration methods have to be visually inspected to detect failures. We propose a method to automate this validation process. Two reference images from the dataset are selected by an expert user avoiding images with poor contrast, animal movement or low quality, and both are co-registered using anatomical landmarks. All the remaining images in the dataset are then registered to every reference with an automatic two-step algorithm based on Mutual Information. The known transformation relating both references allows measuring the registration consistency, which is a good estimator of the accuracy of the alignment process, for every image in the dataset. This value can be used to assess the quality of the registration and therefore detect the incorrect results. We have applied this validation process on a large dataset of 120 FDG-PET rat brain images obtained with a rotating PET scanner. The registration consistency was calculated for every image in the dataset and values below 1.65 mm (PET image resolution) were considered as successful registrations. 116 images were correctly registered with an average error of 0.839 mm, while in four images the proposed method detected a registration failure. Two of these failures were due to very low image quality and these studies were discarded from the study, while the other two were correctly aligned after applying a manual pre-alignment step. Our approach requires minimal user interaction and provides automatic assessment of the registration error, making it unnecessary to visually inspect and check every registration result.This work was supported by projects CIBER CB06/01/0079 (Ministerio de Sanidad y Consumo) and CDTEAM (CENIT program, Ministerio de Industria)

The pangenome of hexaploid bread wheat

There is an increasing understanding that variation in gene presence–absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene pres- ence–absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 102 genes, a core genome of 81 070 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal sin- gle nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at http://appliedbioinformatics.com.au/cgi-bin/ gb2/gbrowse/WheatPan/, and data are available to download from http://wheatgenome.info/wheat_ge nome_databases.php

IAA : Información y actualidad astronómica (37)

Sumario : SgrA*: nuestro aletargado monstruo galáctico.-- Una mirada no tan limitada al universo.-- CLASH.-- CIENCIA EN HISTORIAS. Una breve, muy breve, historia de los autómatas.-- DECONSTRUCCIÓN Y otros ENSAYOS. El extraño caso de Henrietta Leavitt y Erasmus Cefeido.-- EL “MOBY DICK” DE... René Duffard (IAA-CSIC).-- ACTUALIDAD.-- ENTRE BASTIDORES.-- SALA LIMPIA.-- CIENCIA: PILARES E INCERTIDUMBRES... La misteriosa materia oscura.-- AGENDA/RECOMENDADOS.N

Indentificación de Fases de la Diabetes Espontánea de un Biomodelo Murino mediante Análisis Multidimensional de Datos

Biomodels used in the study of diabetes allow to evaluate genetic and environmental factors. Our aim was to characterize individuals of eSS, a genetically diabetic line of rats. We applied multivariate analysis, using the values obtained during the performance of oral glucose tolerance tests, presence of glucosuria, together with other physiological and environmental characteristics totalling 9 variables. Previously, an assignation of missing values of glucosuria was carried out through an artificial neural network classifier. To characterize individuals, principal componentes analysis was carried out. On describing data structure in a graphical representation of factorial coordinates, the first axe separated individuals according to glycemias, age and weight and the second opposed biomass in early ages to litter size. The cluster analysis defined a typology based on five classes. When these results were correlated with clinical classification, it was possible to separate eSS males from the youngest rats with low body weight, aglucosuric, with normal fasting glycemia but impaired glucose tolerance, up to diabetic individuals, older, with higher biomass and glucosuric. This methodology allows to identify stages in the progression of the diabetic syndromeLos biomodelos utilizados para el estudio de la diabetes permiten evaluar factores genéticos y ambientales. Nuestro propósito fue caracterizar individuos de la línea de ratas gen´eticamente diabéticas eSS utilizando, mediante análisis multivariado, los valores de la curva de tolerancia  lúcida y de glucosuria, junto con otras características fisiológicas y ambientales totalizando 9 variables. Se asignaron valores faltantes de glucosuria mediante un clasificador neuronal. Para la caracterizaci´on de los individuos se aplicó el método de componentes principales y al efectuar la descripción de la estructura de los datos mediante representación gráfica en ejes factoriales, el primer eje separó los individuos según las glucemias, edad y peso y el segundo opuso la biomasa en edades tempranas con el tamaño de camada. El análisis en clusters definió una partición en 5 clases. Al relacionar los resultados con la clasificación clínica fue posible tipificar a los machos eSS desde los más jóvenes con menor peso, aglucosúricos, con glucemia de ayuno normal pero con alteración de la tolerancia a la glucosa hasta los diabéticos, de mayor peso y edad y glucosúricos, posibilitándose así la identificación de fases en la progresión del síndrome