Microarrays as a functional approach to the transcriptome

Knowing a cell’s transcriptome is a fundamental requisite in order to analyze its response to the environment. Microarrays have supposed a revolution on this field as they are able to yield an overview of gene expression at any environmental condition on a genome-wide scale. This technique consists in the hybridisation of a nucleic acid sample, previously marked, with a probe (which might be made up of cDNA, oligonucleotides or PCR products) anchored to a solid surface (made of glass, plastic, silicon...) giving as a result a dot grid which reveals, after image analysis, which genes are being expressed. Nevertheless, this only can be achieved if information on the species genome has been generated. Different kinds of expression microarrays exist attending to the probe’s nature and the method used in its synthesis. In this poster two of these will be treated: Spotted Microarrays, for which the probe is synthesised prior to its fixation to the array and allow the analysis of two targets simultaneously. They can be easily customized, but lack high reproducibility and sensitivity. Oligonucleotide Microarrays, which are characterized by the direct printing of the probe on the array. In this case the probes consist on, invariably, oligonucleotides that are complementary to a small fraction of the gene it is representing at the microarray. Their application is somewhat restricted. This fact, however, makes them more reproducible. Currently, the approach towards the transcriptome studies from the Next Generation Sequencing technologies offers a large volume of information in a short amount of time needing less previous information on the target organism than that needed by microarrays, but their expensive price limits their use. The versatility of the latter, together with their reduced costs in comparison to other techniques, makes them an interesting resource in applications that may need less complexity

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

Molecular characterization of MicroRNA-silenced TNL-1 (MIST1) and its role in plant defense

miRNAs are sequence-dependent negative regulators of gene expression involved in many relevant plant processes, including immunity. Activation of defence genes can negatively impact plant fitness, and thus needs to be fine-tuned. miRNA-mediated regulation of gene expression is mediated by the activity of DCL proteins that induce cleavage of target transcripts. We have described miR825-5p as involved in the regulation of immunity. This miRNA specifically targets R genes of the TNL family. We have characterized the regulatory system formed by miRNA825-5p and its main target MIST1. This miRNA only triggers the RDR6-DCL4-dependent production of phasiRNAs from MIST1. MIST1 is the NLR gene from which the most phasiRNAs are produced in Arabidopsis. We reported that pri-miR825 is down-regulated after PAMP-perception and demonstrated that plants with altered levels of miR825-5p exhibit altered PTI-associated phenotypes. In addition, MIST1 has been described to be regulated by other mechanisms like nonsense mediated decay or polyubiquitination. We have characterized the expression pattern of both MIR825 and MIST1 and are currently studying the putative molecular role of MIST1 in defence apart from its demonstrated role as a miRNA825-5p-linked regulatory hub for TNLs regulation in Arabidopsis thaliana.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

The When and Where: How development modulates immunity through a miRNA-NLR-phasiRNA network

Plants possess a battery of dedicated intracellular immune receptors known as nucleotide-binding leucine-rich repeat proteins (NLRs) involved in recognition of pathogen-derived effectors and activation of effector-triggered immunity (ETI). In a recent work, we report a two-tiered regulatory network in Arabidopsis mediated by a microRNA (miR825-5p) and a wave of secondary NLR-derived phased small RNAs (phasi-NLRs) involved in silencing dozens of NLR genes encoding Toll/interleukin-1 NLRs (TNLs). In our model, targeting of MIST1 (microRNA-silenced TNL1) transcripts by miR825-5p, triggers the generation of phasi-NLRs that subsequently silence a wide network of TNL-encoding genes and reinforce the silencing of MIST1. Current knowledge regarding how these networks are modulated contribute to immunity during different developmental stages is scarce. Through generation of GUS-based A. thaliana reporter lines we have characterized the expression pattern of both MIR825 and MIST1 genes and the domain activity of miR825-5p. A comprehensive analysis of RNA and small RNA-seq datasets, unravelled a hitherto unknown connection between miR825-5p/phasi-NLR mediated regulation of NLRs and plant development. Further analysis supports the notion that the action of this regulatory mechanism is restricted to control NLR expression in leaves. We are working to understand how the changes on miRNA/phasi-NLR levels during developmental stages modulate the immune response and the biological impact of this developmental-dependent regulation on plant health. Our results point to a developmentally regulated sRNA-based control of NLR expression in Arabidopsis and shed light on how levels of these regulatory molecules (miRNAs and phasi-NLRs) are modulated during development or in an organ specific manner to fine-tune NLR expression.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Regulación de genes de resistencia de la familia TIR-NBS-LRR mediada por miRNA/phasiRNA durante la interacción con P. syringae

