Caracterización molecular de la biodiversidad

El denominado Código de Barras de la Vida (Barcode of Life) es un sistema de identificación de especies por medio del análisis de secuencias específicas de DNA obtenidas a partir de una muestra de tejido de cualquier organismo eucariota. Se basa en la amplificación y secuenciación de un fragmento de DNA que, a modo de código de barras, permite la identificación de una especie en base a su comparación con bases de datos de secuencias moleculares, Barcode of Life Database (BOLD), mediante herramientas bioinformáticas. La secuencia de los genes que se seleccionan debe ser poco variable entre individuos de la misma especie pero diferir mucho entre éstas. En animales se analiza el patrón de variación de nucleótidos en la región de 648 pb del gen mitocondrial de la enzima citocromo c oxidasa I (COI), mientras que en plantas aporta más información el análisis de la secuencia de dos regiones génicas del DNA cloroplastídico: matK y rbcL. Estos “códigos de barras genéticos” han permitido crear los denominados Barcode Index Numbers (BINs) que identifican secuencias de DNA similares con los grupos definidos por los taxónomos como especies. Este método es una herramienta complementaria a la identificación taxonómica tradicional que permite la identificación de especies polimórficas o crípticas y permite describir la biodiversidad de un enclave, bien porque parte de sus especies aún no hayan sido identificadas formalmente o porque se encuentran en un estadio del desarrollo que impide su identificación exacta. Es interesante también su utilización en la conservación, para el control del tráfico ilegal de huevos o semillas. En la Universidad de Málaga pusimos a punto este sistema para la identificación de especies de moluscos del litoral y pretendemos implantarlo en el Jardín Botánico de dicha universidad.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Thymine starvation causes abortive initiation of chromosome replication critical for cell death in Escherichia coli

Presentado en: XXXVI Congreso SEBBM (Sociedad Española de Bioquímica y Biología Molecular), Madrid, 4-6 septiembre, 2013Thymineless death (TLD), a phenomenon in which thymine auxotrophy becomes lethal when cells are starved for thymine, can be prevented by rifampicin addition. In this work, we have obtained evidence indicating that among the effects of RNA polymerase inhibition by rifampicin, the inhibition of chromosomal replication initiation is the process responsible for TLD suppression. We show that diminishing, abolishing or increasing the transcription level around oriC alleviates TLD by limiting the chromosomal initiation capacity (ChIC) generated under thymine starvation. TLD suppression was eliminated by DnaA inactivation or the deletion in the left half of the replication origin or deletion of the DnaA-boxes located in the right half of the oriC region. In accordance with these data, two-dimensional DNA electrophoresis gels showed an accumulation of simple-Y and bubble arc replication intermediates, as well as recombination structures at the oriC region during thymine starvation. None of these structures were observed under genetic or physiological conditions that suppress TLD. These results demonstrate that abortive initiations of chromosome replication occur under thymine starvation, supporting the idea that these events are a critical target for the lethal damage caused by thymine starvation and that results in TLD.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

How cyclical do cyclically-adjusted balances remain? An EU study

Observed budget balances are an imperfect indicator of the fiscal policy stance, because fluctuations in economic activity induce automatic changes in the balance, hence the use of cyclically-adjusted balances (CAB). However, this paper shows that CABs (as measured through one of the two methods currently used by the Commission) tend to be systematically overestimated during downturns and underestimated during expansions. The dominant source of this distortion arises from the filtering of revenues deemed to be cyclical, possibly signalling a problem with the computation of elasticities. The effect of the items which are assumed not to move with the cycle is non significant, but this overall result conceals offseting effects: public investment turns to be significantly procyclical and interest payments and transfers to firms are countercyclical.Structural balances, output gap

Analysis of hypervariable DNA sequences by NGS technologies: QuasiFlow

The development of Next Generation Sequencing (NGS) technologies has allowed deep characterization of highly variable sequences such as viral or mitochondrial genomes. With respect to RNA and ssDNA viruses, their low replication fidelity generates viral populations consisting of complex mutant spectra termed viral quasispecies. Their study is of special interest as they can be considered a phenotypic reservoir1. Similarly, heteroplasmy of human mitochondrial genomes, in which different sequences are found within a single individual, might have important clinical consequences. For the analysis of the mutant spectrum of such hypervariable sequences from NGS data, we have developed QuasiFlow, a workflow designed in AutoFlow2 that uses Illumina reads. QuasiFlow provides information about DNA variability, such as SNPs, indels and recombination events (Figure 1). Furthermore, it allows haplotype reconstruction of viral quasispecies and characterization of its diversity through normalized Shannon index, nucleotide diversity and mutation networks. Quasiflow performs also a comparative study among samples, based on correlation, ANOVA and PCA analysis, in order to determine which parameters are affected by the experiment and how the samples behave according to their biological origin. In this work, we have applied QuasiFlow to analyze the population structure of the begomovirus Tomato yellow leaf curl virus (TYLCV) infectious clone inoculated in Arabidopsis thaliana plants, using HiSeq or MiSeq reads. Their analysis allowed detection of minor quasispecies variants with a frequency of 10-4 to 10-5 and reconstructed the haplotypes present in the sample. In addition, QuasiFlow was used to discover variants and recombinants in mixed infections of tomato plants. These results show the fast generation of recombinant genomes in geminivirus mixed infections and demonstrate the potential of QuasiFlow for the analysis of mutant spectra using Illumina MiSeq sequencing data. We have extended the use of QuasiFlow to the analysis of highly variable sequences such as the mitochondrial DNA. For that, we have analyzed DNA Illumina Miseq reads from 47 human mitochondrial samples from different cell lines obtained from the NCBI SRA database. Quasiflow generated automatically SNPs, SNP frequencies, indels and analyzed up to 23 variables using PCA analysis and performed an hierarchical clustering of the samples. Our analysis was able to detect pathological variants presented in a frequency lower than 1%.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. This research was funded by Junta de Andalucía and EU through the ERDF 2014-2020, Projects P10-CVI-6075 to M. G.C. and P10-CVI-6561 to A.G-P

