Empleabilidad de los primeros egresados y egresadas del máster de Biotecnología Sanitaria de la UPO

Motivación: Una vez terminada la primera edición del máster de Biotecnología Sanitaria, quisimos evaluar la empleabilidad de los estudiantes recién egresados.Métodos: Para ello, se preparó una ficha con varias preguntas muy concretas en torno a la actual actividad profesional de los estudiantes y su posible relación con la realización del máster. Las fichas fueron rellenadas por todos los estudiante y posteriormente se analizaron los resultados de forma cuantitativa, pero también se revisaron las respuestas personales de cada estudiante.Resultados: El resultado final destaca un alto nivel de empleabilidad entre los estudiantes de la primera promoción del máster.Conclusiones: Este resultado creemos que está especialmente ligado al 2º curso del máster, en el que los estudiantes suelen realizar su trabajo fin de máster en una empresa o laboratorio de investigación

Implementación y puesta a punto de un algoritmo de búsqueda automatizada de secuencias homólogas

Motivación: El término “homología” hace referencia al origen evolutivo común entre dos proteínas que han divergido, presentando características comunes a nivel de secuencia y estructura (Fitch, 1970). Generalmente, la búsqueda de proteínas homólogas a una proteína de interés se realiza de forma manual, mediante el uso del algoritmo PSI-BLAST, ya sea en un ordenador propio o en un portal web como el del NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi). La búsqueda de homólogos de forma manual es tediosa y requiere de mucho tiempo y conocimientos básicos de bioinformática. Una alternativa para la búsqueda de homólogos es el uso de algoritmos de acceso abierto disponibles en la web. Adicionalmente, existen muchas bases de datos que recogen conjuntos de proteínas homólogas previamente formados. El problema principal, tanto de los algoritmos como de las bases de datos es su dificultad de uso, ya que por lo general ninguno de estos recursos está destinado ni preparado para investigadores de laboratorio. Resultados: Se ha desarrollado una herramienta escrita en lenguaje de programación Perl para la búsqueda automatizada de proteínas homólogas a una secuencia inicial de interés. El funcionamiento del algoritmo se ha probado con distintos conjuntos de secuencias, a partir de cuyos resultados se han optimizado los parámetros que rigen su funcionamiento. El algoritmo desarrollado es eficiente (sensible, específico y rápido), exhaustivo a la hora de buscar secuencias homólogas y admite el uso de bases de datos del propio usuario. La modificación de los parámetros por defecto permite que el usuario pueda primar un mejor dato de sensibilidad en detrimento del valor de especificidad, o viceversa. Adicionalmente, se ha diseñado una aplicación web de libre acceso para cualquier usuario (http://www.bioinfocabd.upo.es/cgi-bin/orthoFinder/ortholog2.cgi) para el uso del algoritmo. Sólo es necesario subir un archivo con la secuencia de interés para iniciar la ejecución básica del programa, usando los parámetros óptimos por defecto. La simplicidad de la interfaz facilita la ejecución del algoritmo por parte del usuario. Los resultados de una búsqueda están disponibles generalmente en menos de dos minutos, y quedan allí almacenados durante una semana para posibles consultas recurrentes. La facilidad de uso del programa por medio de la aplicación web, así como el método de presentación de los resultados, permiten generar una interfaz de uso del programa por y para distintos tipos de usuarios