Durante un estrés biótico, las plantas modulan la expresión de una batería de genes involucrados en la respuesta de defensa, proceso donde recientemente se ha determinado el papel esencial que desempeña el silenciamiento génico. El silenciamiento génico es un mecanismo de regulación de la expresión génica, donde destacan como principales moléculas efectoras los pequeños RNAs (sRNAs). En plantas, estos sRNAs, son clasificados en pequeños RNAs interferentes (siRNAs) o microRNAs (miRNAs), presentando tamaños similares (20-24 nt) pero difiriendo en su biogénesis y modo de acción. Los miRNAs son pequeños RNAs de cadena sencilla que actúan regulando negativamente la expresión de genes, mediante su unión al complejo RISC (Rna Induced Silencing Complex) y en una forma dependiente de secuencia. En nuestro laboratorio, mediante el análisis de datos transcriptómicos, y el uso de herramientas bioinformáticas, identificamos un miRNA* de 22 nt como potencial regulador de la expresión de genes de resistencia (“R”) del tipo TIR-NBS-LRR. Posteriormente hemos validado dicha regulación y caracterizado los patrones de expresión tanto del Pri-miRNA como de un gen “R” regulado por este, en diferentes tejidos y estadios del desarrollo, así como durante la interacción con P. syringae. Por otro lado, hemos generado plantas transgénicas que presentan niveles alterados del miRNA* (incremento y reducción) y hemos observado que muestran fenotipos alterados de PTI y una mayor/menor colonización de P. syringae. Finalmente hemos identificado la producción de sRNAs (phasiRNAs) a partir del gen de resistencia, en una forma dependiente de miRNA*-RDR6-DCL4, pudiendo estos sRNAs secundarios regular otros transcritos de la misma familia de genes de resistencia.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Effect of an Intensive Weight-Loss Lifestyle Intervention on Kidney Function: A Randomized Controlled Trial