VII Encuentros con la Ciencia

La séptima edición de esta iniciativa aborda la teoría de la evolución y su implicación en el mundo actual a través de un recorrido por la vida y la obra de Charles Darwin

Efficacy of the tissue regenerating agent (RGTA) in the treatment of neurotrophic corneal ulcers and persistent epithelial defects

Purpose : To report the results obtained in a series of 58 eyes with chronic corneal ulcers and persistent epithelial defects resistant to conventional therapy and treated with 0.01% poly-carboxymethylglucose sulfate (RGTA, Cacicol®). Methods : A prospective study was made of 58 eyes of patients with corneal ulcers and persistent epithelial lesions secondary to neurotrophic disorders, caustic damage, ulcerated metaherpetic lesions, Stevens-Johnson syndrome, peripheral ulcerative keratitis and severe dry eye, among other conditions. The ulcers were essentially chronic and slow-evolving, with mean vertical and horizontal diameters of 2.4 and 2.7 mm, respectively (range 1-5.5 mm). All patients had been previously treated with classical tear substitutes, and some had also received blood products, topical cyclosporine, corticosteroids, amniotic membrane coverings, therapeutic contact lenses and/or a vitamin-based eye ointment. The patients received an initial dose of one drop in the morning every 48 hours during 10 days. After evaluation of the effects of treatment, new dosing schemes were prescribed for those patients who had improved their clinical condition though without complete resolution of the disease. Results : Important variation was observed in the time to recovery of corneal integrity, ranging from a few days to some weeks, depending on the severity and etiology of the case. Full healing was recorded in 50 patients. The patients with large neurotrophic ulcers showed improvement of the lesions, with a decrease in lesion size after 15 days of treatment. Eight eyes did not achieve complete healing. In the case of severe ulceration and when a positive effect was observed after one month, treatment was continued with spacing of the applications until complete healing was achieved. All patients reported subjective improvement. The drug showed immediate efficacy in 11 eyes with epithelialisation disorders following PRK or trauma, with recovery of tissue integrity after the first treatment period. Conclusions : The tissue regenerating agent (RGTA, Cacicol®) is an interesting and effective topical adjuvant product for the treatment of severe and chronic corneal ulcers resistant to conventional treatment. Its efficacy remains to be confirmed in the context of double-blind, randomised clinical trials

Analysis of viral quasispecies by NGS technologies: quasiflow

We have developed QuasiFlow, a workflow designed in AutoFlow that takes advantage of NGS technologies to reconstruct quasispecies based in Illumina reads. QuasiFlow characterises and computes several key parameters, such as recombination events, SNPs, transitions, transversions, indels, quasispecies reconstruction, normalized Shannon index, nucleotide diversity and mutation networks. Moreover, it performs a comparative study of the samples comprising correlation, ANOVA and PCA analyses of the previously obtained virus population parameters. Using QuasiFlow we have analysed Illumina MiSeq reads from DNA samples obtained in mixed infections of ssDNA begomovirus in tomato plants amplified by rolling circle amplification. Further, we have extended the use of QuasiFlow to the analysis of the highly variable mitochondrial DNA. For that, we have used DNA Illumina MiSeq reads from 47 human mitochondrial samples from different cell lines obtained from the NCBI SRA databaseUniversidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Quantifying the effect of Tmax extreme events on local adaptation to climate change of maize crop in Andalusia for the 21st century

Extreme events of Tmax can threaten maize production on Andalusia (Ruiz-Ramos et al., 2011). The objective of this work is to attempt a quantification of the effects of Tmax extreme events on the previously identified (Gabaldón et al., 2013) local adaptation strategies to climate change of irrigated maize crop in Andalusia for the first half of the 21st century

Experiencias de una red docente: aprendizaje significativo en ciencias y tecnología mediante gamificación

En el aprendizaje de los contenidos de materias científico-técnicas es especialmente importante la motivación del estudiante mediante referencias y ejercicios de casos reales donde se trata de reducir la memorización de muchos conceptos reforzando el aprendizaje significativo. De este modo, el método de aprendizaje significativo basado en gamificación se lleva a cabo mediante el uso de técnicas, elementos y dinámicas propias de los juegos y el ocio en actividades docentes con el fin de potenciar la motivación, así como de reforzar la conducta para solucionar problemas, mejorar la productividad, obtener objetivos, activar el aprendizaje y evaluar a los alumnos. En esta comunicación se explicará el proceso de puesta en común, diseño, desarrollo y evaluación de las experiencias de una Red Docente que ha empleado la gamificación como metodología para conseguir el aprendizaje significativo de los alumnos. La acción se ha llevado a cabo en las asignaturas de segundo cuatrimestre en los Estudios de Grado de Química, Biología, Ciencias Ambientales, Ingeniería de la salud, Bioquímica e Ingeniería de Telecomunicación de la Universidad de Málaga que imparten los profesores que componen la Red Docente. Para llevarla a cabo los profesores han conseguido una ayuda para fomentar la creación e implantación de redes docentes de excelencia gracias al Plan Propio Integral de Docencia de la Universidad de Málaga.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech