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Projects

 

Program for Theoretical and Computational Biology

This project is coordinated by the Institute for Integrative Systems Biology I2SysBio) and the Universidad San Francisco de Quito. The project explores the presence of microorganisms with electricity generating potential of microbial communities present in the sediments of salt lagoons and salt flats of San Cristóbal Island in the Galapagos archipelago. Galapagos explores the production of electricity from environmental samples, characterizes the metagenomic content of microbial communities and the correlation of the presence of power species with environmental parameters such as pH, salinity, temperature and dissolved oxygen.
This project is coordinated by the Institute for Integrative Systems Biology I2SysBio) and the ICTS The Canfranc Underground Laboratory. The project studies the content and the spatial variability of the microbial communities present in limestone rocks samples from the Pyrenees at hundreds meters deep thanks to access thought the Somport tunnel, located in the Central Pyrenees and linking the Aragon (Spain) and Aspe (France) valleys. Gollum explores a little known extreme environment, characterized by few nutrients, various physicochemical substrates, low levels of any type of radiation and small temperature fluctuations. The presence of native DNA and the identification of a high archaea contents and its correlation with present metals are some of the most relevant results and open the possibility of multiple questions, starting by resolving whether genomic material identified corresponds to relic DNA or, on the contrary, to living microorganisms isolated from the outside since tens of millions of years.
 

Program for Systems Biology of Molecular Interactions and Regulation

As consequence of the exposition to stress-inductors plants trigger a complex regulatory response that results in adaptation to adverse conditions. In general, these environmental conditions are the major limiting factors for development and productivity in agricultural species. Consequently, the molecular basis of the mechanisms that regulate the response to stress has been extensively studied. Current and predicted environmental conditions altered as consequence of climate change, pose a serious challenge for extensive agricultural production in the near future. Conditioned by this new scenario has been a need to implement innovative strategies to attempts understand the mechanisms that are triggered in the plant exposed to multiple stresses. However, commonly, these approaches are not focused in the changes produced at the level of non-coding RNAs, although increasingly evidence suggests to them a major role in biological plant-processes. Recently we have identified and characterized small ncRNAs (sncRNAs) that exhibit differential expression associated to diverse (biotic and/or abiotic) stress conditions. Based in these evidences was computationally inferred a sncRNAs-mediated network that predicted to regulates the stress-response in melon plants. According our functional model this regulatory-network is constituted by specific sncRNAs (stress-receptors) that by means of intermediate sncRNAs spread stress-induced signal to the sncRNAs-core responsible to regulate the global response to stress. Based in these evidences we enunciate as general objective of our proposal characterize and functionally validate the regulatory pathways mediated by sncRNAs involved in stress-response in cucurbits. We expect use this knowledge as enhancer to develop biotechnological tools that will enhance the tolerance of crops to stress multiple.
 

Program for Pathogen Systems Biology

Una consecuencia fundamental de la teoría darwiniana de la evolución por selección natural es la explicación de la adaptación como resultado de un proceso natural. Sin embargo, los mecanismos genéticos subyacentes no están todavía resueltos y constituyen un tema fundamental en Biología Evolutiva. Las técnicas de Secuenciación de Nueva Generación (NGS) permiten abordar cuestiones evolutivas a una escala antes impensable. No obstante, la rápida evolución de estas tecnologías dificulta mucho su aplicación, sobre todo en sus aspectos analíticos y bioinformáticos, ya que se tienen que resolver muchos problemas e imprevistos de gestión, almacenamiento, transmisión, análisis o interpretación, lo que representa un desafío muy importante en este campo.
Genomic defenses against viruses in plants are actually part of a broader and conserved interconnected system used for a plethora of mechanisms in eukaryotes, including the regulation of gene expression by endogenous siRNAs and other types of small RNAs (sRNAs), defense against genomic invaders like transposons and establishment of the heterochromatin.
Tuberculosis remains the first cause of adult death by a single infectious agent worldwide, despite a century of research leading to valuable tools to reduce tuberculosis mortality. Therefore, innovative approaches are needed to palliate the dramatic burden of tuberculosis damage on mankind. Our knowledge of the interplay between bacterial virulence and human immunity remains insufficient in the context of tuberculosis. I therefore propose to explore host-pathogen associations as a mean to decipher yet unknown mechanisms underlying tuberculosis in Africa.
We use directed evolution for creating modified viruses that selectively infect and destroy tumors (oncolytic viruses). Cancer cells typically show innate immunity defects, which makes them highly susceptible to viral infections. By adapting a virus to tumors in the laboratory, it is possible to enhance the ability of this particular virus to kill cancer cells and to stimulate an immune response against the tumor. This may open new avenues for cancer therapy. We are currently focusing our efforts on vesicular stomatitis virus, a simple RNA virus with a natural tropism towards cancer cells.
La resistencia a los antibióticos representa una de las mayores amenazas a la salud pública mundial. Nuestro grupo de investigación trabaja desde hace años en la aplicación de los métodos y conceptos de la evolución y genética de poblaciones molecular al estudio de microorganismos patógenos, en lo que se conoce como epidemiología molecular. Además de trabajar en cuestiones de interés científico, tomamos problemas y devolvemos resultados relevantes a las autoridades sanitarias, logrando una interesante aplicación de una disciplina biológica básica. En este contexto, en este proyecto nos planteamos estudiar una amplia colección prospectiva de aislados de una bacteria de gran interés para la salud pública, Klebsiella pneumoniae, para analizar los procesos evolutivos que afectan a su dinámica en la población de la Comunidad Valenciana, con especial interés en cepas resistentes a antibióticos. Por su relevancia clínica y para la salud pública, nos centraremos en cepas productoras de beta-lactamasas de espectro extendido y/o carbapenemasas.
The main goal of this project is to define the effect of all possible mutations in a viral capsid, and to understand how different cellular and environmental pressures can alter the viability of such mutations in the capsid.
We investigate the ability of viruses to spread as groups (collective infectious units) and how this promotes the evolution of social interactions among viruses. For this, we use model viruses (vesicular stomatitis) as well as human (enteroviruses) and insect (baculoviruses) pathogens. Infecting hosts as groups may allow viruses to better counteract antiviral responses and may promote cooperation among different viral genetic variants, but may also favor the evolution of cheater viruses.
Cellular molecular chaperones are a group of conserved and abundant proteins that oversee protein folding and help maintain protein homeostasis. The goal of this project is to define all the chaperones and co-chaperones involved in the replication of respiratory syncytial virus, the single most important respiratory pathogen in children.
Las resistencias a antibióticos y antivirales representan una de las mayores amenazas para la salud y un asunto de gran importancia económica, según reconocen organismos internacionales como la OMS o la OCDE. Siendo el resultado de procesos naturales pero acelerados por la intervención humana, son múltiples los factores que influyen en su aparición y expansión. Por tanto, las estrategias adoptadas y en estudio para controlar las resistencias deben contemplar intervenciones a diversos niveles. Desde el grupo de investigación “Evolución y Salud” de la Universitat de València planteamos un proyecto que integra dos de nuestras principales líneas de trabajo, la evolución experimental y la epidemiología molecular, en un único objetivo: analizar cómo optimizar las estrategias de administración de medicamentos con el fin de retardar o evitar la expansión de resistencias. Para ello, aplicaremos diferentes diseños de evolución experimental en condiciones controladas de laboratorio usando dos microorganismos diferentes: una bacteria (Pseudomonas aeruginosa) y un virus de RNA (rinovirus humano). El sistema experimental también contempla dos entornos básicos, uno in vitro (cultivos) y otro in vivo (usando el modelo murino para ambos patógenos). El desarrollo de las resistencias será evaluado funcionalmente y se analizarán a intervalos regulares la aparición y dinámica de variantes genéticos responsables de la resistencia. Para ello emplearemos técnicas de ultra-secuenciación que nos permitirán evaluar la variabilidad genética y su distribución a lo largo del genoma de cada población, así como los efectos derivados de las mutaciones de resistencia.
It is generally assumed that genetic variability in host species for susceptibility to infection will necessarily condition the evolution of pathogens populations, either by driving them to the diversification of the pathogen into strains that track the different host defence alleles (e.g., antigenic diversity), or by canalization of the pathogen to infect only the most susceptible genotypes. Associated to these processes of diversification or specialization, virulence may or may not increase concomitantly. In any case, pathogen's fitness must be optimized.
 

Program for Evolutionary Systems Biology of Symbionts

The project proposes the development of two types of tools to study gene functions in aphids. On one side, the project proposes an alternative RNAi methodology which consists in providing aphids with a continuous supply of the dsRNA required to trigger the RNAi by including it in a plant virus that infects the plant the aphid naturally feeds on. This technique, called VIGS (Virus Induced Gene Silencing), is a tool successfully used in the silencing of plant genes. Secondly, we intend to develop the CRISPR / Cas methodology in aphids. In addition to investigating the extension of these techniques to aphids, we will investigate the role of candidate genes that we have identified so far as good candidates to regulate several polyphenisms in aphids (including the reproductive polyphenism).
The project aims at identifying and characterizing the key elements governing the mode of reproduction in aphids. We are particularly interested in elucidating the molecular basis responsible for the switch from parthenogenesis to sexual reproduction and analyzing what role (if any) play in this process the circadian clock genes.
The main objective is to learn the role science communication plays on the origin of beliefs, perceptions and knowledge concerning scientific issues. To achieve this aim, we will carry out five citizen consultations in Lisbon (Portugal), Valencia (Spain), Vicenza (Italy), Trnava (Slovakia) and Lodz (Poland), with the participation of a total of 500 citizensabout four science “hot” topics: vaccines, use of complementary and alternative medicines, climate change, food safety. The researchers aim at gaining a deeper insight into the public understanding of science and identify current science communication models.
Mutualistic symbiosis between bacteria and eukaryotic hosts is a widespread phenomenon in nature. Two different symbiotic system exist in insects, endosymbiosis, in which intracellular mutualistic bacteria play an essential nutritional role, and ectosymbiosis, formed mainly by bacteria in the gut, which function is still not well understood. Cockroaches are special because the two symbiotic system coexist in a single individual.
Mutualistic symbiotic bacteria, whether intracellular (endosymbionts) or complex exosymbiont communities stored in organs (such as the gut) of their eukaryotic hosts, may be exploited to affect their hosts by modification or artificial development of new capabilities. Obtaining robust experimental models is of paramount importance to achieve a deeper understanding of these systems prior to manipulating them. In this project, we will work with the endosymbiont Blattabacterium and the exosymbionts found in the digestive system of the cockroach Blattella germanica, as well as some selected species of Lepidoptera.
 

Program for Applied Systems Biology and Synthetic Biology

The central intent of SETH is the generation of a knowledge base, a suite of useful strains and a portfolio of matching genetic technologies for enabling a new type of large-scale industrial and environmental processes mediated by whole bacterial cells but executed under (very) low-water conditions. This endeavor builds on the success of the precedent HELIOS project but goes much beyond by capitalizing on the wealth of biological activities found in desiccation-tolerant bacteria and their repurposing for the design of live catalysts able to work under an unprecedented variety of physicochemical settings.
The main objective is to exchange information and knowledge between countries affected by diseases caused by Xylella fastidiosa in order to gather all available data on the bacterium, its vectors, the situation of affected crops in Ibero-American countries and the prevention and control activities that are being carried out. The aim is to generate knowledge to contribute to the development of a technological alert and surveillance system that allows local or national governments to take the necessary measures to follow, contain and eradicate the disease.
The main objective is to learn the role science communication plays on the origin of beliefs, perceptions and knowledge concerning scientific issues. To achieve this aim, we will carry out five citizen consultations in Lisbon (Portugal), Valencia (Spain), Vicenza (Italy), Trnava (Slovakia) and Lodz (Poland), with the participation of a total of 500 citizensabout four science “hot” topics: vaccines, use of complementary and alternative medicines, climate change, food safety. The researchers aim at gaining a deeper insight into the public understanding of science and identify current science communication models.
We propose to gather the most relevant stakeholders of all the aspects of standardisation in biology in Europe in a co-creation scenario; to empirically test cultural (lab-centric) standardisation practices and promote a consensus conceptual and technical redefinitionof biological standards; and, finally, to foster a realistic and flexible toolbox of standard biological parts, including a reduced set of specialised chassis for specific applications as well as a renewed conceptual framework to inform policy makers, scientific and other societal actors.
The project is part of the group's ongoing research line, aimed to provide knowledge bases and derived technological strategies to improve the efficiency of wine yeasts in all the industrial processes where they participate: dry active biomass production and wine fermentation. The specific objectives of this project are oriented to study the integration of the different nutrient signaling pathways and mechanisms of adaptation to oxidative stress in industrial conditions, and to characterize and improve the technological performance of non-conventional yeasts of oenological interest.
The general objective is to increase our knowledge about bacterial communities living on artificial surfaces (solar panels) under extreme conditions, so that we can understand the molecular mechanisms that make their survival possible and apply this knowledge to develop biotechnological applications.
 
 
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