Introduction: Large randomized trials testing the effect of a multifactorial weight-loss lifestyle intervention including Mediterranean diet (MedDiet) on renal function are lacking. Here, we evaluated the 1-year efficacy of an intensive weight-loss intervention with an energy-reduced MedDiet (erMedDiet) plus increased physical activity (PA) on renal function. Methods: Randomized controlled "PREvención con DIeta MEDiterránea-Plus"(PREDIMED-Plus) trial is conducted in 23 Spanish centers comprising 208 primary care clinics. Overweight/obese (n = 6,719) adults aged 55-75 years with metabolic syndrome were randomly assigned (1:1) to an intensive weight-loss lifestyle intervention with an erMedDiet, PA promotion, and behavioral support (intervention) or usual-care advice to adhere to an energy-unrestricted MedDiet (control) between September 2013 and December 2016. The primary outcome was 1-year change in estimated glomerular filtration rate (EGFR). Secondary outcomes were changes in urine albumin-to-creatinine ratio (UACR), incidence of moderately/severely impaired EGFR (<60 mL/min/1.73 m2) and micro-to macroalbuminuria (UACR ≥30 mg/g), and reversion of moderately (45 to <60 mL/min/1.73 m2) to mildly impaired GFR (60 to <90 mL/min/1.73 m2) or micro-to macroalbuminuria. Results: After 1 year, EGFR declined by 0.66 and 1.25 mL/min/1.73 m2 in the intervention and control groups, respectively (mean difference, 0.58 mL/min/1.73 m2; 95% CI: 0.15-1.02). There were no between-group differences in mean UACR or micro-to macroalbuminuria changes. Moderately/severely impaired EGFR incidence and reversion of moderately to mildly impaired GFR were 40% lower (HR 0.60; 0.44-0.82) and 92% higher (HR 1.92; 1.35-2.73), respectively, in the intervention group. Conclusions: The PREDIMED-Plus lifestyle intervention approach may preserve renal function and delay CKD progression in overweight/obese adults.This work was supported by the official Spanish Institutions for funding scientific biomedical research, CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN) and Instituto de Salud Carlos III (ISCIII), through the Fondo de Investigación para la Salud (FIS), which is cofunded by the European Regional Development Fund (5 coordinated FIS projects leaded by J.S.-S and J.V., including the following projects: PI13/00673, PI13/00492, PI13/00272, PI13/01123, PI13/00462, PI13/00233, PI13/02184, PI13/00728, PI13/01090, PI13/01056, PI14/01722, PI14/00636, PI14/00618, PI14/00696, PI14/01206, PI14/01919, PI14/00853, PI14/01374, PI14/00972, PI14/00728, PI14/01471, PI16/00473, PI16/00662, PI16/01873, PI16/01094, PI16/00501, PI16/00533, PI16/00381, PI16/00366, PI16/01522, PI16/01120, PI17/00764, PI17/01183, PI17/00855, PI17/01347, PI17/00525, PI17/01827, PI17/00532, PI17/00215, PI17/01441, PI17/00508, PI17/01732, PI17/00926; PI19/00957, PI19/00386, PI19/00309, PI19/01032, PI19/00576, PI19/00017, PI19/01226, PI19/00781, PI19/01560, and PI19/01332); the Especial Action Project entitled Implementación y evaluación de una intervención intensiva sobre la actividad física Cohorte PREDIMED-Plus grant to J.S.-S.; the European Research Council (Advanced Research Grant 2014–2019; agreement #340918) granted to M.Á.M.-G.; the Recercaixa (No. 2013ACUP00194) grant to J.S.-S.; grants from the Consejería de Salud de la Junta de Andalucía (PI0458/2013, PS0358/2016, and PI0137/2018); the PROMETEO/2017/017 grant from the Generalitat Valenciana; the SEMERGEN grant; funds from the European Regional Development Fund (CB06/03); International Nut & Dried Fruit Council – FESNAD (Long-term effects of an energyrestricted Mediterranean diet on mortality and cardiovascular disease 2014–2015, No. 201302) (PI: M.Á.M.-G.); the AstraZeneca Young Investigators Award in Category of Obesity and T2D 2017 (PI: D.R.); grant of support to research groups No. 35/2011 (Balearic Islands Gov.; FEDER funds) (J.A.T. and C.B.); the JR17/00022 (ISCIII) grant to O.C.; the Boosting young talent call grant program for the development of IISPV research projects 2019–2021 (Ref.: 2019/IISPV/03 grant to A.D.-L.); the Societat Catalana d’Endocrinologia i Nutrició (SCEN) Clinical-Research Grant 2019 (IPs: J.S.-S. and A.D.-L.). Collaborative Nutrition and/or Obesity Project for Young Researchers 2019 supported by CIBEROBN entitled Lifestyle Interventions and Chronic Kidney Disease: Inflammation, Oxidative Stress and Metabolomic Profile (LIKIDI study) grant to A.D.-L

re-habitar El Carmen : Un proyecto sobre patrimonio contemporáneo

El proyecto _re-HABITAR suponía para el propio proceder de la institución un avance más allá del reconocimiento, registro, inventario o protección patrimonial de la arquitectura del siglo XX y del Movimiento Moderno para posicionarse en la acción preventiva y conservativa de ese legado contemporáneo. Para ello, la praxis patrimonial se aferraba a un modelo: el de la vivienda social en España en la segunda mitad del siglo XX; a un caso concreto: el de la barriada de Nuestra Señora del Carmen (Recasens Méndez-Queipo de Llano, 1958); y a un requisito fundamental: analizar un objeto vivo y en uso, aún con la presencia de quienes lo vivieron y usaron desde su origen

IKZF1plus is a frequent biomarker of adverse prognosis in Mexican pediatric patients with B-acute lymphoblastic leukemia

BackgroundRecurrent genetic alterations contributing to leukemogenesis have been identified in pediatric B-cell Acute Lymphoblastic Leukemia (B-ALL), and some are useful for refining classification, prognosis, and treatment selection. IKZF1plus is a complex biomarker associated with a poor prognosis. It is characterized by IKZF1 deletion coexisting with PAX5, CDKN2A/2B, or PAR1 region deletions. The mutational spectrum and clinical impact of these alterations have scarcely been explored in Mexican pediatric patients with B-ALL. Here, we report the frequency of the IKZF1plus profile and the mutational spectrum of IKZF1, PAX5, CDKN2A/2B, and ERG genes and evaluate their impact on overall survival (OS) in a group of patients with B-ALL.MethodsA total of 206 pediatric patients with de novo B-ALL were included. DNA was obtained from bone marrow samples at diagnosis before treatment initiation. A custom-designed next-generation sequencing panel was used for mutational analysis. Kaplan-Meier analysis was used for OS estimation.ResultsWe identified the IKZF1plus profile in 21.8% of patients, which was higher than that previously reported in other studies. A significantly older age (p=0.04), a trend toward high-risk stratification (p=0.06), and a decrease in 5-year Overall Survival (OS) (p=0.009) were observed, although heterogeneous treatment protocols in our cohort would have impacted OS. A mutation frequency higher than that reported was found for IKZF1 (35.9%) and CDKN2A/2B (35.9%) but lower for PAX5 (26.6%). IKZF1MUT group was older at diagnosis (p=0.0002), and most of them were classified as high-risk (73.8%, p=0.02), while patients with CDKN2A/2BMUT had a higher leukocyte count (p=0.01) and a tendency toward a higher percentage of blasts (98.6%, &gt;50% blasts, p=0.05) than the non-mutated patients. A decrease in OS was found in IKZF1MUT and CDKN2A/2BMUT patients, but the significance was lost after IKZF1plus was removed.DiscussionOur findings demonstrated that Mexican patients with B-ALL have a higher prevalence of genetic markers associated with poor outcomes. Incorporating genomic methodologies into the diagnostic process, a significant unmet need in low- and mid-income countries, will allow a comprehensive identification of relevant alterations, improving disease classification, treatment selection, and the general outcome

