Open Access
Induction of radiata pine somatic embryogenesis at high temperatures provokes a long-term decrease in DNA methylation/hydroxymethylation and differential expression of stress-related genes
(MDPI, 2020) Castander Olarieta, Ander; Pereira, Catia; Sales, Ester; Meijón, Mónica; Arrillaga, Isabel; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Cañal, María Jesús; Moncaleán, Paloma; Montalbán, Itziar A.; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2
Based on the hypothesis that embryo development is a crucial stage for the formation of stable epigenetic marks that could modulate the behaviour of the resulting plants, in this study, radiata pine somatic embryogenesis was induced at high temperatures (23◦ C, eight weeks, control; 40◦ C, 4 h; 60◦ C, 5 min) and the global methylation and hydroxymethylation levels of emerging embryonal masses and somatic plants were analysed using LC-ESI-MS/ MS-MRM. In this context, the expression pattern of six genes previously described as stress-mediators was studied throughout the embryogenic process until plant level to assess whether the observed epigenetic changes could have provoked a sustained alteration of the transcriptome. Results indicated that the highest temperatures led to hypomethylation of both embryonal masses and somatic plants. Moreover, we detected for the first time in a pine species the presence of 5-hydroxymethylcytosine, and revealed its tissue specificity and potential involvement in heat-stress responses. Additionally, a heat shock protein-coding gene showed a down-regulation tendency along the process, with a special emphasis given to embryonal masses at first subculture and ex vitro somatic plants. Likewise, the transcripts of several proteins related with translation, oxidative stress response, and drought resilience were differentially expressed.
Open Access
Effect of thermal stress on tissue ultrastructure and metabolite profiles during initiation of Radiata pine somatic embryogenesis
(Frontiers Media, 2019) Castander Olarieta, Ander; Montalbán, Itziar A.; Oliveira, Eliana de Medeiros; Dell'Aversana, Emilia; D'Amelia, Luisa; Carillo, Petronia; Steiner, Neusa; Fraga, Hugo Pacheco de Freitas; Guerra, Miguel Pedro; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika
Climate change will inevitably lead to environmental variations, thus plant drought tolerance will be a determinant factor in the success of plantations and natural forestry recovery. Some metabolites, such as soluble carbohydrates and amino acids, have been described as being the key to both embryogenesis efficiency and abiotic stress response, contributing to phenotypic plasticity and the adaptive capacity of plants. For this reason, our main objectives were to evaluate if the temperature during embryonal mass initiation in radiata pine was critical to the success of somatic embryogenesis, to alter the morphological and ultrastructural organization of embryonal masses at cellular level and to modify the carbohydrate, protein, or amino acid contents. The first SE initiation experiments were carried out at moderate and high temperatures for periods of different durations prior to transfer to the control temperature of 23 degrees C. Cultures initiated at moderate temperatures (30 degrees C, 4 weeks and 40 degrees C, 4 days) showed significantly lower initiation and proliferation rates than those at the control temperature or pulse treatment at high temperatures (50 degrees C, 5 min). No significant differences were observed either for the percentage of embryogenic cell lines that produced somatic embryos, or for the number of somatic embryos per gram of embryonal mass. Based on the results from the first experiments, initiation was carried out at 40 degrees C 4 h; 50 degrees C, 30 min; and a pulse treatment of 60 degrees C, 5 min. No significant differences were found for the initiation or number of established lines or for the maturation of somatic embryos. However, large morphological differences were observed in the mature somatic embryos. At the same time, changes observed at cellular level suggested that strong heat shock treatments may trigger the programmed cell death of embryogenic cells, leading to an early loss of embryogenic potential, and the formation of supernumerary suspensor cells. Finally, among all the differences observed in the metabolic profile, it is worth highlighting the accumulation of tyrosine and isoleucine, both amino acids involved in the synthesis of abiotic stress response-related secondary metabolites.
Open Access
Small area variations in non-affective first-episode psychosis: the role of socioeconomic and environmental factors
(Springer, 2023) Gutiérrez, Gerardo; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Aranguren Conde, Lidia; Corrales, Asier; Gil Berrozpe, Gustavo José; Librero, Julián; Sánchez Torres, Ana María; Peralta Martín, Víctor; García de Jalón, Elena; Cuesta, Manuel J.; Martínez, Matilde; Otero, María; Azcárate, Leire; Pereda, Nahia; Monclús, Fernando; Moreno, Laura; Fernández, Alba; Ariz, Mari Cruz; Sabaté, Alba; Aquerreta, Ainhoa; Aguirre, Izaskun; Lizarbe, Tadea; Begué, María José; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2
Background: There is strong evidence supporting the association between environmental factors and increased risk of non-affective psychotic disorders. However, the use of sound statistical methods to account for spatial variations associated with environmental risk factors, such as urbanicity, migration, or deprivation, is scarce in the literature. Methods: We studied the geographical distribution of non-affective first-episode psychosis (NA-FEP) in a northern region of Spain (Navarra) during a 54-month period considering area-level socioeconomic indicators as putative explanatory variables. We used several Bayesian hierarchical Poisson models to smooth the standardized incidence ratios (SIR). We included neighborhood-level variables in the spatial models as covariates. Results: We identified 430 NA-FEP cases over a 54-month period for a population at risk of 365,213 inhabitants per year. NA-FEP incidence risks showed spatial patterning and a significant ecological association with the migrant population, unemployment, and consumption of anxiolytics and antidepressants. The high-risk areas corresponded mostly to peripheral urban regions; very few basic health sectors of rural areas emerged as high-risk areas in the spatial models with covariates. Discussion: Increased rates of unemployment, the migrant population, and consumption of anxiolytics and antidepressants showed significant associations linked to the spatial-geographic incidence of NA-FEP. These results may allow targeting geographical areas to provide preventive interventions that potentially address modifiable environmental risk factors for NA-FEP. Further investigation is needed to understand the mechanisms underlying the associations between environmental risk factors and the incidence of NA-FEP.
Open Access
Cytokinins are involved in drought tolerance of Pinus radiata plants originating from embryonal masses induced at high temperatures
(Oxford University Press, 2021) Castander Olarieta, Ander; Moncaleán, Paloma; Pereira, Catia; Pěnčík, A.; Petřík, I.; Pavlović, I.; Novák, Ondrej; Strnad,Miroslav; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Montalbán, Itziar A.; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika
Vegetative propagation through somatic embryogenesis is an effective method to produce elite varieties and can be applied as a tool to study the response of plants to different stresses. Several studies show that environmental changes during embryogenesis could determine future plant development. Moreover, we previously reported that physical and chemical conditions during somatic embryogenesis can determine the protein, hormone and metabolite profiles, as well as the micromorphological and ultrastructural organization of embryonal masses and somatic embryos. In this sense, phytohormones are key players throughout the somatic embryogenesis process as well as during numerous stress-adaptation responses. In this work, we first applied different higherature regimes (30 °C, 4 weeks; 40 °C, 4 days; 50 °C, 5 min) during induction of Pinus radiata D. Don somatic embryogenesis, together with control temperature (23 °C). Then, the somatic plants regenerated from initiated embryogenic cell lines and cultivated in greenhouse conditions were subjected to drought stress and control treatments to evaluate survival, growth and several physiological traits (relative water content, water potential, photosynthesis, stomatal conductance and transpiration). Based on those preliminary results, even more extreme higherature regimes were applied during induction (40 °C, 4 h; 50 °C, 30 min; 60 °C, 5 min) and the corresponding cytokinin profiles of initiated embryonal masses from different lines were analysed. The results showed that the temperature regime during induction had delayed negative effects on drought resilience of somatic plants as indicated by survival, photosynthetic activity and water- use efficiency. However, high temperatures for extended periods of time enhanced subsequent plant growth in well-watered conditions. Higherature regime treatments induced significant differences in the profile of total cytokinin bases, N6-isopentenyladenine, cis-zeatin riboside and trans-zeatin riboside. We concluded that phytohormones could be potential regulators of stress-response processes during initial steps of somatic embryogenesis and that they may have delayed implications in further developmental processes, determining the performance of the generated plants.
Open Access
Using mortality to predict incidence for rare and lethal cancers in very small areas
(VCH Publishers, 2022) Etxeberria Andueza, Jaione; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2
Incidence and mortality figures are needed to get a comprehensive overview of cancer burden. In many countries, cancer mortality figures are routinely recorded by statistical offices, whereas incidence depends on regional cancer registries. However, due to the complexity of updating cancer registries, incidence numbers become available 3 or 4 years later than mortality figures. It is, therefore, necessary to develop reliable procedures to predict cancer incidence at least until the period when mortality data are available. Most of the methods proposed in the literature are designed to predict total cancer (except nonmelanoma skin cancer) or major cancer sites. However, less frequent lethal cancers, such as brain cancer, are generally excluded from predictions because the scarce number of cases makes it difficult to use univariate models. Our proposal comes to fill this gap and consists of modeling jointly incidence and mortality data using spatio-temporal models with spatial and age shared components. This approach allows for predicting lethal cancers improving the performance of individual models when data are scarce by taking advantage of the high correlation between incidence and mortality. A fully Bayesian approach based on integrated nested Laplace approximations is considered for model fitting and inference. A validation process is also conducted to assess the performance of alternative models. We use the new proposals to predict brain cancer incidence rates by gender and age groups in the health units of Navarre and Basque Country (Spain) during the period 2005-2008.
Open Access
Space-time interactions in bayesian disease mapping with recent tools: making things easier for practitioners
(Edward Arnold, 2022) Urdangarin Iztueta, Arantxa; Ugarte Martínez, María Dolores; Goicoa Mangado, Tomás; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística, Informática y Matemáticas
Spatio-temporal disease mapping studies the distribution of mortality or incidence risks in space and its evolution in time, and it usually relies on fitting hierarchical Poisson mixed models. These models are complex for practitioners as they generally require adding constraints to correctly identify and interpret the different model terms. However, including constraints may not be straightforward in some recent software packages. This paper focuses on NIMBLE, a library of algorithms that contains among others a configurable system for Markov chain Monte Carlo (MCMC) algorithms. In particular, we show how to fit different spatio-temporal disease mapping models with NIMBLE making emphasis on how to include sum-to-zero constraints to solve identifiability issues when including spatio-temporal interactions. Breast cancer mortality data in Spain during the period 1990-2010 is used for illustration purposes. A simulation study is also conducted to compare NIMBLE with R-INLA in terms of parameter estimates and relative risk estimation. The results are very similar but differences are observed in terms of computing time.
Open Access
Alleviating confounding in spatio-temporal areal models with an application on crimes against women in India
(SAGE Publications, 2021) Adin Urtasun, Aritz; Goicoa Mangado, Tomás; Hodges, James S.; Schnell, Patrick M.; Ugarte Martínez, María Dolores; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística, Informática y Matemáticas
Assessing associations between a response of interest and a set of covariates in spatial areal models is the leitmotiv of ecological regression. However, the presence of spatially correlated random effects can mask or even bias estimates of such associations due to confounding effects if they are not carefully handled. Though potentially harmful, confounding issues have often been ignored in practice leading to wrong conclusions about the underlying associations between the response and the covariates. In spatio-temporal areal models, the temporal dimension may emerge as a new source of confounding, and the problem may be even worse. In this work, we propose two approaches to deal with confounding of fixed effects by spatial and temporal random effects, while obtaining good model predictions. In particular, restricted regression and an apparently—though in fact not—equivalent procedure using constraints are proposed within both fully Bayes and empirical Bayes approaches. The methods are compared in terms of fixed-effect estimates and model selection criteria. The techniques are used to assess the association between dowry deaths and certain socio-demographic covariates in the districts of Uttar Pradesh, India.
Open Access
Evaluating recent methods to overcome spatial confounding
(Springer, 2022) Urdangarin Iztueta, Arantxa; Goicoa Mangado, Tomás; Ugarte Martínez, María Dolores; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2; Universidad Pública de Navarra / Nafarroako Unibertsitate Publikoa
The concept of spatial confounding is closely connected to spatial regression, although no general definition has been established. A generally accepted idea of spatial confounding in spatial regression models is the change in fixed effects estimates that may occur when spatially correlated random effects collinear with the covariate are included in the model. Different methods have been proposed to alleviate spatial confounding in spatial linear regression models, but it is not clear if they provide correct fixed effects estimates. In this article, we consider some of those proposals to alleviate spatial confounding such as restricted regression, the spatial+ model, and transformed Gaussian Markov random fields. The objective is to determine which one provides the best estimates of the fixed effects. Dowry death data in Uttar Pradesh in 2001, stomach cancer incidence data in Slovenia in the period 1995–2001 and lip cancer incidence data in Scotland between the years 1975–1980 are analyzed. Several simulation studies are conducted to evaluate the performance of the methods in different scenarios of spatial confounding. Results reflect that the spatial+ method seems to provide fixed effects estimates closest to the true value although standard errors could be inflated
Open Access
Temporal evolution of brain cancer incidence in the municipalities of Navarre and the Basque Country, Spain
(BioMed Central, 2015) Ugarte Martínez, María Dolores; Adin Urtasun, Aritz; Goicoa Mangado, Tomás; Casado, Itziar; Ardanaz, Eva; Larrañaga, Nerea; Estatistika eta Ikerketa Operatiboa; Institute for Advanced Materials and Mathematics - INAMAT2; Estadística e Investigación Operativa; Gobierno de Navarra / Nafarroako Gobernua: proyecto 113 Res. 2186/2014
Background: Brain cancer incidence rates in Spain are below the European’s average. However, there are two regions in the north of the country, Navarre and the Basque Country, ranked among the European regions with the highest incidence rates for both males and females. Our objective here was two-fold. Firstly, to describe the temporal evolution of the geographical pattern of brain cancer incidence in Navarre and the Basque Country, and secondly, to look for specific high risk areas (municipalities) within these two regions in the study period (1986–2008). Methods: A mixed Poisson model with two levels of spatial effects is used. The model also included two levels of spatial effects (municipalities and local health areas). Model fitting was carried out using penalized quasi-likelihood. High risk regions were detected using upper one-sided confidence intervals. Results: Results revealed a group of high risk areas surrounding Pamplona, the capital city of Navarre, and a few municipalities with significant high risks in the northern part of the region, specifically in the border between Navarre and the Basque Country (Gipuzkoa). The global temporal trend was found to be increasing. Differences were also observed among specific risk evolutions in certain municipalities. Conclusions: Brain cancer incidence in Navarre and the Basque Country (Spain) is still increasing with time. The number of high risk areas within those two regions is also increasing. Our study highlights the need of continuous surveillance of this cancer in the areas of high risk. However, due to the low percentage of cases explained by the known risk factors, primary prevention should be applied as a general recommendation in these populations.
Open Access
La necesidad de un manifiesto a favor de la alfabetización estadística: editorial
(Sociedad Estadística e Investigación Operativa (SEIO), 2025-03-27) Casals, Martí ; Daunis i Estadella, Pepus; Galé, Carmen; Goicoa Mangado, Tomás; Patino-Alonso, Carmen; Estadística, Informática y Matemáticas; Estatistika, Informatika eta Matematika; Institute for Advanced Materials and Mathematics - INAMAT2
Imagina leer el siguiente titular en un periódico: “Las personas que consumen café tienen un 50% menos de probabilidad de desarrollar ciertas enfermedades”. A partir de esta lectura, decides aumentar tu consumo diario de café. Sin embargo, antes de tomar esa decisión hay que conocer cómo se ha llegado a dicha conclusión: cuál es el tamaño de la muestra, el diseño del estudio, sobre qué población se aplica, el método de recolección de datos, y valorar si es posible establecer relaciones causales. Este ejemplo ilustra como la falta de conocimiento sobre el procedimiento puede comprometer la validez del estudio y se puede traducir en una interpretación incorrecta o unos resultados sesgados. Una comunicación deficiente puede llevar decisiones mal fundamentadas, incluso en áreas críticas como la salud y el bienestar (Spiegelhalter, 2019).