Genome-wide DNA-(de)methylation is associated with Noninfectious Bud-failure exhibition in Almond (Prunus dulcis [Mill.] D.A.Webb).

Noninfectious bud-failure (BF) remains a major threat to almond production in California, particularly with the recent rapid expansion of acreage and as more intensive cultural practices and modern cultivars are adopted. BF has been shown to be inherited in both vegetative and sexual progeny, with exhibition related to the age and propagation history of scion clonal sources. These characteristics suggest an epigenetic influence, such as the loss of juvenility mediated by DNA-(de)methylation. Various degrees of BF have been reported among cultivars as well as within sources of clonal propagation of the same cultivar. Genome-wide methylation profiles for different clones within almond genotypes were developed to examine their association with BF levels and association with the chronological time from initial propagation. The degree of BF exhibition was found to be associated with DNA-(de)methylation and clonal age, which suggests that epigenetic changes associated with ageing may be involved in the differential exhibition of BF within and among almond clones. Research is needed to investigate the potential of DNA-(de)methylation status as a predictor for BF as well as for effective strategies to improve clonal selection against age related deterioration. This is the first report of an epigenetic-related disorder threatening a major tree crop

Application of genomic and quantitative genetic tools to identify candidate resistance genes for brown rot resistance in peach.

The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar 'Dr. Davis' and a brown rot resistant introgression line, 'F8,1-42', derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot

Implementación de una suite gráfica para reforzar el aprendizaje en representación de contenido multimedia

Las prácticas de las asignaturas en los grados de Ingeniería Informática se diseñan habitualmente para que los estudiantes formulen y construyan la solución a un determinado problema usando algún lenguaje de programación. Este tipo de prácticas son adecuadas cuando el objetivo es el aprendizaje o refinamiento de sus habilidades en ese lenguaje. Sin embargo, si el objetivo es que profundicen sobre las ideas desarrolladas en las clases de teoría, una aproximación más eficiente es proporcionar a los estudiantes una herramienta software que les permita trabajar y analizar conceptos teóricos de forma sencilla y práctica. En el contexto de la información multimedia, la mayoría de las aplicaciones comerciales están orientadas al desarrollo profesional y resultan poco adecuadas desde un punto de vista didáctico. Por esa razón, los autores de este artículo hemos decidido desarrollar una suite gráfica que permita a los estudiantes comprobar de forma visual los conceptos teóricos de la asignatura y analizar el impacto de múltiples factores relacionados con la representación y procesado de imágenes. Con esta herramienta, se evita que los estudiantes tengan que programar directamente las funcionalidades en un lenguaje que no dominan, de forma que pueden invertir su tiempo en trabajar con dicha herramienta y lograr un aprendizaje más profundo.The practical activities for Degrees in Computer Engineering are usually designed to guarantee the students state and obtain the solution for a specific problem using some programming language. This type of activities are suitable when the purpose is to improve their skills in such a language. However, when the purpose is that the students achieve a deeper knowledge about theoretical ideas, a more efficient approach is to provide them a software tool to develop and analyse the theoretical concepts in a simple and practical way. In the context of multimedia information, most commercial applications are focused on professional development and they are not suitable from an educational point of view. For that, we decided to implement a graphic suite which allows the students to visually test the theoretical concepts in the subject, and to analyse the impact of multiple factors related to the representation and processing of images. Using this tool, the students do not need to implement the programme’s features, but they can spend their time on working with the developed tool and achieving a deeper learning.Este trabajo ha sido financiado por la Xunta de Galicia (ED431C 2016-045, ED431G/01) y la Agencia Estatal de Investigación de España (TEC2016-75067-C4-1-R)

Toward the Elucidation of Cytoplasmic Diversity in North American Grape Breeding Programs