Atlas de las praderas marinas de España

Knowledge of the distribution and extent of seagrass habitats is currently the basis of management and conservation policies of the coastal zones in most European countries. This basic information is being requested through European directives for the establishment of monitoring programmes and the implementation of specific actions to preserve the marine environment. In addition, this information is crucial for the quantification of the ecological importance usually attributed to seagrass habitats due to, for instance, their involvement in biogeochemical cycles, marine biodiversity and quality of coastal waters or global carbon budgets. The seagrass atlas of Spain represents a huge collective effort performed by 84 authors across 30 Spanish institutions largely involved in the scientific research, management and conservation of seagrass habitats during the last three decades. They have contributed to the availability of the most precise and realistic seagrass maps for each region of the Spanish coast which have been integrated in a GIS to obtain the distribution and area of each seagrass species. Most of this information has independently originated at a regional level by regional governments, universities and public research organisations, which explain the elevated heterogeneity in criteria, scales, methods and objectives of the available information. On this basis, seagrass habitats in Spain occupy a total surface of 1,541,63 km2, 89% of which is concentrated in the Mediterranean regions; the rest is present in sheltered estuarine areas of the Atlantic peninsular regions and in the open coastal waters of the Canary Islands, which represents 50% of the Atlantic meadows. Of this surface, 71.5% corresponds to Posidonia oceanica, 19.5% to Cymodocea nodosa, 3.1% to Zostera noltii (=Nanozostera noltii), 0.3% to Zostera marina and 1.2% to Halophila decipiens. Species distribution maps are presented (including Ruppia spp.), together with maps of the main impacts and pressures that has affected or threatened their conservation status, as well as the management tools established for their protection and conservation. Despite this considerable effort, and the fact that Spain has mapped wide shelf areas, the information available is still incomplete and with weak precision in many regions, which will require an investment of major effort in the near future to complete the whole picture and respond to demands of EU directives

Implementación de una Gymkhana molecular.

El gran desarrollo de las técnicas de biología molecular de alto rendimiento y la consiguiente generación de datos de secuencias de ADN requiere la capacitación del alumnado, de forma que la asignatura de Bioinformática o sus contenidos aparecen en los en los programas docentes de Grados en carreras de Biociencias. La importancia de esta disciplina científica queda patente en el enorme número de publicaciones especializadas, herramientas y bases de datos disponibles. En la Universidad de Málaga hemos implementado un método de aprendizaje de análisis de secuencias basado en juegos que hemos adaptado a estudiantes del Grado en Biología y a alumnado de enseñanza media. Su principal objetivo es introducir a los estudiantes en las bases de datos moleculares y los sistemas de búsqueda de información sobre genes, proteínas y filogenia molecular. El alumnado realizan un "muestreo de secuencias" al aire libre ocultas en un código QR en formato de gymkhana, que posteriormente analizan en el aula de informática. Este análisis bioinformático comprende la identificación de las secuencias recogidas comparándolas con una base de datos específica mediante análisis de comparación de secuencias por BLAST y la búsqueda de secuencias homólogas en un sistema de bases de datos de secuencias, así como el análisis de las relaciones filogenéticas a partir de las secuencias identificadas mediante el programa Seaview. El contenido didáctico se ha adaptado a la asignatura de Informática del Grado en Biología (Gymkhana molecular) y al alumnado de enseñanza media (Safari molecular).Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech