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Program for Theoretical and Computational Biology

 
The generation of mitotically stable alterations in gene expression due to epigenetic marks is a fast and relatively long-lasting manner for stablishing a genomic memory of past stress events. Environment-triggered deregulation of genetic factors associated with epigenetic machineries can also lead to phenotypic plasticity and stress mitigation. Therefore, host’s epigenetic machinery can pose an important but largely unmeasured selective pressure on pathogens. Plant viruses offer a convenient model for studying this kind of interactions. Firstly, a large-scale evolution experiment for checking how virus populations evolve and interact in plants with compromised or enhanced epigenetic pathways is proposed. Arabidopsis thaliana plants with mutations in key genes associated with active or repressive chromatin marks, including DNA methylation and histone modification, will be challenged against independent lineages of turnip mosaic potyvirus (TuMV).
Massively parallel or next-generation sequencing (NGS) has been a revolution in genetic studies, having important applications in research and in clinics. Some are the study of the genome, transcriptome, microbiome, methylome, genetic diagnosis and personalised medicine, such as pharmacogenetics and the detection of somatic tumour markers, studies of tumour mutations in circulating DNA, determination of the mutation rate for oncology immunotherapy studies. An important application is the study of specific regions of the genome for many clinical or research studies, mainly of one or several genes (NGS panel) due to the high costs of genome-wide studies.
Changes with age of the interactions of the microbiota with its human host and deter-mination of a permanent core of mutualistic symbionts
 

Program for Systems Biology of Molecular Interactions and Regulation

 
The objective of this Project is the “Development of a dual strategy for the mitigation of the damage associated to stress, in tomato productive systems”.
The objective of the project BotVidSENSOR, is the development of a tool for the diagnosis of the "grey rot" disease, caused by B. cinerea, which will allow the EARLY monitoring at the POINT OF NEED of the infections caused by this pathogen in grapevine.
Stress-induced changes in plants (including those produced by pests or pathogens) are usually detected by the appearance of visual symptoms, usually once the adverse effects on crop production have become irreversible.
Environmental stresses (largely facilitated by climate change) limit the productive potential of many agricultural species. Faced with adverse environmental situations, the plant sets in motion multiple processes of gene expression regulation with the aim of counteracting these effects. In our group we study how these complex regulatory networks influenced by the environment play a critical role in modulating plant-environment interactions. This project aims to understand how processes occurring simultaneously at 3 different regulatory levels (siRNAnoma, transcriptome and epigenome) modulate the melon plant response to stress. This knowledge will allow the development of global and innovative crop protection strategies.
New advances in the biological sciences allow the active engineering of proteins and cells for new therapeutic, analytical or synthetic biology approaches. With an expected market worth of billions of dollars by 2020, formal education and research in these fields is not yet well established in continental Europe and requires interdisciplinary skills, combining biology, chemistry and computational sciences with engineering principles. RNAct creates a comprehensive, cross-disciplinary platform to train ESRs, guiding them towards the versatile computational and experimental skills required in this intrinsically multidisciplinary field. RNAct enables ESRs to experience both academic and industrial locations, with support for developing the soft skills they will need to employ and communicate their knowledge. RNAct employs a mix of computational, structural and molecular biology to design and characterize the conformation and function of dynamic proteins, with validation and innovation opportunities in in-cell analytics, therapeutics and synthetic biology, which will help research and companies establish an edge in these competitive fields. We concretely focus on RNA Recognition Motifs (RRMs), which are highly dynamic protein domains with versatile RNA binding functionality. These RRMs play crucial roles in the regulation of in-cell RNA, with very versatile RNA-binding behavior. They could play a key role in synthetic biology.
 