Plants have an intriguing tripartite genetic system: Nuclear genome 9 Mitochondria 9 Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the cytoplasmic diversity among 6073 individuals (comprising cultivars, interspecific hybrids and segregating progenies) are presented. Genotyping by sequencing (GBS) was used to elucidate plastid and mitochondrial DNA sequences, and results were analyzed using multivariate techniques. Single nucleotide polymorphism (SNP) effects were annotated in reference to plastid and mitochondrial genome sequences. The cytoplasmic diversity identified was structured according to synthetic domestication groups (wine and raisin/table gr.ape types) and interspecific-hybridization-driven groups with introgression from North American Vitis species, identifying five cytoplasmic groups and four major clusters. Fifty-two SNP markers were used to describe the diversity of the germplasm. Ten organelle genes showed distinct SNP annotations and effect predictions, of which six were chloroplast-derived and three were mitochondrial genes, in addition to one mitochondrial SNP affecting a nonannotated open reading frame. The results suggest that the application of GBS will aid in the study of cytoplasmic genomes in grapevine, which will enable further studies on the role of cytoplasmic genomes in grapevine germplasm, and then allow the exploitation of these sources of diversity in breeding

Serum osteoprotegerin is associated with pulse pressure in kidney transplant recipients

Pulse pressure (PP) reflects increased large artery stiffness, which is caused, in part, by arterial calcification in patients with chronic kidney disease. PP has been shown to predict both cardiovascular and cerebrovascular events in various patient populations, including kidney transplant (KTX) recipients. Osteoprotegerin (OPG) is a marker and regulator of arterial calcification, and it is related to cardiovascular survival in hemodialysis patients. Here we tested the hypothesis that OPG is associated with increased pulse pressure. We cross-sectionally analyzed the association between serum OPG and PP in a prevalent cohort of 969 KTX patients (mean age: 51 +/- 13 years, 57% male, 21% diabetics, mean eGFR 51 +/- 20 ml/min/1.73 m2). Independent associations were tested in a linear regression model adjusted for multiple covariables. PP was positively correlated with serum OPG (rho = 0.284, p < 0.001). Additionally, a positive correlation was seen between PP versus age (r = 0.358, p < 0.001), the Charlson Comorbidity Index (r = 0.232, p < 0.001), serum glucose (r = 0.172, p < 0.001), BMI (r = 0.133, p = 0.001) and serum cholesterol (r = 0.094, p = 0.003). PP was negatively correlated with serum Ca, albumin and eGFR. The association between PP and OPG remained significant after adjusting for multiple potentially relevant covariables (beta = 0.143, p < 0.001). We conclude that serum OPG is independently associated with pulse pressure in kidney transplant recipients

A Next-generation Marker Genotyping Platform (AmpSeq) in Heterozygous Crops: A Case Study for Marker-assisted Selection in Grapevine

Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates traitassociated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads ( ⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had o10% missing data, and read depth had a median of 220–244 × . Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, lowcost and easily automated analysis

Incidence of cardiovascular events after kidney transplantation and cardiovascular risk scores: study protocol

<p>Abstract</p> <p>Background</p> <p>Cardiovascular disease (CVD) is the major cause of death after renal transplantation. Not only conventional CVD risk factors, but also transplant-specific risk factors can influence the development of CVD in kidney transplant recipients.</p> <p>The main objective of this study will be to determine the incidence of post-transplant CVD after renal transplantation and related factors. A secondary objective will be to examine the ability of standard cardiovascular risk scores (Framingham, Regicor, SCORE, and DORICA) to predict post-transplantation cardiovascular events in renal transplant recipients, and to develop a new score for predicting the risk of CVD after kidney transplantation.</p> <p>Methods/Design</p> <p>Observational prospective cohort study of all kidney transplant recipients in the A Coruña Hospital (Spain) in the period 1981-2008 (2059 transplants corresponding to 1794 patients).</p> <p>The variables included will be: donor and recipient characteristics, chronic kidney disease-related risk factors, pre-transplant and post-transplant cardiovascular risk factors, routine biochemistry, and immunosuppressive, antihypertensive and lipid-lowering treatment. The events studied in the follow-up will be: patient and graft survival, acute rejection episodes and cardiovascular events (myocardial infarction, invasive coronary artery therapy, cerebral vascular events, new-onset angina, congestive heart failure, rhythm disturbances and peripheral vascular disease).</p> <p>Four cardiovascular risk scores were calculated at the time of transplantation: the Framingham score, the European Systematic Coronary Risk Evaluation (SCORE) equation, and the REGICOR (Registre Gironí del COR (Gerona Heart Registry)), and DORICA (Dyslipidemia, Obesity, and Cardiovascular Risk) functions.</p> <p>The cumulative incidence of cardiovascular events will be analyzed by competing risk survival methods. The clinical relevance of different variables will be calculated using the ARR (Absolute Risk Reduction), RRR (Relative Risk Reduction) and NNT (Number Needed to Treat).</p> <p>The ability of different cardiovascular risk scores to predict cardiovascular events will be analyzed by using the c index and the area under ROC curves. Based on the competing risks analysis, a nomogram to predict the probability of cardiovascular events after kidney transplantation will be developed.</p> <p>Discussion</p> <p>This study will make it possible to determine the post-transplant incidence of cardiovascular events in a large cohort of renal transplant recipients in Spain, to confirm the relationship between traditional and transplant-specific cardiovascular risk factors and CVD, and to develop a score to predict the risk of CVD in these patients.</p

Effect of end-stage renal disease on B-lymphocyte subpopulations, IL-7, BAFF and BAFF receptor expression

Background. End-stage renal disease (ESRD) results in increased susceptibility to infections, impaired response to vaccination and diffuse B-cell lymphopenia. However, the precise nature and mechanism of ESRD-induced B-cell lymphopenia remains unclear. Therefore, we studied the distribution of major B-cell subsets, B-cell growth, differentiation and survival factors, IL-7 and BAFF, and their receptors in 21 haemodialysis patients and 21 controls

The critical role of the operating conditions on the Fenton oxidation of 2-chlorophenol: assessment of PCDD/Fs formation

This work assesses the influence of the operating conditions H2O2dose (20 or 100% of the stoichiometric amount), temperature (20 or 70◦C), and the presence of chloride in the oxidation medium in the formation of polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) during Fenton treatment of aqueous samples of 2-chlorophenol, 2-CP, one of the strongest precursor of PCDD/Fs. After 4 h of oxidation in the experiments carried out with 20% H2O2chlorinated phenoxyphenols and biphenyls, which are intermediates in PCDD/Fs formation, as well as PCDD/Fs were observed, resulting in concentrations11 times higher than in the untreated sample. Additionally, when NaCl was also present in the reaction medium, PCDD/Fs were formed at higher extent, with a total concentration 74.4 times higher than in the untreated 2-CP solution. Results depicted a preferential formation of PCDFs over PCDDs, with dominance of lower chlorinated PCDD/Fs (tetra and penta-PCDD/Fs). Besides, the formation of the most toxic PCDD/Fs congeners (2,3,7,8-PCDD/Fs) was not favored under the operating conditions used in this work.Financial support from the projects CTQ2011-25262, CTQ2008-05545 and CTQ2008-00690 (Ministerio de Economía y Competitividad – MINECO (SPAIN) and Fondo Europeo de Desarrollo Regional – FEDER) is gratefully acknowledged

Accurate determination of key surface properties that determine the efficient separation of bovine milk BSA and LF proteins

The aim of this work is to accurately measure fundamental surface properties, i.e., zeta potential, isoelectric point and protein size that determine the optimal separation conditions of Bovine serum albumin and lactoferrin, two high added value food proteins whose similarity in weight makes their separation a scientific and technical challenge. The systematic study of these proteins’ surface properties was performed under different conditions: (i) 3.0 < pH < 10.0, (ii) electrolyte type: KCl, NaCl and CaCl2 and concentration (0.01–0.1 M KCl) and (iii) protein concentration in the range of 0.04–4.0 g L-1 for BSA and 0.01–1.0 g L-1 for LF with the objective of establishing the optimal separation conditions. Finally, the comparison of the experimental and theoretically calculated values revealed significant deviations under specific conditions, highlighting the simplicity of the theoretical assumptions and leading to the conclusion that the use of experimental surface properties is still needed for the correct design of food protein separation processes.Financial support from the Projects CTQ2011-25262, CTM2011- 23912 and CTQ2012- 31639 (Ministerio de Economía y Competitividad-MINECO/SPAIN and Fondo Europeo de Desarrollo Regional-FEDER) is gratefully acknowledged