Sma3s: A three-step modular annotator for large sequence datasets

This is an Open Access article distributed under the terms of the Creative Commons Attribution License.Automatic sequence annotation is an essential component of modern 'omics' studies, which aim to extract information from large collections of sequence data. Most existing tools use sequence homology to establish evolutionary relationships and assign putative functions to sequences. However, it can be difficult to define a similarity threshold that achieves sufficient coverage without sacrificing annotation quality. Defining the correct configuration is critical and can be challenging for non-specialist users. Thus, the development of robust automatic annotation techniques that generate high-quality annotations without needing expert knowledge would be very valuable for the research community. We present Sma3s, a tool for automatically annotating very large collections of biological sequences from any kind of gene library or genome. Sma3s is composed of three modules that progressively annotate query sequences using either: (i) very similar homologues, (ii) orthologous sequences or (iii) terms enriched in groups of homologous sequences. We trained the system using several random sets of known sequences, demonstrating average sensitivity and specificity values of ∼85%. In conclusion, Sma3s is a versatile tool for high-throughput annotation of a wide variety of sequence datasets that outperforms the accuracy of other well-established annotation algorithms, and it can enrich existing database annotations and uncover previously hidden features. Importantly, Sma3s has already been used in the functional annotation of two published transcriptomes.This work has been partially financed by the National Institute for Bioinformatics (www.inab.org), a platform of Genoma España and the EC project ‘Advancing Clinico-Genomic Trials on Cancer’ (contract no. 026996).Peer Reviewe

Improvement of nutritional properties of Cassva (Manihot esculenta) through massive analysis of gene expression

Motivation: Currently, the cassava is the basis of food for more than 1 billion people in the world. In this instance, the modification of the nutritional composition of plant foods is an urgent matter, since the basic nutritional needs of the world population are not yet covered. The identification of the transcription factors that regulate oil biosynthesis could give tools to re-direct sucrose to oil in the root of tuberculous cultures. In cassava, most of the research that has been done has focused on the tuber, with little study of the seeds and their characteristics.In Cassava the factors that direct the flow of carbon towards the different reserve tissues and determine the final composition of the tissue in the plant are not known. The proposed research line aims to deepen the knowledge of the fatty acid biosynthesis in cassava and increase the oil content of the roots. Fundamental knowledge to be able to reach the final objective of increasing the oil content. In addition to improving its nutritional value, while the amount of nutrients that contribute to the body.Methods: There are two lines of research. The computer methods are based on searching for genes involved in the biosynthesis pathway of lipid substrates through databases such as Uniref and UniProt. After a series of genes obtained from other trials, we compared their presence in the Manihot Esculenta genome and verified their function. With homologous genes, we can expand the number of candidate genes.The laboratory methods aim to develop the method of genetic transformation of cassava (Ima M Zainuddin et al., Plant Methods 2012, 8:24) in combination with Agrobacterium. From a horizontal cuttings and an in vitro culture of their apical buds, we get a mother plant from which we can obtain somatic embryos and create new seedlings to be able to transform with differentResults: The following results were obtained after a first search for genes obtained from a compilation base don papers previously made in other related organisms. From that list of candidates genes, there are genes that cease to be candidates because they are not found in Manihot esculenta, these being susy, ATP-PFK and FBAGenes that continue as candidates, for being in the genome of cassava, being PK,GPT2 and PPT1. And for the latter, new genes can be obtained, such as APE2 with identifier 16G010700.1 in JGI Phytozome. It is a translocator of triose-phosphate located in the chloroplast.Conclusions: There is a vision of the future in this line of research to be able to start from a new and broader list of genes involved in the synthesis routes of sucrose and oil that are susceptible to modification.There is still a lot to study to reach the goal, but positive results will come out

Discovery of lost genes in the genome of Acinetobacter baumannii using Anablast

Motivation: Microbial resistance to antibiotics is currently one of the greatest threats in global health. Multiple outbreaks of multi-resistant Acinetobacter baumannii strains have been documented [1] and it is necessary to find new drugs against it, and the finding of new genes in the bacteria could help in this fighting. As A. baumannii is a highly studied organism, it is difficult to find new genes by homology with traditional predictors.For this reason we have chosen the AnABlast program which is a new bioinformatics tool which has been successful in finding out new genes in eukaryotes. This program generates profiles of accumulated alignments in query amino acid sequences using a low-stringency BLAST strategy [2], which highlight regions with evolutionary meaning.Methods: First, we used AnAblast to locate new coding regions in the A. baumannii genome. After that we analyzed the regions found by AnABlast comparing them with known sequences from the GenBank database to look for the genes found in intergenic regions and we obtain a series of candidates that we need to analyze, characterize and validate.Results: We obtained nine candidates that have been characterized analyzing both its evolutionary conservation and function annotation. Eight of them were also found in other strains of A. baumannii and one could be a gene not found until now that needs to be validated.Conclusions: Using the AnABlast program we have found nine possible coding regions not detected by other methods in the reference strain of A. baumannii. Although they need validation, AnAblast has proven itself useful for gene detection in prokaryote