Program for Pathogen Systems Biology

 
The environment is a key factor in the outcome of virus-host interactions, eventually modulating the infection outcome and its severity. Indeed, it has been shown in different organisms that microgravity affects their immunity.
The multidrug-resistant bacteria emergency is a world public health problem requiring the search and development of alternative treatment. Phages, bacteria viruses, stand as an effective biocontrol tool, thanks to their intrinsic properties such as their high specificity and evolutionary capability, as well as being ecologically safe.
La detección de virus patógenos para humanos en aguas residuales es una herramienta muy útil y conocida para la vigilancia epidemiológica.
The objectives of this platform will be the identification of mutations associated with epidemiological/clinical changes of SARS-CoV-2 with special attention to breakthrough infections.
We are part of a joint effort to better understand the effects of mutations in SARS-CoV-2 in real time. This grant aims at building a platform to deal with current and future threats.
We are part of a joint effort to establish a platform for the screening of antivirals against current and future viral threats. The work combines groups that span the full drug discovery and development process.
The emergency of multidrug-resistant bacteria is one of public health’s main issues. The World Health Organisation created a list of multidrug-resistant pathogenic bacteria including critical-priority nosocomial pathogens capable of causing grave infections that are often lethal; such is the case with Klebsiella pneumoniae.
The generation of mitotically stable alterations in gene expression due to epigenetic marks is a fast and relatively long-lasting manner for stablishing a genomic memory of past stress events. Environment-triggered deregulation of genetic factors associated with epigenetic machineries can also lead to phenotypic plasticity and stress mitigation. Therefore, host’s epigenetic machinery can pose an important but largely unmeasured selective pressure on pathogens. Plant viruses offer a convenient model for studying this kind of interactions. Firstly, a large-scale evolution experiment for checking how virus populations evolve and interact in plants with compromised or enhanced epigenetic pathways is proposed. Arabidopsis thaliana plants with mutations in key genes associated with active or repressive chromatin marks, including DNA methylation and histone modification, will be challenged against independent lineages of turnip mosaic potyvirus (TuMV).
Our group research focuses on microorganisms concerning the human health, in order to propose guidelines to the health administration in relation to certain pathogens, diseases related to the microbiota alteration and outbreaks.
 

Program for Evolutionary Systems Biology of Symbionts

 
There is a lot of interest in using bacteriophages for treating diseases caused by multi-drug resistant bacteria. In the project CDEIGENT/2021/008 we will investigate the ability of the bacteriophages to modify the bacterial composition in the human intestine affected by Clostridioides difficile infection using methods of microbial single-cell genomics.
Changes with age of the interactions of the microbiota with its human host and deter-mination of a permanent core of mutualistic symbionts
The objective of the MicroHNSCC project is to identify a specific microbiota pattern with prognostic capacity and to assess whether this pattern modulates the response to chemoradiotherapy of advanced head and neck tumours through its interaction with tumour metabolism.
Our group research focuses on microorganisms concerning the human health, in order to propose guidelines to the health administration in relation to certain pathogens, diseases related to the microbiota alteration and outbreaks.
 

Program for Applied Systems Biology and Synthetic Biology

 
The recycling of multimaterial plastic products, that is, made up of different plastic materials, is key to meeting the recycling targets for 2031 set by the European Commission, which establish that more than 50% of the plastic waste generated in Europe must be recycled, which is well above the 32.5% achieved in 2018.
Anaerobic digestion (AD) of organic matter is a robust technology for biogas synthesis from different types of waste (sewage sludge from water treatment, animal slurry, bio-waste, etc.). The main goal of AD is the production of methane, a renewable energy source that can be used to generate electricity, heat or as vehicle fuel.
This project will contribute to the identification of the molecular mechanism of action of probiotic microorganisms, based on the identification of the synthesis pathways of molecular patterns relevant to their functional action. A double approach is proposed: computational and experimental. Thus, a series of metabolic models will be developed at a genomic scale (GEM) from the annotated sequences of bifidobacteria genomes.
MIPLACE aims at introducing into the circular economy the plastic polymers of polyethylene terephthalate (PET) and polyurethane (PU), which constitute a large part of the plastic waste currently produced. It focuses on the possibility of using microorganisms or parts of them, that use these plastics and transform them into other Bio-PU molecules, which are industrially relevant and more sustainable. On the other hand, and following the principles of the circular economy, we are not only working on their manufacture, but also on the recycling of these Bio-PU products to complete the production of this important material.
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.
 

Innovation Unit (Sinnbiosis)

 

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