Searching for gene clusters related to virulence by coding sequence conservation

Motivation: Due to the increasing world population, the need to improve food production is growing. This can be helped byfighting the pathogens which affect the main crops as maize, wheat, barley and sugar cane. Among those, biotrophic parasitessuch as smut fungi can be found. To study how those microorganisms infect their host, the model system Ustilago maydis canbe used.U. maydis secretes protein effectors to infect its host, and at least 25% of them are known to be grouped in 13 different geneclusters. In addition to these characterized clusters, 7 new clusters have been described in the bibliography but notexperimentally tested. The aim of this work is to find out new clusters with features similar to the known ones (controls), mainlylow conservation, which can affect the infection process.Methods: To achieve this goal, candidate gene clusters were initially discovered based on coding sequence conservation viathe computational tool AnABlast [1], which highlitghted genomic coding region with conservation signal similar to the initialcontrols. Then, the candidates were functionally annotated using the tool Sma3s_v2 [2]. To select the best candidates, aprincipal component analysis (PCA) was done using the following factors, which were trained with the controls: sequenceconservation obtained by a similarity search by Blast against close organisms (Ensembl fungi phylogeny), expression dataduring infection, and signal peptide presence (SignalP and TargetP), usually present in effectors.Currently, a laboratory experiment has been began to elucidate if the chosen candidates affect the pathogenity, deleting themby homologous recombination.Results: We have been able to identify 49 new clusters by comparing their coding signal with those already known. After thesubsequent analysis three of them, and one from the bibliography have been chosen to be tested in laboratory to elucidatetheir virulence phenotype (swelling and tumors).In the PCA our best candidate is located among the clusters previously described as pathogenic, showing genes beingsecreted with high levels of expressionConclusions: In brief, we propose that putative cluster of virulence sequences could be found by the presented strategy. So,it could constitute a new silico approach to find out specific genes involved in different biological processes such as inffection

Nutritional improvement of Manihot esculenta roots by boosting the lipids storage

Motivation: The human population continues to grow and it is necessary to produce more and better quality food to meet the world population's demand. Genetic engineering opens great possibilities to improve the quantity of available food. The cassava (Manihot esculenta) plant is the basis of food for more than 1 billion people in the world. All plants have genes coding for oil biosynthetic pathways and transcription factors that activate the expression of these genes. If these transcription factors are activated in other tissues, like roots, the conversion of sucrose to oil could increase. In this way, crops that accumulate sugars and starch could become more nutritious (2.2 times more energy than carbohydrates). It has been shown that starch and oil can accumulate in the same cell, as is the case for oats (Ekman et al., 2008). In this project, cassava has been chosen as a model plant because it has a high starch content in their edible roots.Methods: Two somatic embryos were obtained from mother plants with ecotype 60444. The in-vitro plants will be transformed by the vector via Agrobacterium tumefaciens. The functional annotation of the cassava proteome was carried out using Sma3s (Casimiro-Soriguer et al., 2017). This annotation will allow us to know the function of the protein-coding genes present in cassava. To know those genes involved in the synthesis of fatty acids they must be filtered. The expression of these genes in different tissues was comparated with ArrayExpress. Posible candidates will be examined in order to choose the most suitable ones to be transformed and expressed in the cassava plants.Results: From 41,381 cassava predicted proteins, 35,889 were scored, meaning Sma3s annotated 86% of the proteome. The list of possible candidates is currently around 600 genes and their expression wilI checked with public database. In vitro plants are growing and the second phase of the transformation will be begun.Conclusions: The project will (i) expand knowledge on cassava, particularly on the development of their storage organs, such as roots and seeds, as well as carbohydrate and lipid metabolism, and (ii) develop a cassava crop modification platform using genetic engineering techniques. This work aims to cover two demands of society, try to mitigate hunger, and on the other hand be able to extrapolate the scientific knowledge generated to other crops of interest to cover the current demand for vegetable oil

Searching for novel genes and pseudogenes in the human Y chromosome based on ancestral coding signals

Motivation: Human Y chromosome has several features that contribute to an extreme variation due to the lack of a homologous partner for crossing over, high rate of sequence amplification and low evolutionary pressure [1]. For these reasons, we think that the Y chromosome could be a perfect candidate in order to discover new coding and fossil regions such as pseudogenes.Genome finding is one of the greatest hits in modern biology. However, in silico identification of small and complex coding sequences is still challenging. Jiménez et al [2] developed AnAblast, a computer tool which has been successful in uncovering new genes, as well as fossil-coding sequences. This program generates profiles of accumulated alignments of conserved coding signals using a low-stringency BLAST strategy [2]. Methods: We have used AnAblast to localizate new coding regions in the chromosome Y. After that, AnAblast-generated profiles were introduced into a genome browser, along with other informative data such as repeats and RNA expression data. The candidate's list obtained was complemented by careful BLAST, InterPro and peaks analysis. Moreover, we performed a search on the tool Genome Data Viewer (GDV) to check each result.Results: We have been able to identify some chromosome Y regions that fulfill different requirements: (1) regions without previous annotations as pseudogenes, genes or non-coding regions (Ensembl track); (2) regions without previous annotations as interspersed repeats and low complexity (RepeatMasker track); and (3) regions with expression profiles (RNA-seq of testis).The best candidate to be a new coding region was localized at Y:9912876-9919657 (-). Blast and InterPro analysis indicated similarity with serine-proteases which are found in rodents and another organism such as Rousettus aegyptiacus (Egyptian fruit bat). After the search on GDV, we observed that only the first bat´s exon was not found in our candidate. In spite of this, we found a methionine codon in our candidate (more specifically in the first exon). Furthermore, the Y chromosome has a 5´-truncated copy of this region.Conclusions: We have found some chromosome Y regions which could be new coding genes or pseudogenes. Thus, this in silico research provides a powerful protocol to search novel genes and fossil regions in the whole human genome. Although we added several RNA-seq tracks that showed the expression of these regions, clinical trials should be performed to verify our candidates

Optimización de la levadura de fisión Schizosaccharomyces pombe para su uso en la búsqueda de compuestos antitumorales

La desregulación del ciclo celular puede dar lugar a enfermedades como el cáncer. La levadura Schizosaccharomyces pombe es un organismo modelo que puede usarse para el estudio del ciclo celular y la búsqueda de nuevos fármacos antitumorales. Desgraciadamente, los microtúbulos de la levadura no son sensibles a algunas drogas muy utilizadas como el Taxol. El objetivo de este estudio es optimizar a S. pombe para poder expresar en ella tubulinas humanas en lugar de las endógenas así como analizar mediante modelización molecular los cambios necesarios para hacer a S. pombe sensible. De esta forma podríamos utilizar esta levadura para hacer búsquedas masivas de nuevos compuestos anticancerígenos

Metaheuristic approaches for optimal broadcasting design in metropolitan MANETs

11th International Conference on Computer Aided Systems Theory. Las Palmas de Gran Canaria, Spain, February 12-16, 2007Mobile Ad-hoc Networks (MANETs) are composed of a set of communicating devices which are able to spontaneously interconnect without any pre-existing infrastructure. In such scenario, broadcasting becomes an operation of tremendous importance for the own existence and operation of the network. Optimizing a broadcasting strategy in MANETs is a multiobjective problem accounting for three goals: reaching as many stations as possible, minimizing the network utilization, and reducing the duration of the operation itself. This research, which has been developed within the OPLINK project (http://oplink.lcc.uma.es), faces a wide study about this problem in metropolitan MANETs with up to seven different advanced multiobjective metaheuristics. They all compute Pareto fronts of solutions which empower a human designer with the ability of choosing the preferred configuration for the network. The quality of these fronts is evaluated by using the hypervolume metric. The obtained results show that the SPEA2 algorithm is the most accurate metaheuristic for solving the broadcasting problem.Publicad